A genetic map of Prunus based on an interspecific cross between peach and almond.
Foolad M R,Arulsekar S,Becerra V,Bliss F A
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
A genetic linkage map of Prunus has been constructed using an interspecific F2 population generated from self-pollinating a single F1 plant from a cross between a dwarf peach selection (54P455) and an almond cultivar 'Padre'. Mendelian segregations were observed for 118 markers including 1 morphological (dw), 6 isozymes, 12 plum genomic, 14 almond genomic and 75 peach mesocarp specific cDNA markers. One hundred and seven markers were mapped to 9 different linkage groups covering about 800 cM map distance, and 11 markers remained unlinked. Three loci identified by three cDNA clones, PC8, PC5 and PC68.1, were tightly linked to the dw locus in linkage group 5. Segregation distortion was observed for approximately one-third of the markers, perhaps due to the interspecific nature and the reproductive (i.e. self-incompatibility) differences between peach and almond. This map will be used for adding other markers and genes controlling important traits, identifying the genomic locations and genetic characterizing of the economically important genes in the genus Prunus, as well as for markerassisted selection in breeding populations. Of particular interest are the genes controlling tree growth and form, and fruit ripening and mesocarp development in peach and almond.
Utility of RAPD markers in identifying genetic linkages to genes of economic interest in peach.
Warburton M L,Becerra-Velásquez V L,Goffreda J C,Bliss F A
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
The identification of molecular markers linked to economically important traits for use in crop improvement is very important in long-lived perennial species. Three-hundred-and-sixty RAPD primers were used with bulked segregant analysis to identify markers linked to loci of specific interest in peach [(Prunus persica) L. Batch] and peach x almond [(Prunus dulcis) Batch] crosses. The traits analyzed included flesh color, adhesion, and texture; pollen fertility; plant stature; and three isozyme loci. The Mendelian behavior of the RAPD loci was established, and RAPD markers were mapped relative to the loci controlling flesh color, adhesion, and texture, and the isozyme loci Mdh-1, 6Pgd-2 and Aat-1, as well as the existing RFLP genetic linkage map constructed previously using a peach x almond F2 population. This technique has facilitated rapid identification of RAPD and RFLP markers that are linked to the traits under study. Loci controlling these traits mapped predominantly to linkage groups 2 and 3 of the peach genetic linkage map. Linkages to genes with both dominant and co-dominant alleles were identified, but linkages to dominant genes were more difficult to find. In several crosses, RAPD marker bands proved to be allelic. One co-dominant RAPD formed a heteroduplex band in heterozygous individuals and in mixtures of alternate homozygotes. The Mendelian behavior of the RAPD loci studied was established and the results suggest that RAPD markers will be useful for plant improvement in peach.
Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication.
Akagi Takashi,Hanada Toshio,Yaegaki Hideaki,Gradziel Thomas M,Tao Ryutaro
DNA research : an international journal for rapid publication of reports on genes and genomes
Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.
Heterogeneity in the entire genome for three genotypes of peach [Prunus persica (L.) Batsch] as distinguished from sequence analysis of genomic variants.
Fresnedo-Ramírez Jonathan,Martínez-García Pedro J,Parfitt Dan E,Crisosto Carlos H,Gradziel Thomas M
BACKGROUND:Peach [Prunus persica (L.) Batsch] is an economically important fruit crop that has become a genetic-genomic model for all Prunus species in the family Rosaceae. A doubled haploid reference genome sequence length of 227.3 Mb, a narrow genetic base contrasted by a wide phenotypic variability, the generation of cultivars through hybridization with subsequent clonal propagation, and the current accessibility of many founder genotypes, as well as the pedigree of modern commercial cultivars make peach a model for the study of inter-cultivar genomic heterogeneity and its shaping by artificial selection. RESULTS:The quantitative genomic differences among the three genotypes studied as genomic variants, included small variants (SNPs and InDels) and structural variants (SV) (duplications, inversions and translocations). The heirloom cultivar 'Georgia Belle' and an almond by peach introgression breeding line 'F8,1-42' are more heterogeneous than is the modern cultivar 'Dr. Davis' when compared to the peach reference genome ('Lovell'). A pair-wise comparison of consensus genome sequences with 'Lovell' showed that 'F8,1-42' and 'Georgia Belle' were more divergent than were 'Dr. Davis' and 'Lovell'. CONCLUSIONS:A novel application of emerging bioinformatics tools to the analysis of ongoing genome sequencing project outputs has led to the identification of a range of genomic variants. Results can be used to delineate the genomic and phenotypic differences among peach genotypes. For crops such as fruit trees, the availability of old cultivars, breeding selections and their pedigrees, make them suitable models for the study of genome shaping by artificial selection. The findings from the study of such genomic variants can then elucidate the control of pomological traits and the characterization of metabolic pathways, thus facilitating the development of protocols for the improvement of Prunus crops.
Phenolic contents and bioactive potential of peach fruit extracts.
Mokrani Abderrahmane,Krisa Stéphanie,Cluzet Stéphanie,Da Costa Grégory,Temsamani Hamza,Renouf Elodie,Mérillon Jean-Michel,Madani Khodir,Mesnil Marc,Monvoisin Arnaud,Richard Tristan
Several cultivars of peach fruit (Prunus persica L.) were investigated. Their phenolic composition and concentration were assessed by LC-MS. Concentrations were calculated in mg per g of dry weight extract. Their antioxidant capacity (Folin-Ciocalteu, ORAC, DPPH, ABTS, PFRAP and ICA), inhibitory property against β-amyloid and α-synuclein fibril formation and protective capacity against Aβ-induced toxicity on PC12 cell lines (viability assessed by MTT assay and intracellular ROS production by DCFH-DA assay) were evaluated. Fifteen different phenolic compounds were identified and quantified. In particular, new isorhamnetin derivatives were identified. Phenolic contents were ranged between 19 and 82mg/g. Spring Belle extract had the highest content and Romea the lowest. Except for the ICA assay, a good correlation between phenolic content and the antioxidant capacities of peach fruit extracts was found, indicating that phenolic compounds are major contributors to their antioxidant capacity. Results indicate that the phenolic extract of peach cultivars inhibits Aβ and αS fibril formation and protects PC12 cell lines against Aβ-induced toxicity.
Comparative proteomic analysis of floral color variegation in peach.
Zhou Yong,Wu Xinxin,Zhang Zhen,Gao Zhihong
Biochemical and biophysical research communications
Variegation in flower is a special trait in ornamental peach (Prunus persica L.). To investigate the mechanism of color variegation, we used a combination of two dimensional gel electrophoresis and mass spectrometry to explore the proteomic profiles between variegated flower (VF) and red flower (RF) buds of the peach cultivar 'Sahong Tao'. More than 500 highly reproducible protein spots (P < 0.05) were detected and 72 protein spots showed a greater than two-fold difference in their values. We identified 70 proteins that may play roles in petal coloration. The mRNA levels of the corresponding genes were detected using quantitative RT-PCR. The results show that most of the proteins are involved in energy and metabolism, which provide energy and substrates. We found that LDOX, WD40, ACC, and PPO II are related to the pigment biosynthetic pathway. The activity of PPO enzyme was further validated and showed the higher with significant differences in RF compared with the VF ones. Moreover, the four UCH proteins are involved in protein fate and may be important in post-translational modifications in peach flowers. Our study is the first comparative proteomic analysis of floral variegation and will contribute to further investigations into the molecular mechanism of flower petal coloration in ornamental peach.
Archaeological evidence for peach (Prunus persica) cultivation and domestication in China.
Zheng Yunfei,Crawford Gary W,Chen Xugao
The cultivated/domesticated peach (Prunus persica var. persica; Rosaceae, subgenus Amygdalus; synonym: Amygdalus persica) originated in China, but its wild ancestor, as well as where, when, and under what circumstances the peach was domesticated, is poorly known. Five populations of archaeological peach stones recovered from Zhejiang Province, China, document peach use and evolution beginning ca. 8000 BP. The majority of the archaeological sites from which the earliest peach stones have been recovered are from the Yangzi River valley, indicating that this is where early selection for favorable peach varieties likely took place. Furthermore, peach stone morphology through time is consistent with the hypothesis that an unknown wild P. persica was the ancestor of the cultivated peach. The oldest archaeological peach stones are from the Kuahuqiao (8000-7000 BP) and Tianluoshan (7000-6500 BP) sites and both stone samples segregate into two size groups, suggesting early selection of preferred types. The first peach stones in China most similar to modern cultivated forms are from the Liangzhu culture (ca. 5300 to 4300 BP), where the peach stones are significantly larger and more compressed than earlier stones. Similar peach stones are reported from Japan much earlier (6700-6400 BP). This large, compressed-stone peach was introduced to Japan and indicates a yet unidentified source population in China that was similar to the Liangzhu culture peach. This study proposes that the lower Yangzi River valley is a region, if not the region, of early peach selection and domestication and that the process began at least 7500 years ago.
Prunus transcription factors: breeding perspectives.
Bianchi Valmor J,Rubio Manuel,Trainotti Livio,Verde Ignazio,Bonghi Claudio,Martínez-Gómez Pedro
Frontiers in plant science
Many plant processes depend on differential gene expression, which is generally controlled by complex proteins called transcription factors (TFs). In peach, 1533 TFs have been identified, accounting for about 5.5% of the 27,852 protein-coding genes. These TFs are the reference for the rest of the Prunus species. TF studies in Prunus have been performed on the gene expression analysis of different agronomic traits, including control of the flowering process, fruit quality, and biotic and abiotic stress resistance. These studies, using quantitative RT-PCR, have mainly been performed in peach, and to a lesser extent in other species, including almond, apricot, black cherry, Fuji cherry, Japanese apricot, plum, and sour and sweet cherry. Other tools have also been used in TF studies, including cDNA-AFLP, LC-ESI-MS, RNA, and DNA blotting or mapping. More recently, new tools assayed include microarray and high-throughput DNA sequencing (DNA-Seq) and RNA sequencing (RNA-Seq). New functional genomics opportunities include genome resequencing and the well-known synteny among Prunus genomes and transcriptomes. These new functional studies should be applied in breeding programs in the development of molecular markers. With the genome sequences available, some strategies that have been used in model systems (such as SNP genotyping assays and genotyping-by-sequencing) may be applicable in the functional analysis of Prunus TFs as well. In addition, the knowledge of the gene functions and position in the peach reference genome of the TFs represents an additional advantage. These facts could greatly facilitate the isolation of genes via QTL (quantitative trait loci) map-based cloning in the different Prunus species, following the association of these TFs with the identified QTLs using the peach reference genome.
A 1.7-Mb chromosomal inversion downstream of a PpOFP1 gene is responsible for flat fruit shape in peach.
Plant biotechnology journal
Flat peaches have become popular worldwide due to their novelty and convenience. The peach flat fruit trait is genetically controlled by a single gene at the S locus, but its genetic basis remains unclear. Here, we report a 1.7-Mb chromosomal inversion downstream of a candidate gene encoding OVATE Family Protein, designated PpOFP1, as the causal mutation for the peach flat fruit trait. Genotyping of 727 peach cultivars revealed an occurrence of this large inversion in flat peaches, but absent in round peaches. Ectopic overexpression of PpOFP1 resulted in oval-shaped leaves and shortened siliques in Arabidopsis, suggesting its role in repressing cell elongation. Transcriptional activation of PpOFP1 by the chromosomal inversion may repress vertical elongation in flat-shaped fruits at early stages of development, resulting in the flat fruit shape. Moreover, PpOFP1 can interact with fruit elongation activator PpTRM17, suggesting a regulatory network controlling fruit shape in peach. Additionally, screening of peach wild relatives revealed an exclusive presence of the chromosomal inversion in P. ferganensis, supporting that this species is the ancestor of the domesticated peach. This study provides new insights into mechanisms underlying fruit shape evolution and molecular tools for genetic improvement of fruit shape trait in peach breeding programmes.
An integrated approach for increasing breeding efficiency in apple and peach in Europe.
Laurens Francois,Aranzana Maria José,Arus Pere,Bassi Daniele,Bink Marco,Bonany Joan,Caprera Andrea,Corelli-Grappadelli Luca,Costes Evelyne,Durel Charles-Eric,Mauroux Jehan-Baptiste,Muranty Hélène,Nazzicari Nelson,Pascal Thierry,Patocchi Andrea,Peil Andreas,Quilot-Turion Bénédicte,Rossini Laura,Stella Alessandra,Troggio Michela,Velasco Riccardo,van de Weg Eric
Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond.
An improved strategy based on RAPD markers efficiently identified 95 peach cultivars.
Yu M L,Wang W Y,Ma R J,Shen Z J,Fang J G
Genetics and molecular research : GMR
DNA markers have useful applications in cultivar identification. A novel analysis approach called cultivar identification diagram (CID) was developed using DNA markers in the separation of plant individuals. This new strategy is less time- and cost-consuming, has reliable results, and was constructed for fingerprinting. Ten 11-mer primers were used to amplify the genotypes; all 95 peach genotypes (from the National Peach Germplasm Repository, in Nanjing, China) were distinguished by a combination of 54 primers. The utilization of the CID among these 95 peach cultivars was also verified by the identification of three randomly chosen groups of cultivars. This identification showed some advantages including the use of fewer primers and easy separation of all cultivars by the corresponding primers marked in the right position on the CID. This peach CID could provide the information to separate any peach cultivars of these 95, which may be of help to the peach industry in China and for the utilization of DNA markers to identify other plant species.
Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm.
Verde Ignazio,Bassil Nahla,Scalabrin Simone,Gilmore Barbara,Lawley Cynthia T,Gasic Ksenija,Micheletti Diego,Rosyara Umesh R,Cattonaro Federica,Vendramin Elisa,Main Dorrie,Aramini Valeria,Blas Andrea L,Mockler Todd C,Bryant Douglas W,Wilhelm Larry,Troggio Michela,Sosinski Bryon,Aranzana Maria José,Arús Pere,Iezzoni Amy,Morgante Michele,Peace Cameron
Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs.The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species.
High-density multi-population consensus genetic linkage map for peach.
da Silva Linge Cassia,Antanaviciute Laima,Abdelghafar Asma,Arús Pere,Bassi Daniele,Rossini Laura,Ficklin Stephen,Gasic Ksenija
Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars 'Zin Dai' and 'Crimson Lady' (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae.
Evolutionary Genomics of Peach and Almond Domestication.
Velasco Dianne,Hough Josh,Aradhya Mallikarjuna,Ross-Ibarra Jeffrey
G3 (Bethesda, Md.)
The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide [Formula: see text] values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.
Genome-Wide Analysis and Identification of the Gene Family in Peach.
Guan Dan,Hu Xiao,Diao Donghui,Wang Fang,Liu Yueping
International journal of molecular sciences
The Auxin/indole-3-acetic acid () repressor genes down-regulate the auxin response pathway during many stages of plant and fruit development. In order to determine if and how participate in governing texture and hardness in stone fruit maturation, we identified 23 genes in peach, confirmed by the presence of four conserved domains. In this work, we used fluorescence microscopy with PpIAA-GFP fusion reporters to observe their nuclear localization. We then conducted PCR-based differential expression analysis in "melting" and "stony hard" varieties of peach, and found that in the "melting" variety, nine exhibited peak expression in the S4-3 stage of fruit maturation, with showing the highest (>120-fold) induction. The expression of six peaked in the S4-2 stage, with expressed the most highly. Only showed higher expression in the "stony hard" variety than in the "melting" variety, both peaking in the S3 stage. In contrast, had the highest relative expression in buds, flowers, young and mature leaves, and roots. Our study provides insights into the expression patterns of developmental regulators in response to auxin during fruit maturation, thus providing insight into their potential development as useful markers for quantitative traits associated with fruit phenotype.
Transcriptome analysis and transient transformation suggest an ancient duplicated MYB transcription factor as a candidate gene for leaf red coloration in peach.
Zhou Ying,Zhou Hui,Lin-Wang Kui,Vimolmangkang Sornkanok,Espley Richard V,Wang Lu,Allan Andrew C,Han Yuepeng
BMC plant biology
BACKGROUND:Leaf red coloration is an important characteristic in many plant species, including cultivars of ornamental peach (Prunus persica). Peach leaf color is controlled by a single Gr gene on linkage group 6, with a red allele dominant over the green allele. Here, we report the identification of a candidate gene of Gr in peach. RESULTS:The red coloration of peach leaves is due to accumulation of anthocyanin pigments, which is regulated at the transcriptional level. Based on transcriptome comparison between red- and green-colored leaves, an MYB transcription regulator PpMYB10.4 in the Gr interval was identified to regulate anthocyanin pigmentation in peach leaf. Transient expression of PpMYB10.4 in tobacco and peach leaves can induce anthocyain accumulation. Moreover, a functional MYB gene PpMYB10.2 on linkage group 3, which is homologous to PpMYB10.4, is also expressed in both red- and green-colored leaves, but plays no role in leaf red coloration. This suggests a complex mechanism underlying anthocyanin accumulation in peach leaf. In addition, PpMYB10.4 and other anthocyanin-activating MYB genes in Rosaceae responsible for anthocyanin accumulation in fruit are dated to a common ancestor about 70 million years ago (MYA). However, PpMYB10.4 has diverged from these anthocyanin-activating MYBs to generate a new gene family, which regulates anthocyanin accumulation in vegetative organs such as leaves. CONCLUSIONS:Activation of an ancient duplicated MYB gene PpMYB10.4 in the Gr interval on LG 6, which represents a novel branch of anthocyanin-activating MYB genes in Rosaceae, is able to activate leaf red coloration in peach.
Fine mapping and identification of a candidate gene for a major locus controlling maturity date in peach.
Pirona Raul,Eduardo Iban,Pacheco Igor,Da Silva Linge Cassia,Miculan Mara,Verde Ignazio,Tartarini Stefano,Dondini Luca,Pea Giorgio,Bassi Daniele,Rossini Laura
BMC plant biology
BACKGROUND:Maturity date (MD) is a crucial factor for marketing of fresh fruit, especially those with limited shelf-life such as peach (Prunus persica L. Batsch): selection of several cultivars with differing MD would be advantageous to cover and extend the marketing season. Aims of this work were the fine mapping and identification of candidate genes for the major maturity date locus previously identified on peach linkage group 4. To improve genetic resolution of the target locus two F2 populations derived from the crosses Contender x Ambra (CxA, 306 individuals) and PI91459 (NJ Weeping) x Bounty (WxBy, 103 individuals) were genotyped with the Sequenom and 9K Illumina Peach Chip SNP platforms, respectively. RESULTS:Recombinant individuals from the WxBy F2 population allowed the localisation of maturity date locus to a 220 kb region of the peach genome. Among the 25 annotated genes within this interval, functional classification identified ppa007577m and ppa008301m as the most likely candidates, both encoding transcription factors of the NAC (NAM/ATAF1, 2/CUC2) family. Re-sequencing of the four parents and comparison with the reference genome sequence uncovered a deletion of 232 bp in the upstream region of ppa007577m that is homozygous in NJ Weeping and heterozygous in Ambra, Bounty and the WxBy F1 parent. However, this variation did not segregate in the CxA F2 population being the CxA F1 parent homozygous for the reference allele. The second gene was thus examined as a candidate for maturity date. Re-sequencing of ppa008301m, showed an in-frame insertion of 9 bp in the last exon that co-segregated with the maturity date locus in both CxA and WxBy F2 populations. CONCLUSIONS:Using two different segregating populations, the map position of the maturity date locus was refined from 3.56 Mb to 220 kb. A sequence variant in the NAC gene ppa008301m was shown to co-segregate with the maturity date locus, suggesting this gene as a candidate controlling ripening time in peach. If confirmed on other genetic materials, this variant may be used for marker-assisted breeding of new cultivars with differing maturity date.
Characteristics and regulatory pathway of the PrupeSEP1 SEPALLATA gene during ripening and softening in peach fruits.
Li Jinjin,Li Fang,Qian Ming,Han Mingyu,Liu Hangkong,Zhang Dong,Ma Juanjuan,Zhao Caiping
Plant science : an international journal of experimental plant biology
SEPALLATA genes are members of a subfamily of MADS-box transcription factors, and have essential roles in floral organ development and fruit ripening. In this study, the PrupeSEP1 gene was cloned from peach flesh. Its deduced amino acid sequence was very similar to that of MdMADS8 and MdMADS9 in apple and MADS-RIN-like in strawberry. During storage of melting flesh (MF) peach, the pattern of SEP1 expression was similar to that of ethylene biosynthesis and ethylene signal transduction-related gene expression (EIN2 and ETR2). The SEP1 expression level was correlated with that of EIN2 and ETR2. Furthermore, in MF, cell wall modification-related genes (Endo-PG3, EXP2 and PME3), N-glycan processing genes (β-Hex2 and α-Man) and Lox1 exhibited similar expression patterns to that of SEP1. However, in non-melting flesh (NMF) peach, the SEP1 expression pattern was different from that of MF peach. Moreover, in NMF, only EXP2, LOX1, and α-Man expression patterns were similar to that of SEP1. After SEP1 expression was inhibited by virus-induced gene silencing technique (VIGS) in MF peach, compared with the control, the fruit remained firm and fruit softening was delayed. While expression levels of the ripening and softening related genes, ACS2, EIN2, PME1, Endo-PG3, ACO1, ETR2,β-Hex2 and Lox1, were significantly decreased in SEP1-silenced peach, the transcription of EXP2 and PME3 were significantly enhanced except at the harvest stage. Yeast one-hybrid verification showed SEP1 can interact with promoter of target genes PGs. Our results indicate SEP1 may regulate fruit ripening and softening of MF peaches, while this regulation may be lost in the NMF peaches.
Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm.
Micheletti Diego,Dettori Maria Teresa,Micali Sabrina,Aramini Valeria,Pacheco Igor,Da Silva Linge Cassia,Foschi Stefano,Banchi Elisa,Barreneche Teresa,Quilot-Turion Bénédicte,Lambert Patrick,Pascal Thierry,Iglesias Ignasi,Carbó Joaquim,Wang Li-Rong,Ma Rui-Juan,Li Xiong-Wei,Gao Zhong-Shan,Nazzicari Nelson,Troggio Michela,Bassi Daniele,Rossini Laura,Verde Ignazio,Laurens François,Arús Pere,Aranzana Maria José
Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.
Identification of a new allele of the Dw gene causing brachytic dwarfing in peach.
Cantín Celia M,Arús Pere,Eduardo Iban
BMC research notes
OBJECTIVE:Peach brachytic dwarfism determined by Dwarf gene (Dw) is an undesired trait segregating in some peach breeding programs. Recently, a single nucleotide polymorphism (SNP) mutation in the gibberellin insensitive dwarf 1 (GID1) peach gene causing brachytic dwarfism was described. In this research we wanted to validate this marker in an F population of the 'Nectavantop' peach cultivar (Nv) to include it as a marker assisted selection tool for peach breeding programs. RESULTS:The observed segregation of the trait was in agreement with that of a recessive gene, the individuals homozygous for the recessive allele (dwdw) presenting the dwarf genotype. Dw was mapped to the distal part of linkage group 6 as previously described. The SNP marker based on the causal mutation previously described did not segregate in Nv F population. The sequence of the GID1c gene in Nv revealed a second SNP in its coding sequence which cosegregated with the dwarf phenotype. This SNP was predicted by the SNAP software to cause a major functional change and was validated in the dwarf peach cultivar 'Small sunning'. These results suggest the existence of at least two independent mutations of the Dw gene causing the peach brachytic dwarf phenotype.
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.
,Verde Ignazio,Abbott Albert G,Scalabrin Simone,Jung Sook,Shu Shengqiang,Marroni Fabio,Zhebentyayeva Tatyana,Dettori Maria Teresa,Grimwood Jane,Cattonaro Federica,Zuccolo Andrea,Rossini Laura,Jenkins Jerry,Vendramin Elisa,Meisel Lee A,Decroocq Veronique,Sosinski Bryon,Prochnik Simon,Mitros Therese,Policriti Alberto,Cipriani Guido,Dondini Luca,Ficklin Stephen,Goodstein David M,Xuan Pengfei,Del Fabbro Cristian,Aramini Valeria,Copetti Dario,Gonzalez Susana,Horner David S,Falchi Rachele,Lucas Susan,Mica Erica,Maldonado Jonathan,Lazzari Barbara,Bielenberg Douglas,Pirona Raul,Miculan Mara,Barakat Abdelali,Testolin Raffaele,Stella Alessandra,Tartarini Stefano,Tonutti Pietro,Arús Pere,Orellana Ariel,Wells Christina,Main Dorrie,Vizzotto Giannina,Silva Herman,Salamini Francesco,Schmutz Jeremy,Morgante Michele,Rokhsar Daniel S
Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
RNA-Seq analysis unveils gene regulation of fruit size cooperatively determined by velocity and duration of fruit swelling in peach.
Gu Chao,Zhou Yu-Hang,Shu Wei-Sheng,Cheng Hai-Yan,Wang Lu,Han Yue-Peng,Zhang Yu-Yan,Yu Ming-Liang,Joldersma Dirk,Zhang Shao-Ling
Fruit swelling determines fruit size and usually occurs in two distinct time periods in peach. However, little is known about the gene regulation of fruit swelling. In this study, measurements of longitudinal and transverse diameters in developing and ripening peach fruits unveiled two periods of fruit swelling: the first swelling ends at approximately 65 days after flower blooming (DAFB) and the second swelling starts at approximately 75 DAFB. Comparisons of diameters sizes and development periods among cultivars and accessions revealed a cooperative regulation of swelling velocity and swelling duration, which leads to final determination of fruit size. Furthermore, RNA-sequencing was conducted for fruits at the initial swelling, non-swelling interval between the two swellings (hereafter, 'the interval'), second swelling and ripening stages. A total of 110 and 128 differentially expressed genes were screened from fruits in the first and second swelling, respectively. Besides, the nine most differentially expressed genes located within the reported quantitative trait locations (QTLs) of fruit size in peach were detected in both the first and second swelling stages. Those genes have been reported to be involved in mediating cell size, which indicates the occurrence of both cell proliferation and cell expansion in each of the two major periods of fruit swelling. In addition, a potential gene regulation network is proposed herein and could be used to elucidate the molecular mechanism of peach fruit swellings mediated by multiple key genes.
Identification of EIL and ERF Genes Related to Fruit Ripening in Peach.
Zhou Hui,Zhao Lei,Yang Qiurui,Amar Mohamed Hamdy,Ogutu Collins,Peng Qian,Liao Liao,Zhang Jinyun,Han Yuepeng
International journal of molecular sciences
Peach () is a climacteric fruit with a relatively short shelf life due to its fast ripening or softening process. Here, we report the association of gene families encoding ethylene insensitive-3 like (EIL) and ethylene response factor (ERF) with fruit ripening in peach. In total, 3 and 12 PpERFs were highly expressed in fruit, with the majority showing a peak of expression at different stages. All three EILs could activate ethylene biosynthesis genes and . One out of the 12 , termed , is a homolog of ripening-associated in tomato, with a consistently high expression throughout fruit development and an ability to activate and . Additionally, four subgroup F PpERFs harboring the EAR repressive motif were able to repress the promoter but could also activate the promoter. Promoter deletion assay revealed that PpEILs and PpERFs could participate in transcriptional regulation of through either direct or indirect interaction with various cis-elements. Taken together, these results suggested that all three and are candidates involved in ethylene biosynthesis, and EAR motif-containing may function as activator or repressor of ethylene biosynthesis genes in peach. Our study provides an insight into the roles of EILs and ERFs in the fruit ripening process.
A candidate PpRPH gene of the D locus controlling fruit acidity in peach.
Wang Lu,Jiang Xiaohan,Zhao Li,Wang Furong,Liu Yudi,Zhou Hui,He Huaping,Han Yuepeng
Plant molecular biology
KEY MESSAGE:A candidate gene, designate PpRPH, in the D locus was identified to control fruit acidity in peach. Fruit acidity has a strong impact on organoleptic quality of fruit. Peach fruit acidity is controlled by a large-effect D locus on chromosome 5. In this study, the D locus was mapped to a 509-kb interval, with two markers, 5dC720 and 5C1019, co-segregating with the non-acid/acid trait of peach fruit. Within this interval, a candidate gene encoding a putative small protein, designated PpRPH, showed a consistency between gene expression and fruit acidity, with up- and down-regulation in non-acidic and acidic fruits, respectively. Transient ectopic expression of PpRPH in tobacco leaves caused an increase of pH by approximately 40% compared to the control transformed with empty vector. Whereas, the concentrations of citrate and malate decreased significantly by 22% and 37%, respectively, with respect to the empty vector control. All these results suggest that PpRPH is a strong candidate gene of the D locus. These findings contribute to our overall understanding of the complex mechanism underlying fruit acidity in peach as well as that in other fruit crops.
Fruit quality of Redhaven and Royal Glory peach cultivars on seven different rootstocks.
Orazem Primoz,Stampar Franci,Hudina Metka
Journal of agricultural and food chemistry
Two peach cultivars, Redhaven and Royal Glory, grafted on seven different rootstocks (Adesoto, Barrier 1, GF 677, Ishtara, Monegro, Penta, and peach seedling) were analyzed for tree vigor and yield. Fruit of similar ripeness (fruit firmness) was analyzed in terms of pomological (fruit weight, soluble solids content) and biochemical parameters (individual sugars, organic acids, phenolic acids in the flesh and peel, as well as flavonols and anthocyanins in the peel). A uniform effect of rootstock on tree size was evident in the cases of both cultivars. The Ishtara rootstock induced weak tree growth; Adesoto, Penta and peach seedling semivigorous growth; and Barrier 1, GF 677, and Monegro vigorous tree growth. We recorded higher yields in the Redhaven cultivar, while no significant differences in yield in the fourth growing season were found among the rootstocks for each cultivar. Rootstock had no effect on soluble solids in the Redhaven cultivar, while in the Royal Glory it did. Penta yielded the highest soluble solids content levels, while Adesoto and Monegro were associated with low levels. In the fruit from both cultivars, the rootstock had a significant influence on individual sugars, organic acids, and phenolic acids in the pulp. We also found that phenolic acids in the pulp and skin were more affected by the rootstock than other secondary metabolites analyzed, regardless of the cultivar.
Comparative transcriptome analysis reveals key genes potentially related to soluble sugar and organic acid accumulation in watermelon.
Gao Lei,Zhao Shengjie,Lu Xuqiang,He Nan,Zhu Hongju,Dou Junling,Liu Wenge
Soluble sugars and organic acids are important components of fruit flavor and have a strong impact on the overall organoleptic quality of watermelon (Citrullus lanatus) fruit. Several studies have analyzed the expression levels of the genes related to soluble sugar accumulation and the dynamic changes in their content during watermelon fruit development and ripening. Nevertheless, to date, there have been no reports on the organic acid content in watermelon or the genes regulating their synthesis. In this study, the soluble sugars and organic acids in watermelon were measured and a comparative transcriptome analysis was performed to identify the key genes involved in the accumulation of these substances during fruit development and ripening. The watermelon cultivar '203Z' and its near-isogenic line (NIL) 'SW' (in the '203Z' background) were used as experimental materials. The results suggested that soluble sugar consist of fructose, glucose and sucrose while malic-, citric-, and oxalic acids are the primary organic acids in watermelon fruit. Several differentially expressed genes (DEGs) related to soluble sugar- and organic acid accumulation and metabolism were identified. These include the DEGs encoding raffinose synthase, sucrose synthase (SuSy), sucrose-phosphate synthase (SPSs), insoluble acid invertases (IAI), NAD-dependent malate dehydrogenase (NAD-cyt MDH), aluminum-activated malate transporter (ALMT), and citrate synthase (CS). This is the first report addressing comparative transcriptome analysis via NILs materials in watermelon fruit. These findings provide an important basis for understanding the molecular mechanism that leads to soluble sugar and organic acid accumulation and metabolism during watermelon fruit development and ripening.
Sugar Profile of Kernels as a Marker of Origin and Ripening Time of Peach (Prunus persicae L.).
Stanojević Marija,Trifković Jelena,Akšić Milica Fotirić,Rakonjac Vera,Nikolić Dragan,Šegan Sandra,Milojković-Opsenica Dušanka
Plant foods for human nutrition (Dordrecht, Netherlands)
Large amounts of fruit seeds, especially peach, are discarded annually in juice or conserve producing industries which is a potential waste of valuable resource and serious disposal problem. Regarding the fact that peach seeds can be obtained as a byproduct from processing companies their exploitation should be greater and, consequently more information of cultivars' kernels and their composition is required. A total of 25 samples of kernels from various peach germplasm (including commercial cultivars, perspective hybrids and vineyard peach accessions) differing in origin and ripening time were characterized by evaluation of their sugar composition. Twenty characteristic carbohydrates and sugar alcohols were determined and quantified using high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC/PAD). Sucrose, glucose and fructose are the most important sugars in peach kernels similar to other representatives of the Rosaceae family. Also, high amounts of sugars in seeds of promising hybrids implies that through conventional breeding programs peach kernels with high sugar content can be obtained. In addition, by the means of several pattern recognition methods the variables that discriminate peach kernels arising from diverse germplasm and different stage of maturity were identified and successful models for further prediction were developed. Sugars such as ribose, trehalose, arabinose, galactitol, fructose, maltose, sorbitol, sucrose, iso-maltotriose were marked as most important for such discrimination.
Functional Analysis Reveals the Regulatory Role of Encoding Tonoplast Sugar Transporter in Sugar Accumulation of Peach Fruit.
Peng Qian,Wang Lu,Ogutu Collins,Liu Jingjing,Liu Li,Mollah Md Dulal Ali,Han Yuepeng
International journal of molecular sciences
Sugar content is related to fruit sweetness, and the complex mechanisms underlying fruit sugar accumulation still remain elusive. Here, we report a peach gene encoding tonoplast sugar transporter that is located in the quantitative trait loci (QTL) interval on Chr5 controlling fruit sucrose content. One derived Cleaved Amplified Polymorphic Sequence (dCAPS) marker was developed based on a nonsynonymous G/T variant in the third exon of . Genotyping of peach cultivars with the dCAPS marker revealed a significant difference in fruit sugar content among genotypes. is located in the tonoplast, and substitution of glutamine by histidine caused by the G/T variation has no impact on subcellular location. The expression profile of exhibited a consistency with the sugar accumulation pattern, and its transient silencing significantly inhibited sugar accumulation in peach fruits. All of these results demonstrated the role of in regulating sugar accumulation in peach fruit. In addition, cis-elements for binding of MYB and WRKY transcript factors were found in the promoter sequence of , suggesting a gene regulatory network of fruit sugar accumulation. Our results are not only helpful for understanding the mechanisms underlying fruit sugar accumulation, but will also be useful for the genetic improvement of fruit sweetness in peach breeding programs.
Inter-Species Comparative Analysis of Components of Soluble Sugar Concentration in Fleshy Fruits.
Dai Zhanwu,Wu Huan,Baldazzi Valentina,van Leeuwen Cornelis,Bertin Nadia,Gautier Hélène,Wu Benhong,Duchêne Eric,Gomès Eric,Delrot Serge,Lescourret Françoise,Génard Michel
Frontiers in plant science
The soluble sugar concentration of fleshy fruit is a key determinant of fleshy fruit quality. It affects directly the sweetness of fresh fruits and indirectly the properties of processed products (e.g., alcohol content in wine). Despite considerable divergence among species, soluble sugar accumulation in a fruit results from the complex interplay of three main processes, namely sugar import, sugar metabolism, and water dilution. Therefore, inter-species comparison would help to identify common and/or species-specific modes of regulation in sugar accumulation. For this purpose, a process-based mathematical framework was used to compare soluble sugar accumulation in three fruits: grape, tomato, and peach. Representative datasets covering the time course of sugar accumulation during fruit development were collected. They encompassed 104 combinations of species (3), genotypes (30), and growing conditions (19 years and 16 nutrient and environmental treatments). At maturity, grape showed the highest soluble sugar concentrations (16.5-26.3 g/100 g FW), followed by peach (2.2 to 20 g/100 g FW) and tomato (1.4 to 5 g/100 g FW). Main processes determining soluble sugar concentration were decomposed into sugar importation, metabolism, and water dilution with the process-based analysis. Different regulation modes of soluble sugar concentration were then identified, showing either import-based, dilution-based, or import and dilution dual-based. Firstly, the higher soluble sugar concentration in grape than in tomato is a result of higher sugar importation. Secondly, the higher soluble sugar concentration in grape than in peach is due to a lower water dilution. The third mode of regulation is more complicated than the first two, with differences both in sugar importation and water dilution (grape vs. cherry tomato; cherry tomato vs. peach; peach vs. tomato). On the other hand, carbon utilization for synthesis of non-soluble sugar compounds (namely metabolism) was conserved among the three fruit species. These distinct modes appear to be quite species-specific, but the intensity of the effect may significantly vary depending on the genotype and management practices. These results provide novel insights into the drivers of differences in soluble sugar concentration among fleshy fruits.
Agronomical parameters, sugar profile and antioxidant compounds of "Catherine" peach cultivar influenced by different plum rootstocks.
Font i Forcada Carolina,Gogorcena Yolanda,Moreno María Ángeles
International journal of molecular sciences
The influence of seven plum rootstocks (Adesoto, Monpol, Montizo, Puebla de Soto 67 AD, PM 105 AD, St. Julien GF 655/2 and Constantí 1) on individual and total sugars, as well as on antioxidant content in fruit flesh of "Catherine" peaches, was evaluated for three years. Agronomical and basic fruit quality parameters were also determined. At twelve years after budding, significant differences were found between rootstocks for the different agronomic and fruit quality traits evaluated. The Pollizo plum rootstocks Adesoto and PM 105 AD seem to induce higher sweetness to peach fruits, based on soluble solids content, individual (sucrose, fructose and sorbitol) and total sugars. A clear tendency was also observed with the rootstock Adesoto, inducing the highest content of phenolics, flavonoids, vitamin C and relative antioxidant capacity (RAC). Thus, the results of this study demonstrate the significant effect of rootstock on the sugar profile and phytochemical characteristics of peach fruits. In addition, this work shows the importance of the sugar profile, because specific sugars play an important role in peach flavour quality, as well as the studied phytochemical compounds when looking for high quality peaches with enhanced health properties.
Relationship between polyphenol oxidase activity and nutrition, maturity and quality parameters in flat peach.
Pascual Miquel,Villar Josep M,Lordan Joan,Fonseca Francisco,Falguera Víctor,Rufat Josep
Journal of the science of food and agriculture
BACKGROUND:Polyphenol oxidase (PPO) is one of the main factors that determine postharvest stability and therefore commercial possibilities of peach orchards. Since the activity of this enzyme depends on several variables of different nature, stating the relationships among them is essential to manage crop inputs so as to achieve the desired quality. RESULTS:Multivariate projection techniques were used to identify these relationships throughout on-tree maturation in flat peach samples that had received different fertilisation doses, but harvested in equal conditions of soluble solids, fruit weight, diameter, firmness and skin and flesh colour. A relatively low fertilisation dose that was enough to avoid any lack of nutrients provided the lowest crop yield, but also with the lowest PPO activity. Fruit N/Ca ratio turned out to be a better indicator of PPO activity than isolated nitrogen or calcium content. Nutrient analyses on leaves did not have strong correlations with any significant parameter. The most useful variables to predict PPO activity before harvest were fruit firmness and skin colour, both of them read at the onset of on-tree maturation. CONCLUSION:High fertilisation doses resulted in greater yields, but also with higher PPO activity, which is detrimental for the commercial chances of the fruit.
A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach.
Vendramin Elisa,Pea Giorgio,Dondini Luca,Pacheco Igor,Dettori Maria Teresa,Gazza Laura,Scalabrin Simone,Strozzi Francesco,Tartarini Stefano,Bassi Daniele,Verde Ignazio,Rossini Laura
Nectarines play a key role in peach industry; the fuzzless skin has implications for consumer acceptance. The peach/nectarine (G/g) trait was described as monogenic and previously mapped on chromosome 5. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F2 progeny from the cross 'Contender' (C, peach) x 'Ambra' (A, nectarine). Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. This marker was shown to efficiently discriminate between peach and nectarine plants, indicating that a unique mutational event gave rise to the nectarine trait and providing a useful diagnostic tool for early seedling selection in peach breeding programs.
The crucial role of PpMYB10.1 in anthocyanin accumulation in peach and relationships between its allelic type and skin color phenotype.
Tuan Pham Anh,Bai Songling,Yaegaki Hideaki,Tamura Takayuki,Hihara Seisuke,Moriguchi Takaya,Oda Kenji
BMC plant biology
BACKGROUND:Red coloration of fruit skin is one of the most important traits in peach (Prunus persica), and it is mainly due to the accumulation of anthocyanins. Three MYB10 genes, PpMYB10.1, PpMYB10.2, and PpMYB10.3, have been reported as important regulators of red coloration and anthocyanin biosynthesis in peach fruit. In this study, contribution of PpMYB10.1/2/3 to anthocyanin accumulation in the fruit skin was investigated in the Japanese peach cultivars, white-skinned 'Mochizuki' and red-skinned 'Akatsuki'. We then investigated the relationships between allelic type of PpMYB10.1 and skin color phenotype in 23 Japanese peach cultivars for future establishment of DNA-marker. RESULTS:During the fruit development of 'Mochizuki' and 'Akatsuki', anthocyanin accumulation was observed only in the skin of red 'Akatsuki' fruit in the late ripening stages concomitant with high mRNA levels of the last step gene leading to anthocyanin accumulation, UDP-glucose:flavonoid-3-O-glucosyltransferase (UFGT). This was also correlated with the expression level of PpMYB10.1. Unlike PpMYB10.1, expression levels of PpMYB10.2/3 were low in the skin of both 'Mochizuki' and 'Akatsuki' throughout fruit development. Moreover, only PpMYB10.1 revealed expression levels associated with total anthocyanin accumulation in the leaves and flowers of 'Mochizuki' and 'Akatsuki'. Introduction of PpMYB10.1 into tobacco increased the expression of tobacco UFGT, resulting in higher anthocyanin accumulation and deeper red transgenic tobacco flowers; however, overexpression of PpMYB10.2/3 did not alter anthocyanin content and color of transgenic tobacco flowers when compared with wild-type flowers. Dual-luciferase assay showed that the co-infiltration of PpMYB10.1 with PpbHLH3 significantly increased the activity of PpUFGT promoter. We also found close relationships of two PpMYB10.1 allelic types, MYB10.1-1/MYB10.1-2, with the intensity of red skin coloration. CONCLUSION:We showed that PpMYB10.1 is a major regulator of anthocyanin accumulation in red-skinned peach and that it activates PpUFGT transcription. PpMYB10.2/3 may be involved in functions other than anthocyanin accumulation in peach. The peach cultivars having two MYB10.1-2 types resulted in the white skin color. By contrast, those with two MYB10.1-1 or MYB10.1-1/MYB10.1-2 types showed respective red or pale red skin color. These findings contribute to clarifying the molecular mechanisms of anthocyanin accumulation and generating gene-based markers linked to skin color phenotypes.
Comparative Transcriptome Profiling in a Segregating Peach Population with Contrasting Juiciness Phenotypes.
Del Pozo Talía,Miranda Simón,Latorre Mauricio,Olivares Felipe,Pavez Leonardo,Gutiérrez Ricardo,Maldonado Jonathan,Hinrichsen Patricio,Defilippi Bruno G,Orellana Ariel,González Mauricio
Journal of agricultural and food chemistry
Cold storage of fruit is one of the methods most commonly employed to extend the postharvest lifespan of peaches ( Prunus persica (L.) Batsch). However, fruit quality in this species is affected negatively by mealiness, a physiological disorder triggered by chilling injury after long periods of exposure to low temperatures during storage and manifested mainly as a lack of juiciness, which ultimately modifies the organoleptic properties of peach fruit. The aim of this study was to identify molecular components and metabolic processes underlying mealiness in susceptible and nonsusceptible segregants. Transcriptome and qRT-PCR profiling were applied to individuals with contrasting juiciness phenotypes in a segregating F population. Our results suggest that mealiness is a multiscale phenomenon, because juicy and mealy fruit display distinctive reprogramming processes affecting translational machinery and lipid, sugar, and oxidative metabolism. The candidate genes identified may be useful tools for further crop improvement.
Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach.
Falchi Rachele,Vendramin Elisa,Zanon Laura,Scalabrin Simone,Cipriani Guido,Verde Ignazio,Vizzotto Giannina,Morgante Michele
The Plant journal : for cell and molecular biology
Peach flesh color (white or yellow) is among the most popular commercial criteria for peach classification, and has implications for consumer acceptance and fruit nutritional quality. Despite the increasing interest in improving cultivars of both flesh types, little is known about the genetic basis for the carotenoid content diversity in peach. Here we describe the association between genotypes at a locus encoding the carotenoid cleavage dioxygenase 4 (PpCCD4), localized in pseudomolecule 1 of the Prunus persica reference genome sequence, and the flesh color for 37 peach varieties, including two somatic revertants, and three ancestral relatives of peach, providing definitive evidence that this locus is responsible for flesh color phenotype. We show that yellow peach alleles have arisen from various ancestral haplotypes by at least three independent mutational events involving nucleotide substitutions, small insertions and transposable element insertions, and that these mutations, despite being located within the transcribed portion of the gene, also result in marked differences in transcript levels, presumably as a consequence of differential transcript stability involving nonsense-mediated mRNA decay. The PpCCD4 gene provides a unique example of a gene for which humans, in their quest to diversify phenotypic appearance and qualitative characteristics of a fruit, have been able to select and exploit multiple mutations resulting from a variety of mechanisms.
Antioxidant capacity, quality, and anthocyanin and nutrient contents of several peach cultivars [Prunus persica (L.) Batsch] grown in Spain.
Reig G,Iglesias I,Gatius F,Alegre S
Journal of agricultural and food chemistry
Antioxidant capacity, quality, and anthocyanin and nutrient contents of 106 peach cultivars from different breeding programs were evaluated at the Estació Experimental de Lleida, IRTA (Catalonia, Spain), during two growing seasons (2010 and 2011). High variability was found among cultivars within each quality trait, where different cultivars were scored as the best and the worst. For example, a 5-fold range (2.17-12.07 g of malic acid L⁻¹), 6-fold range (144.20-711.73 μg of Trolox g⁻¹ of FW), and 11-fold range (0.70-11.43 mg of cyanidin-3-glucoside kg⁻¹ of FW) were observed in titratable acidity, relative antioxidant capacity, and anthocyanin content, respectively. The breeding program within each fruit type (melting peach, nectarine, and flat peach) and qualitative pomological traits also had significant effects on the quality. Nevertheless, each breeding program had specific characteristics that distinguished it from the others. Even so, within each breeding program, there is high variability among cultivars. Therefore, growers should not base their strategy exclusively on the choice of breeding program. Principal component analysis for each fruit type (melting peach, nectarine, nonmelting peach, and flat peach) allowed a selection of a set of cultivars from different breeding programs with the highest quality performance. For example, cultivars such as 'Azurite', 'IFF 1230', 'Amiga', 'Fire Top', 'African Bonnigold', 'Ferlot', 'Mesembrine', and 'Platifirst' had higher sweetness and flavor compared to the others. Therefore, this study could help breeders to make decisions for the selection of new cultivars able to improve the quality features of fruit intake, technicians to know better quality performance of peach cultivars, and consumers to meet their expectations for fruit with high health benefits and a specific taste.
Carotenoid cleavage in chromoplasts of white and yellow-fleshed peach varieties.
Giberti Samuele,Giovannini Daniela,Forlani Giuseppe
Journal of the science of food and agriculture
BACKGROUND:In peach fruit, carotenoid accumulation in the mesocarp causes the difference between yellow and white genotypes. The latter are generally characterized by a peculiar and more intense aroma, because of higher release of volatiles deriving from dioxygenase-catalysed breakdown of the tetraterpene skeleton. The rate of carotenoid oxidation was investigated in peach (Prunus persica L.) fruits harvested at various stages of development. Two couples of white and yellow-fleshed isogenic varieties and an ancestral white-fleshed genotype were analysed, which had previously shown to differ in Carotenoid Cleavage Dioxygenase 4 allelic composition resulting in various combinations of putatively active/inactive proteins. RESULTS:Carotenoid bleaching activity was localized in the insoluble fraction of fruit flesh chromoplasts. Higher rates of trans-β-apo-8'-carotenal than β-carotene bleaching suggest that the first cleavage reaction is the rate-limiting step. Consistently, HPLC analysis did not show the appearance of coloured intermediates in reaction mixtures. High levels of substrate breakdown were found during the initial phases of fruit development in all genotypes examined, whereas significant differences were evident during the second exponential growth phase and ripening onset. Also, the ratio of carotene versus carotenale utilization varied significantly. CONCLUSION:Pattern comparison among activity levels measured in vitro on chromoplast enriched fractions suggests that cleavage enzyme(s) other than Carotenoid Cleavage Dioxygenase 4 play a significant role in carotenoid breakdown during fruit development and ripening. © 2018 Society of Chemical Industry.
Genetic variation, population structure and linkage disequilibrium in peach commercial varieties.
Aranzana Maria José,Abbassi El-Kadri,Howad Werner,Arús Pere
BACKGROUND:Peach [Prunus persica (L.) Batsch] is one of the most economically important fruit crops that, due to its genetic and biological characteristics (small genome size, taxonomic proximity to other important species and short juvenile period), has become a model plant in genomic studies of fruit trees. Our aim was an in-depth study of the extent, distribution and structure of peach genetic variation in North American and European commercial varieties as well as old Spanish varieties and several founders used in the early USA peach breeding programmes. For this we genotyped 224 peach cultivars using 50 SSRs evenly distributed along the 8 linkage groups of the Prunus reference map. RESULTS:Genetic distance analysis based on SSRs divided the peach cultivars in three main groups based mainly on their fruit characteristics: melting flesh peaches, melting flesh nectarines and non-melting varieties. Whereas non-melting flesh peaches had a higher number of alleles than melting peaches and nectarines, they were more homozygous. With some exceptions ('Admiral Dewey', 'Early Crawford' and 'Chinese Cling'), the founder US cultivars clustered together with the commercial melting peaches, indicating that their germplasm is well represented in modern cultivars. Population structure analysis showed a similar subdivision of the sample into subpopulations. Linkage disequilibrium (LD) analysis in three unstructured, or barely structured, subpopulations revealed a high level of LD conservation in peach extending up to 13-15 cM. CONCLUSIONS:Using a much larger set of SSRs, our results confirm previous observations on peach variability and population structure and provide additional tools for breeding and breeders' rights enforcement. SSR data are also used for the estimation of marker mutation rates and allow pedigree inferences, particularly with founder genotypes of the currently grown cultivars, which are useful to understand the evolution of peach as a crop. Results on LD conservation can be explained by the self-pollinating nature of peach cultivated germplasm and by a bottleneck that occurred at the beginning of modern breeding practices. High LD suggests that the development of whole-genome scanning approaches is suitable for genetic studies of agronomically important traits in peach.
Assessment of organic acid accumulation and its related genes in peach.
Zheng Beibei,Zhao Li,Jiang Xiaohan,Cherono Sylvia,Liu JingJing,Ogutu Collins,Ntini Charmaine,Zhang Xiujun,Han Yuepeng
Fruit acidity is an important determinant of peach organoleptic quality, but its regulatory mechanism remains elusive. Measurement of organic acids in ripe fruits of seventy-five peach cultivars revealed the predominant components malate and citrate, accompanied by quinate. Organic acid accumulation increased at early stages of fruit growth, but exhibited a more dramatic reduction in low-acid cultivar during later stages of fruit development compared to high-acid cultivars. Low-acid cultivars showed citrate degradation and less transport of malate into the vacuole due to up- and down-regulation of a GABA pathway gene GAD and a malate transporter gene ALMT9, respectively. The NAD-MDH1 gene might control the rate-limiting step in malate synthesis, while three genes, PDK, PK, and ADH, could affect citrate synthesis through the pyruvate-to-acetyl-CoA-to-citrate pathway. Altogether, these results suggested that malate accumulation is controlled at the level of metabolism and vacuolar storage, while metabolism is crucial for citrate accumulation in peach.
Comparative Transcriptome and Microscopy Analyses Provide Insights into Flat Shape Formation in Peach ().
Guo Jian,Cao Ke,Li Yong,Yao Jia-Long,Deng Cecilia,Wang Qi,Zhu Gengrui,Fang Weichao,Chen Changwen,Wang Xinwei,Guan Liping,Ding Tiyu,Wang Lirong
Frontiers in plant science
Fruit shape is an important external characteristic that consumers use to select preferred fruit cultivars. In peach, the flat fruit cultivars have become more and more popular worldwide. Genetic markers closely linking to the flat fruit trait have been identified and are useful for marker-assisted breeding. However, the cellular and genetic mechanisms underpinning flat fruit formation are still poorly understood. In this study, we have revealed the differences in fruit cell number, cell size, and in gene expression pattern between the traditional round fruit and modern flat fruit cultivars. Flat peach cultivars possessed significantly lower number of cells in the vertical axis because cell division in the vertical direction stopped early in the flat fruit cultivars at 15 DAFB (day after full bloom) than in round fruit cultivars at 35 DAFB. This resulted in the reduction in vertical development in the flat fruit. Significant linear relationship was observed between fruit vertical diameter and cell number in vertical axis for the four examined peach cultivars ( = 0.9964) at maturation stage, and was also observed between fruit vertical diameter and fruit weight ( = 0.9605), which indicated that cell number in vertical direction contributed to the flat shape formation. Furthermore, in RNA-seq analysis, 4165 differentially expressed genes (DEGs) were detected by comparing RNA-seq data between flat and round peach cultivars at different fruit development stages. In contrast to previous studies, we discovered 28 candidate genes potentially responsible for the flat shape formation, including 19 located in the mapping site and 9 downstream genes. Our study indicates that flat and round fruit shape in peach is primarily determined by the regulation of cell production in the vertical direction during early fruit development.
Quantitative trait loci affecting reproductive phenology in peach.
Romeu José F,Monforte Antonio J,Sánchez Gerardo,Granell Antonio,García-Brunton Jesús,Badenes María L,Ríos Gabino
BMC plant biology
BACKGROUND:The reproductive phenology of perennial plants in temperate climates is largely conditioned by the duration of bud dormancy, and fruit developmental processes. Bud dormancy release and bud break depends on the perception of cumulative chilling and heat during the bud development. The objective of this work was to identify new quantitative trait loci (QTLs) associated to temperature requirements for bud dormancy release and flowering and to fruit harvest date, in a segregating population of peach. RESULTS:We have identified QTLs for nine traits related to bud dormancy, flowering and fruit harvest in an intraspecific hybrid population of peach in two locations differing in chilling time accumulation. QTLs were located in a genetic linkage map of peach based on single nucleotide polymorphism (SNP) markers for eight linkage groups (LGs) of the peach genome sequence. QTLs for chilling requirements for dormancy release and blooming clustered in seven different genomic regions that partially coincided with loci identified in previous works. The most significant QTL for chilling requirements mapped to LG1, close to the evergrowing locus. QTLs for heat requirement related traits were distributed in nine genomic regions, four of them co-localizing with QTLs for chilling requirement trait. Two major loci in LG4 and LG6 determined fruit harvest time. CONCLUSIONS:We identified QTLs associated to nine traits related to the reproductive phenology in peach. A search of candidate genes for these QTLs rendered different genes related to flowering regulation, chromatin modification and hormone signalling. A better understanding of the genetic factors affecting crop phenology might help scientists and breeders to predict changes in genotype performance in a context of global climate change.
Deep RNA-Seq uncovers the peach transcriptome landscape.
Wang Lu,Zhao Shuang,Gu Chao,Zhou Ying,Zhou Hui,Ma Juanjuan,Cheng Jun,Han Yuepeng
Plant molecular biology
Peach (Prunus persica) is one of the most important of deciduous fruit trees worldwide. To facilitate isolation of genes controlling important horticultural traits of peach, transcriptome sequencing was conducted in this study. A total of 133 million pair-end RNA-Seq reads were generated from leaf, flower, and fruit, and 90 % of reads were mapped to the peach draft genome. Sequence assembly revealed 1,162 transcription factors and 2,140 novel transcribed regions (NTRs). Of these 2,140 NTRs, 723 contain an open reading frame, while the rest 1,417 are non-coding RNAs. A total of 9,587 SNPs were identified across six peach genotypes, with an average density of one SNP per ~5.7 kb. The top of chromosome 2 has higher density of expressed SNPs than the rest of the peach genome. The average density of SSR is 312.5/Mb, with tri-nucleotide repeats being the most abundant. Most of the detected SSRs are AT-rich repeats and the most common di-nucleotide repeat is CT/TC. The predominant type of alternative splicing (AS) events in peach is exon-skipping isoforms, which account for 43 % of all the observed AS events. In addition, the most active transcribed regions in peach genome were also analyzed. Our study reveals for the first time the complexity of the peach transcriptome, and our results will be helpful for functional genomics research in peach.
Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach.
Rawandoozi Zena J,Hartmann Timothy P,Carpenedo Silvia,Gasic Ksenija,da Silva Linge Cassia,Cai Lichun,Van de Weg Eric,Byrne David H
BACKGROUND:Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time. RESULTS:Phenotypic data of seven F low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40-46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles. CONCLUSIONS:A multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.
New insights into the properties of pubescent surfaces: peach fruit as a model.
Fernández Victoria,Khayet Mohamed,Montero-Prado Pablo,Heredia-Guerrero José Alejandro,Liakopoulos Georgios,Karabourniotis George,Del Río Víctor,Domínguez Eva,Tacchini Ignacio,Nerín Cristina,Val Jesús,Heredia Antonio
The surface of peach (Prunus persica 'Calrico') is covered by a dense indumentum, which may serve various protective purposes. With the aim of relating structure to function, the chemical composition, morphology, and hydrophobicity of the peach skin was assessed as a model for a pubescent plant surface. Distinct physicochemical features were observed for trichomes versus isolated cuticles. Peach cuticles were composed of 53% cutan, 27% waxes, 23% cutin, and 1% hydroxycinnamic acid derivatives (mainly ferulic and p-coumaric acids). Trichomes were covered by a thin cuticular layer containing 15% waxes and 19% cutin and were filled by polysaccharide material (63%) containing hydroxycinnamic acid derivatives and flavonoids. The surface free energy, polarity, and work of adhesion of intact and shaved peach surfaces were calculated from contact angle measurements of water, glycerol, and diiodomethane. The removal of the trichomes from the surface increased polarity from 3.8% (intact surface) to 23.6% and decreased the total surface free energy chiefly due to a decrease on its nonpolar component. The extraction of waxes and the removal of trichomes led to higher fruit dehydration rates. However, trichomes were found to have a higher water sorption capacity as compared with isolated cuticles. The results show that the peach surface is composed of two different materials that establish a polarity gradient: the trichome network, which has a higher surface free energy and a higher dispersive component, and the cuticle underneath, which has a lower surface free energy and higher surface polarity. The significance of the data concerning water-plant surface interactions is discussed within a physiological context.
Nitrogen fertilization rates in a subtropical peach orchard: effects on tree vigor and fruit quality.
Rubio Ames Zilfina,Brecht Jeffrey K,Olmstead Mercy A
Journal of the science of food and agriculture
BACKGROUND:Nitrogen is a key component of crop production and is commonly related to increases in yield and fruit size. The N fertilization rates used for low-chill peach cultivars were adapted from other peach production regions, where environmental and soil conditions are different. The growth and production as well as the effect on fruit physical and compositional attributes of two low-chill peach cultivars - 'TropicBeauty' (TB) and 'UFSharp' (UFS) - with five different N fertilization rates (0 (N0), 45 (N1), 90 (N2), 179 (N3) and 269 (N4) kg ha applied each year from 2011 to 2017) were examined. RESULTS:Peach trees under higher N rates had higher pruning weights compared to the lower N0 or N1 rates. Yield was only affected in 2017 for the two cultivars tested. Physical attributes were inconsistently affected by N. Fruit from the higher N rates had lower a* value (more green) than fruit from the trees under low or zero N. While fruit firmness was not affected by N, fruit from trees under zero/low N had higher total soluble solids in some years. CONCLUSION:Considering that N is recycled in the trees, being retained and reused each season to resume growth, it is important to address peach orchard fertilization based on peach tree N status. The results of this experiment show that an increase in N beyond what is required for tree maintenance does not increase yield. In addition, reducing N does not strongly affect fruit quality, although the color and soluble solids results suggest that lower N rates may advance fruit maturation. © 2019 Society of Chemical Industry.
Genetic Transformation in Peach ( L.): Challenges and Ways Forward.
Ricci Angela,Sabbadini Silvia,Prieto Humberto,Padilla Isabel Mg,Dardick Chris,Li Zhijian,Scorza Ralph,Limera Cecilia,Mezzetti Bruno,Perez-Jimenez Margarita,Burgos Lorenzo,Petri Cesar
Plants (Basel, Switzerland)
Almost 30 years have passed since the first publication reporting regeneration of transformed peach plants. Nevertheless, the general applicability of genetic transformation of this species has not yet been established. Many strategies have been tested in order to obtain an efficient peach transformation system. Despite the amount of time and the efforts invested, the lack of success has significantly limited the utility of peach as a model genetic system for trees, despite its relatively short generation time; small, high-quality genome; and well-studied genetic resources. Additionally, the absence of efficient genetic transformation protocols precludes the application of many biotechnological tools in peach breeding programs. In this review, we provide an overview of research on regeneration and genetic transformation in this species and summarize novel strategies and procedures aimed at producing transgenic peaches. Promising future approaches to develop a robust peach transformation system are discussed, focusing on the main bottlenecks to success including the low efficiency of -mediated transformation, the low level of correspondence between cells competent for transformation and those that have regenerative competence, and the high rate of chimerism in the few shoots that are produced following transformation.
Association Mapping Analysis for Fruit Quality Traits in Using SNP Markers.
Font I Forcada Carolina,Guajardo Verónica,Chin-Wo Sebastian Reyes,Moreno María Ángeles
Frontiers in plant science
The identification of genes involved in variation of peach fruit quality would assist breeders to create new cultivars with improved fruit quality. Peach is a genetic and genomic model within the Rosaceae. A large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from the peach genome sequence was used in this study. A set of 94 individuals from a peach germplasm collection was phenotyped and genotyped, including local Spanish and modern cultivars maintained at the Experimental Station of Aula Dei, Spain. Phenotypic evaluation based on agronomical, pomological and fruit quality traits was performed at least 3 years. A set of 4,558 out of a total of 8,144 SNPs markers developed by the Illumina Infinium BeadArray (v1.0) technology platform, covering the peach genome, were analyzed for population structure analysis and genome-wide association studies (GWAS). Population structure analysis identified two subpopulations, with admixture within them. While one subpopulation contains only modern cultivars, the other one is formed by local Spanish and several modern cultivars from international breeding programs. To test the marker trait associations between markers and phenotypic traits, four models comprising both general linear model (GLM) and mixed linear model (MLM) were selected. The MLM approach using co-ancestry values from population structure and kinship estimates (K model) identified a maximum of 347 significant associations between markers and traits. The associations found appeared to map within the interval where many candidate genes involved in different pathways are predicted in the peach genome. These results represent a promising situation for GWAS in the identification of SNP variants associated to fruit quality traits, potentially applicable in peach breeding programs.
Phenotypic characterization of qualitative parameters and antioxidant contents in peach and nectarine fruit and changes after jam preparation.
Drogoudi Pavlina,Gerasopoulos Dimitrios,Kafkaletou Mina,Tsantili Eleni
Journal of the science of food and agriculture
BACKGROUND:Sugars and antioxidants in peaches contribute to fresh fruit quality and nutrition; however, information on widely grown cultivars and changes induced after peach jam preparation is limited. In the present study, colour, sugars and antioxidant parameters were determined in fruit and jam from 45 peach and nectarine cultivars. RESULTS:Pronounced varietal differences were found in sorbitol (42-fold range), total phenolics (TPs) and antioxidant capacities (10- to 19-fold range). Sorbitol levels were greater in non-melting peach, followed by nectarine, and lower values were found in melting peach cultivars. Late-harvested peach and nectarine cultivars tended to have a higher soluble solid content and antioxidant potential. Cultivars with relatively high antioxidant contents produced darker and redder jams, containing more antioxidants, than the jam or the fruit from the other cultivars. Jam-TPs were reduced by 48% compared to fruit-TPs, with greater reduction being noted in high antioxidant cultivars. The most favorable jam organoleptic characteristics were found in 'Morsiani 90', 'Amiga', 'Romea' and 'Alirosada', as well as in non-melting compared to melting peach cultivars. CONCLUSION:The best cultivars for each fruit flesh type and jam were identified. Peach jam could be an alternative substitute when fresh fruit is not available and when it is prepared with high antioxidant cultivars. © 2016 Society of Chemical Industry.
Assessment of Sugar Components and Genes Involved in the Regulation of Sucrose Accumulation in Peach Fruit.
Vimolmangkang Sornkanok,Zheng Hongyu,Peng Qian,Jiang Quan,Wang Huiliang,Fang Ting,Liao Liao,Wang Lu,He Huaping,Han Yuepeng
Journal of agricultural and food chemistry
Soluble sugar contents in mature fruits of 45 peach accessions were quantified using gas chromatography analysis. Sucrose is the predominant sugar in mature fruit, followed by glucose and fructose, which have similar concentrations. Overall, sucrose metabolism and accumulation are crucial determinants of sugar content in peach fruit, and there is a wide range of sucrose concentrations among peach genotypes. To understand the mechanisms regulating sucrose accumulation in peach fruit, expression profiles of genes involved in sucrose metabolism and transport were compared among four genotypes. Two sucrose-cleaving enzyme genes (SUS4 and NINV8), one gene involved in sucrose resynthesis (SPS3), and three sugar transporter genes (SUT2, SUT4, and TMT2) were prevalently expressed in peach fruit, and their expression levels are significantly correlated with sucrose accumulation. In contrast, the VAINV genes responsible for sucrose cleavage in the vacuole were weakly expressed in mature fruit, suggesting that the sucrose-cleaving reaction is not active in the vacuole of sink cells of mature peach fruit. This study suggests that sucrose accumulation in peach fruit involves the coordinated interaction of genes related to sucrose cleavage, resynthesis, and transport, which could be helpful for future peach breeding.
Variation in minerals, phenolics and antioxidant activity of peel and pulp of different varieties of peach (Prunus persica L.) fruit from Pakistan.
Manzoor Maleeha,Anwar Farooq,Mahmood Zahed,Rashid Umer,Ashraf Muhammad
Molecules (Basel, Switzerland)
Peach (Prunus persica L.), being a potential source of bioactive compounds, has been demonstrated to have medicinal benefits. In this study variation of minerals and antioxidant characteristics (total phenolic contents, total flavonoid contents, reducing power, inhibition of peroxidation using linoleic acid system and DPPH free radical scavenging activity) between peel and pulp parts of different peach varieties, namely Golden, Shireen, and Shahpasand were investigated. The peel and pulp extracts, derived from the varieties analyzed, exhibited an appreciable amount of total phenolics (TP) and total flavonoids (TF), ranging from 1,209.3-1,354.5, 711.7-881.3 mg GAE/100 g and 599.7-785.5, 301.3-499.7 mg CE/100 g on a dry weight basis, respectively. Reducing power of peel and pulp extracts (12.5 mg/mL concentration) ranged from 2.57-2.77 and 1.54-1.99.The inhibition of linoleic acid peroxidation and DPPH scavenging activity of the extracts varied from 70.8-80.9% and 66.8-76.5% in peels, and 51.9-60.1% and 43.4-49.1% in pulps. The mineral analysis revealed that the content of K was highest in both parts of the peach fruit followed by Mg, Ca, Fe, Mn and Zn. The results of our present study indicate that peach peel had significantly higher levels of minerals, antioxidant capacity and phenolics than those of the pulp, suggesting the intake of unpeeled peach as a potential source of high-value components. The peach peel can be a useful as a viable source of natural antioxidants for functional foods and nutraceutical applications.
The contribution of stored malate and citrate to the substrate requirements of metabolism of ripening peach (Prunus persica L. Batsch) flesh is negligible. Implications for the occurrence of phosphoenolpyruvate carboxykinase and gluconeogenesis.
Famiani Franco,Farinelli Daniela,Moscatello Stefano,Battistelli Alberto,Leegood Richard C,Walker Robert P
Plant physiology and biochemistry : PPB
The first aim of this study was to determine the contribution of stored malate and citrate to the substrate requirements of metabolism in the ripening flesh of the peach (Prunus persica L. Batsch) cultivar Adriatica. In the flesh, stored malate accumulated before ripening could contribute little or nothing to the net substrate requirements of metabolism. This was because there was synthesis and not dissimilation of malate throughout ripening. Stored citrate could potentially contribute a very small amount (about 5.8%) of the substrate required by metabolism when the whole ripening period was considered, and a maximum of about 7.5% over the latter part of ripening. The second aim of this study was to investigate why phosphoenolpyruvate carboxykinase (PEPCK) an enzyme utilised in gluconeogenesis from malate and citrate is present in peach flesh. The occurrence and localisation of enzymes utilised in the metabolism of malate, citrate and amino acids were determined in peach flesh throughout its development. Phosphoenolpyruvate carboxylase (essential for the synthesis of malate and citrate) was present in the same cells and at the same time as PEPCK and NADP-malic enzyme (both utilised in the dissimilation of malate and citrate). A hypothesis is presented to explain the presence of these enzymes and to account for the likely occurrence of gluconeogenesis.
Rootstock and fruit canopy position affect peach [Prunus persica (L.) Batsch] (cv. Rich May) plant productivity and fruit sensorial and nutritional quality.
Gullo Gregorio,Motisi Antonio,Zappia Rocco,Dattola Agostino,Diamanti Jacopo,Mezzetti Bruno
The right combination of rootstock and training system is important for increased yield and fruit sensorial and nutritional homogeneity and quality with peach [Prunus persica (L.) Batsch]. We investigated the effects of rootstock and training system on these parameters, testing the effect of vigorous GF677 and weaker Penta rootstock on 'Rich May' peach cultivar. Fruit position effects regarding photosynthetically active radiation availability, along the canopy profile using the Y training system, were investigated. The positive relationships between total polyphenols content and antioxidant capacity according to canopy vigour and architecture were determined for the two scion/stock combinations. Changes in fruit epicarp colour and content of bioactive compounds were also determined. Lower-vigour trees from Penta rootstock grafting yielded larger fruit with improved skin overcolour, and greater total polyphenols content and antioxidant capacity. GF677 rootstock produced more vigorous trees with fruit with lower sensorial and nutritional parameters. Canopy position strongly affects fruit sensorial and nutritional qualities. These data define potential for improvements to peach production efficiency and fruit quality, particularly for southern Europe peach cultivation conditions.
Deciphering the interplay among genotype, maturity stage and low-temperature storage on phytochemical composition and transcript levels of enzymatic antioxidants in Prunus persica fruit.
Manganaris George A,Drogoudi Pavlina,Goulas Vlasios,Tanou Georgia,Georgiadou Egli C,Pantelidis George E,Paschalidis Konstantinos A,Fotopoulos Vasileios,Manganaris Athanasios
Plant physiology and biochemistry : PPB
The aim of this study was to understand the antioxidant metabolic changes of peach (cvs. 'Royal Glory', 'Red Haven' and 'Sun Cloud') and nectarine fruits (cv. 'Big Top') exposed to different combinations of low-temperature storage (0, 2, 4 weeks storage at 0 °C, 90% R.H.) and additional ripening at room temperature (1, 3 and 5 d, shelf life, 20 °C) with an array of analytical, biochemical and molecular approaches. Initially, harvested fruit of the examined cultivars were segregated non-destructively at advanced and less pronounced maturity stages and qualitative traits, physiological parameters, phytochemical composition and antioxidant capacity were determined. 'Big Top' and 'Royal Glory' fruits were characterized by slower softening rate and less pronounced ripening-related alterations. The coupling of HPLC fingerprints, consisted of 7 phenolic compounds (chlorogenic, neochlorogenic acid, catechin, epicatechin, rutin, quecetin-3-O-glucoside, procyanidin B1) and spectrophotometric methods disclosed a great impact of genotype on peach bioactive composition, with 'Sun Cloud' generally displaying the highest contents. Maturity stage at harvest did not seem to affect fruit phenolic composition and no general guidelines for the impact of cold storage and shelf-life on individual phenolic compounds can be extrapolated. Subsequently, fruit of less pronounced maturity at harvest were used for further molecular analysis. 'Sun Cloud' was proven efficient in protecting plasmid pBR322 DNA against ROO attack throughout the experimental period and against HO attack after 2 and 4 weeks of cold storage. Interestingly, a general down-regulation of key genes implicated in the antioxidant apparatus with the prolongation of storage period was recorded; this was more evident for CAT, cAPX, Cu/ZnSOD2, perAPX3 and GPX8 genes. Higher antioxidant capacity of 'Sun Cloud' fruit could potentially be linked with compounds other than enzymatic antioxidants that further regulate peach fruit ripening.
Construction of a high-density SNP-based genetic map and identification of fruit-related QTLs and candidate genes in peach [Prunus persica (L.) Batsch].
Shi Pei,Xu Ze,Zhang Shaoyu,Wang Xianju,Ma Xiaofei,Zheng Jicheng,Xing Libo,Zhang Dong,Ma Juanjuan,Han Mingyu,Zhao Caiping
BMC plant biology
BACKGROUND:High-density genetic mapping is a valuable tool for mapping loci that control specific traits for perennial fruit trees. Peach is an economically important fruit tree and a model Rosaceae species for genomic and genetic research. In peach, even though many molecular markers, genetic maps and QTL mappings have been reported, further research on the improvement of marker numbers, map densities, QTL accuracy and candidate gene identification is still warranted. RESULTS:A high-density single nucleotide polymorphism (SNP)-based peach linkage map was constructed using specific locus amplified fragment sequencing (SLAF-seq). This genetic map consisted of 7998 SLAF markers, spanning 1098.79 cM with an average distance of 0.17 cM between adjacent markers. A total of 40 QTLs and 885 annotated candidate genes were detected for 10 fruit-related traits, including fruit weight (FW), fruit diameter (FD), percentage of red skin colour (PSC), eating quality (EQ), fruit flavour (FV), red in flesh (RF), red around pit (RP), adherence to pit (AP), fruit development period (FDP) and fruit fibre content (FFC). Eighteen QTLs for soluble solid content (SSC) were identified along LGs 1, 4, 5, and 6 in 2015 and 2016, and 540 genes were annotated in QTL intervals. Thirty-two QTLs for fruit acidity content (FA) were detected on LG1, and 2, 4, 5, 6, and 1232 candidate genes were identified. The expression profiles of 2 candidate genes for SSC and 4 for FA were analysed in parents and their offspring. CONCLUSIONS:We constructed a high-density genetic map in peach based on SLAF-seq, which may contribute to the identification of important agronomic trait loci. Ninety QTLs for 12 fruit-related traits were identified, most of which overlapped with previous reports, and some new QTLs were obtained. A large number of candidate genes for fruit-related traits were screened and identified. These results may improve our understanding of the genetic control of fruit quality traits and provide useful information in marker-assisted selection for fruit quality in peach breeding programmes.
Investigation of the aroma of commercial peach (Prunus persica L. Batsch) types by Proton Transfer Reaction-Mass Spectrometry (PTR-MS) and sensory analysis.
Bianchi Tiago,Weesepoel Yannick,Koot Alex,Iglesias Ignasi,Eduardo Iban,Gratacós-Cubarsí Marta,Guerrero Luis,Hortós Maria,van Ruth Saskia
Food research international (Ottawa, Ont.)
The aim of this study was to investigate the aroma and sensory profiles of various types of peaches (Prunus persica L. Batsch.). Forty-three commercial cultivars comprising peaches, flat peaches, nectarines, and canning peaches (pavías) were grown over two consecutive harvest years. Fruits were assessed for chemical aroma and sensory profiles. Chemical aroma profile was obtained by proton transfer reaction-mass spectrometry (PTR-MS) and spectral masses were tentatively identified with PTR-Time of Flight-MS (PTR-Tof-MS). Sensory analysis was performed at commercial maturity considering seven aroma/flavor attributes. The four types of peaches showed both distinct chemical aroma and sensory profiles. Flat peaches and canning peaches showed most distinct patterns according to discriminant analysis. The sensory data were related to the volatile compounds by partial least square regression. γ-Hexalactone, γ-octalactone, hotrienol, acetic acid and ethyl acetate correlated positively, and benzeneacetaldehyde, trimethylbenzene and acetaldehyde negatively to the intensities of aroma and ripe fruit sensory scores.
Profiling sugar metabolism during fruit development in a peach progeny with different fructose-to-glucose ratios.
Desnoues Elsa,Gibon Yves,Baldazzi Valentina,Signoret Véronique,Génard Michel,Quilot-Turion Bénédicte
BMC plant biology
BACKGROUND:Fruit taste is largely affected by the concentration of soluble sugars and organic acids and non-negligibly by fructose concentration, which is the sweetest-tasting sugar. To date, many studies investigating the sugars in fruit have focused on a specific sugar or enzyme and often on a single variety, but only a few detailed studies addressing sugar metabolism both as a whole and dynamic system are available. In commercial peach fruit, sucrose is the main sugar, followed by fructose and glucose, which have similar levels. Interestingly, low fructose-to-glucose ratios have been observed in wild peach accessions. A cross between wild peach and commercial varieties offers an outstanding possibility to study fruit sugar metabolism. RESULTS:This work provides a large dataset of sugar composition and the capacities of enzymes that are involved in sugar metabolism during peach fruit development and its genetic diversity. A large fraction of the metabolites and enzymes involved in peach sugar metabolism were assayed within a peach progeny of 106 genotypes, of which one quarter displayed a low fructose-to-glucose ratio. This profiling was performed at six stages of growth using high throughput methods. Our results permit drawing a quasi-exhaustive scheme of sugar metabolism in peach. The use of a large number of genotypes revealed a remarkable robustness of enzymatic capacities across genotypes and years, despite strong variations in sugar composition, in particular the fructose-to-glucose ratio, within the progeny. A poor correlation was also found between the enzymatic capacities and the accumulation rates of metabolites. CONCLUSIONS:These results invalidate the hypothesis of the straightforward enzymatic control of sugar concentration in peach fruit. Alternative hypotheses concerning the regulation of fructose concentration are discussed based on experimental data. This work lays the foundation for a comprehensive study of the mechanisms involved in sugar metabolism in developing fruit.
Water scarcity conditions affect peach fruit size and polyphenol contents more severely than other fruit quality traits.
Rahmati Mitra,Vercambre Gilles,Davarynejad Gholamhossein,Bannayan Mohammad,Azizi Majid,Génard Michel
Journal of the science of food and agriculture
BACKGROUND:The literature abounds with the impacts of drought conditions on the concentration of non-structural compounds (NSC) in peach fruits without distinction as to the direct effect of drought on fruit metabolism and its indirect effect through dilution. Moreover, there is a need to investigate the sensitivity of the fruit composition to progressive water deficit in semi-arid conditions, as well as the origin of variations in fruit composition - not only in carbohydrates and organic acids, but also in secondary metabolites such as polyphenols. RESULTS:The increase in stress intensity resulted in smaller fruits and a reduction in yield. Drought increased fruit dry matter content, structural dry matter (SDM) content and firmness due to lower water import to fruits, although drought reduced fruit surface conductance and its transpiration. Drought significantly affected the concentrations of each NSC either through the decrease in dilution and/or modifications of their metabolism. The increase in hexoses and sorbitol concentrations of fruits grown under drought conditions resulted in an increase in the sweetness index but not near harvest. Malic acid concentration and content:SDM ratio increased as drought intensified, whereas those of citric and quinic acids decreased. Polyphenol concentration and content increased under severe drought. CONCLUSION:The increase in stress intensity strongly affected fruit mass. The concentration of total carbohydrates and organic acid at harvest increased mainly through a decrease in fruit dilution, whereas the concentrations of polyphenols were also strongly affected through an impact on their metabolism.
Evaluation of fruit quality, bioactive compounds and total antioxidant activity of flat peach cultivars.
Di Vaio Claudio,Marallo Nadia,Graziani Giulia,Ritieni Alberto,Di Matteo Antonio
Journal of the science of food and agriculture
BACKGROUND:Fruit quality traits (fresh weight, dry weight, soluble solids content, titratable acidity and firmness) as well as the content of bioactive compounds (phenolic compounds) and total antioxidant activity were evaluated in four commercial cultivars of peach (Greta, Ufo 4, Rome Star and Ufo 6) and four of nectarine (Neve, Planet 1, Maria Carla and Mesembrina) differing in fruit shape (standard or flat) and flesh colour (white or yellow), important cultivars of the Italian and foreign market. The higher fruit organoleptic quality and nutritional profile of flat peach and nectarine cultivars make them candidates for exploiting new market opportunities and the chance to improve profits of farmers. RESULTS:The results showed that assayed quality parameters differed greatly among cultivars. In particular, flesh color and fruit shape accounted for most of the variation in traits underlying organoleptic and nutritional quality. CONCLUSION:Overall data suggested that the flat white-fleshed nectarine Planet 1, the yellow-fleshed nectarine Mesembrina and the yellow-fleshed peach Ufo 6, because of their profiles in terms of soluble solids content, titratable acidity and bioactive compounds, have the greatest potential to meet current consumer requirements.
Sugars in peach fruit: a breeding perspective.
Cirilli Marco,Bassi Daniele,Ciacciulli Angelo
The last decade has been characterized by a decrease in peach (Prunus persica) fruit consumption in many countries, foremost due to unsatisfactory quality. The sugar content is one of the most important quality traits perceived by consumers, and the development of novel peach cultivars with sugar-enhanced content is a primary objective of breeding programs to revert the market inertia. Nevertheless, the progress reachable through classical phenotypic selection is limited by the narrow genetic bases of peach breeding material and by the complex quantitative nature of the trait, which is deeply affected by environmental conditions and agronomical management. The development of molecular markers applicable in MAS or MAB has become an essential strategy to boost the selection efficiency. Despite the enormous advances in 'omics' sciences, providing powerful tools for plant genotyping, the identification of the genetic bases of sugar-related traits is hindered by the lack of adequate phenotyping methods that are able to address strong within-plant variability. This review provides an overview of the current knowledge of the metabolic pathways and physiological mechanisms regulating sugar accumulation in peach fruit, the main advances in phenotyping approaches and genetic background, and finally addressing new research priorities and prospective for breeders.
Development of a rapid and direct method for the determination of organic acids in peach fruit using LC-ESI-MS.
Sandín-España Pilar,Mateo-Miranda M,López-Goti Carmen,De Cal A,Alonso-Prados José Luis
An accurate, simple and rapid liquid chromatography mass spectrometry method for the determination of organic acids in peach fruit has been developed. Direct injection and sample clean-up with a mixed-mode sorbent was compared. The best results for the determination of gluconic, oxalic, malic, citric and fumaric acids were obtained with only a simple dilution and filtration step, and nylon filters should be avoided since some organic acids are retained by them. It is the first time that gluconic acid has been determined in peach fruit. Different parameters involved in the separation and detection process have been optimized. Since matrix effects were observed in the peach commodity, organic acids were quantified by the standard addition method. All validation parameters of the method were found acceptable of all organic acids. Finally, the method was successfully applied to the analysis of samples of peach from two cultivars.
Transcriptome analysis of peach (Prunus persica L. Batsch) during the late stage of fruit ripening.
Pan H F,Sheng Y,Gao Z H,Chen H L,Qi Y J,Yi X K,Qin G H,Zhang J Y
Genetics and molecular research : GMR
Fruit ripening is a complex developmental process, the details of which remain largely unknown in fleshy fruits. In this paper, the fruit flesh of two peach varieties, "Zhongyou9" (a nectarine; Prunus persica L. Batsch) and its mutant "Hongyu", was analyzed by RNA-seq technology during two stages of ripening at 20-day intervals. One hundred and eighty significant upregulated and two hundred and thirty-five downregulated genes were identified in the experiment. Many of these genes were related to plant hormones, chlorophyll breakdown, accumulation of aroma and flavor volatiles, and stress. To the best of our knowledge, this is the first transcriptome analysis of peach ripening, and our data will be useful for further studies of the molecular basis of fruit ripening.
A deletion affecting an LRR-RLK gene co-segregates with the fruit flat shape trait in peach.
In peach, the flat phenotype is caused by a partially dominant allele in heterozygosis (Ss), fruits from homozygous trees (SS) abort a few weeks after fruit setting. Previous research has identified a SSR marker (UDP98-412) highly associated with the trait, found suitable for marker assisted selection (MAS). Here we report a ∼10 Kb deletion affecting the gene PRUPE.6G281100, 400 Kb upstream of UDP98-412, co-segregating with the trait. This gene is a leucine-rich repeat receptor-like kinase (LRR-RLK) orthologous to the Brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) group. PCR markers suitable for MAS confirmed its strong association with the trait in a collection of 246 cultivars. They were used to evaluate the DNA from a round fruit derived from a somatic mutation of the flat variety 'UFO-4', revealing that the mutation affected the flat associated allele (S). Protein BLAST alignment identified significant hits with genes involved in different biological processes. Best protein hit occurred with AtRLP12, which may functionally complement CLAVATA2, a key regulator that controls the stem cell population size. RT-PCR analysis revealed the absence of transcription of the partially deleted allele. The data support PRUPE.6G281100 as a candidate gene for flat shape in peach.
Disentangling the Effects of Water Stress on Carbon Acquisition, Vegetative Growth, and Fruit Quality of Peach Trees by Means of the QualiTree Model.
Rahmati Mitra,Mirás-Avalos José M,Valsesia Pierre,Lescourret Françoise,Génard Michel,Davarynejad Gholam H,Bannayan Mohammad,Azizi Majid,Vercambre Gilles
Frontiers in plant science
Climate change projections predict warmer and drier conditions. In general, moderate to severe water stress reduce plant vegetative growth and leaf photosynthesis. However, vegetative and reproductive growths show different sensitivities to water deficit. In fruit trees, water restrictions may have serious implications not only on tree growth and yield, but also on fruit quality, which might be improved. Therefore, it is of paramount importance to understand the complex interrelations among the physiological processes involved in within-tree carbon acquisition and allocation, water uptake and transpiration, organ growth, and fruit composition when affected by water stress. This can be studied using process-based models of plant functioning, which allow assessing the sensitivity of various physiological processes to water deficit and their relative impact on vegetative growth and fruit quality. In the current study, an existing fruit-tree model (QualiTree) was adapted for describing the water stress effects on peach ( L. Batsch) vegetative growth, fruit size and composition. First, an energy balance calculation at the fruit-bearing shoot level and a water transfer formalization within the plant were integrated into the model. Next, a reduction function of vegetative growth according to tree water status was added to QualiTree. Then, the model was parameterized and calibrated for a late-maturing peach cultivar ("Elberta") under semi-arid conditions, and for three different irrigation practices. Simulated vegetative and fruit growth variability over time was consistent with observed data. Sugar concentrations in fruit flesh were well simulated. Finally, QualiTree allowed for determining the relative importance of photosynthesis and vegetative growth reduction on carbon acquisition, plant growth and fruit quality under water constrains. According to simulations, water deficit impacted vegetative growth first through a direct effect on its sink strength, and; secondly, through an indirect reducing effect on photosynthesis. Fruit composition was moderately affected by water stress. The enhancements performed in the model broadened its predictive capabilities and proved that QualiTree allows for a better understanding of the water stress effects on fruit-tree functioning and might be useful for designing innovative horticultural practices in a changing climate scenario.
A kinetic model of sugar metabolism in peach fruit reveals a functional hypothesis of a markedly low fructose-to-glucose ratio phenotype.
Desnoues Elsa,Génard Michel,Quilot-Turion Bénédicte,Baldazzi Valentina
The Plant journal : for cell and molecular biology
The concentrations of sugars in fruit vary with fruit development, environment and genotype. In general, there were weak correlations between the variations in sugar concentrations and the activities of enzymes directly related with the synthesis or degradation of sugars. This finding suggests that the relationships between enzyme activities and metabolites are often non-linear and are difficult to assess. To simulate the concentrations of sucrose, glucose, fructose and sorbitol during the development of peach fruit, a kinetic model of sugar metabolism was developed by taking advantage of recent profiling data. Cell compartmentation (cytosol and vacuole) was described explicitly, and data-driven enzyme activities were used to parameterize equations. The model correctly accounts for both annual and genotypic variations, which were observed in 10 genotypes derived from an interspecific cross. They provided important information on the mechanisms underlying the specification of phenotypic differences. In particular, the model supports the hypothesis that a difference in fructokinase affinity could be responsible for a low fructose-to-glucose ratio phenotype, which was observed in the studied population.
Inhibitory Potential against Digestive Enzymes Linked to Obesity and Type 2 Diabetes and Content of Bioactive Compounds in 20 Cultivars of the Peach Fruit Grown in Poland.
Nowicka Paulina,Wojdyło Aneta,Laskowski Piotr
Plant foods for human nutrition (Dordrecht, Netherlands)
The presented study provides important insights on the health properties of Prunus persica fruit related to their polyphenol and carotenoid profiles, antioxidant capacity and in vitro potential to inhibit enzymes relevant to type 2 diabetes (α-amylase, α-glucosidase) and obesity (pancreatic lipase) management. Such results have not been published so far. The study showed substantial differences in the chemical composition of peach fruit depending on the cultivar. At the same time, it demonstrated some common features of selected cultivars - the varieties with light flesh ('Spring Time'; 'Madison') were characterized by a high content of phenolic acids and flavonols, thus exhibiting high activity against α-amylase, while the yellow varieties with high content of carotenoids ('Harrow Diamond'; 'Harrow Beauty') showed high inhibitory activity toward porcine pancreatic lipase. Finally, it has been shown that peach fruit is an interesting raw material with a varied chemical composition and nutritional value, especially with high inhibitory potential against digestive enzymes linked to obesity and type 2 diabetes, strongly determined by the cultivar.
Genome re-sequencing reveals the evolutionary history of peach fruit edibility.
Yu Yang,Fu Jun,Xu Yaoguang,Zhang Jiewei,Ren Fei,Zhao Hongwei,Tian Shilin,Guo Wei,Tu Xiaolong,Zhao Jing,Jiang Dawei,Zhao Jianbo,Wu Weiying,Wang Gaochao,Ma Rongcai,Jiang Quan,Wei Jianhua,Xie Hua
Peach (Prunus persica) is an economically important fruit crop and a well-characterized model for studying Prunus species. Here we explore the evolutionary history of peach using a large-scale SNP data set generated from 58 high-coverage genomes of cultivated peach and closely related relatives, including 44 newly re-sequenced accessions and 14 accessions from a previous study. Our analyses suggest that peach originated about 2.47 Mya in southwest China in glacial refugia generated by the uplift of the Tibetan plateau. Our exploration of genomic selection signatures and demographic history supports the hypothesis that frugivore-mediated selection occurred several million years before the eventual human-mediated domestication of peach. We also identify a large set of SNPs and/or CNVs, and candidate genes associated with fruit texture, taste, size, and skin color, with implications for genomic-selection breeding in peach. Collectively, this study provides valuable information for understanding the evolution and domestication of perennial fruit tree crops.
Refining the Genomic Region Containing a Major Locus Controlling Fruit Maturity in Peach.
Elsadr H,Sherif S,Banks T,Somers D,Jayasankar S
Maturity date (MD), defined as the duration between the first calendar day of the year and maturity, and fruit development period (FDP), defined as the duration between full bloom and maturity, are highly variable in peach [Prunus persica (L.) Batsch]. There is a need to discover molecular markers associated with these traits in order to enhance the efficiency and reliability of breeding for extending the harvest season in peach. An association mapping population consisting of 132 peach accessions was phenotypically evaluated for MD and FDP, and genotypically characterized using the genotyping-by-sequencing (GBS) approach. The phenotypic and genotypic data collected were used to conduct a genome-wide association study (GWAS). The GWAS identified three SNPs on chromosome 4 that are significantly associated with both FDP and MD. These three SNPs covered a region of 43,067 bp; we referred to this region as the MD/FDP locus. Seven genes were identified in the MD/FDP locus. One or more of these genes is believed to regulate some aspect of maturity in peach. The data reported here is expected to aid in marker-assisted seedling selection (MASS) targeted towards widening peach germplasm for maturity, particularly early maturity.
Hot air and UV-C treatments promote anthocyanin accumulation in peach fruit through their regulations of sugars and organic acids.
Zhou Dandan,Li Rui,Zhang Hui,Chen Shaoxia,Tu Kang
In our present study, we aimed to explore the effects of hot air and UV-C on anthocyanins and the interaction among anthocyanin, sucrose and organic acids in peaches during postharvest storage. Peaches were treated with hot air or UV-C and stored at 1 °C for 35 days. The results showed that both treatments significantly enhanced the accumulation of anthocyanins and suppressed the degradation of sucrose, citric and malic acids. An in vitro test verified that sucrose, citric and malic acid penetrated the tissue and then induced the biosynthesis of anthocyanins by up regulating anthocyanin-related enzymes. In addition, hot air and UV-C directly enhanced the activities and gene expression of related enzymes to promote the accumulation of anthocyanins. PAL, ANS and UFGT played crucial roles in the biosynthesis of anthocyanins in peach fruit after harvest, and these three enzymes can be stimulated by HA, UV-C, sucrose, citric and malic acid.
An integrated peach genome structural variation map uncovers genes associated with fruit traits.
Guo Jian,Cao Ke,Deng Cecilia,Li Yong,Zhu Gengrui,Fang Weichao,Chen Changwen,Wang Xinwei,Wu Jinlong,Guan Liping,Wu Shan,Guo Wenwu,Yao Jia-Long,Fei Zhangjun,Wang Lirong
BACKGROUND:Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored. RESULTS:Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in Prupe.4G186800, which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of PpMYB10.1 is associated with flesh color around the stone. In addition, a 1.67 Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1, regulates flat shape formation. CONCLUSIONS:The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.
Determination of Biochemical Composition in Peach ( L. Batsch) Accessions Characterized by Different Flesh Color and Textural Typologies.
Serra Sara,Anthony Brendon,Masia Andrea,Giovannini Daniela,Musacchi Stefano
Foods (Basel, Switzerland)
The rising interest in beneficial health properties of polyphenol compounds in fruit initiated this investigation about biochemical composition in peach mesocarp/exocarp. Biochemical evaluation of phenolic compounds and ascorbic acid were quantified through high-performance liquid chromatography (HPLC) in relation to three flesh colors (white, yellow and red) and four flesh typologies (melting, non-melting, slow softening and stony hard) within six commercial cultivars and eight breeding selections of peach/nectarine in 2007. While in 2008, quality and sensorial analyses were conducted on only three commercial cultivars ('Big Top', 'Springcrest' and 'Ghiaccio 1'). The red flesh selection demonstrated the highest levels of phenolic compounds (in mesocarp/exocarp) and ascorbic acid. Total phenolic concentration was approximately three-fold higher in the exocarp than the mesocarp across all accessions. Breeding selections generally reported higher levels of phenolics than commercial cultivars. Flesh textural typologies justified firmness differences at harvest, but minimally addressed variations in quality and phenolic compounds. Flesh pigmentation explained variation in the biochemical composition, with the red flesh accession characterized by an abundancy of phenolic compounds and a high potential for elevated antioxidant activity. Sensorial analyses ranked the cultivar with high soluble solids concentration:titratable acidity (SSC:TA) and reduced firmness the highest overall. Red flesh is a highly desirable trait for breeding programs aiming to improve consumption of peaches selected for nutraceutical properties.
Comparative mapping and marker-assisted selection in Rosaceae fruit crops.
Dirlewanger Elisabeth,Graziano Enrique,Joobeur Tarek,Garriga-Calderé Francesc,Cosson Patrick,Howad Werner,Arús Pere
Proceedings of the National Academy of Sciences of the United States of America
The development of saturated linkage maps using transferable markers, restriction fragment length polymorphisms, and micro-satellites has provided a foundation for fruit tree genetics and breeding. A Prunus reference map with 562 such markers is available, and a further set of 13 maps constructed with a subset of these markers has allowed genome comparison among seven Prunus diploid (x = 8) species (almond, peach, apricot, cherry, Prunus ferganensis, Prunus davidiana, and Prunus cerasifera); marker colinearity was the rule with all of them. Preliminary results of the comparison between apple and Prunus maps suggest a high level of synteny between these two genera. Conserved genomic regions have also been detected between Prunus and Arabidopsis. By using the data from different linkage maps anchored with the reference Prunus map, it has been possible to establish, in a general map, the position of 28 major genes affecting agronomic characters found in different species. Markers tightly linked to the major genes responsible for the expression of important traits (disease/pest resistances, fruit/nut quality, self-incompatibility, etc.) have been developed in apple and Prunus and are currently in use for marker-assisted selection in breeding programs. Quantitative character dissection using linkage maps and candidate gene approaches has already started. Genomic tools such as the Prunus physical map, large EST collections in both Prunus and Malus, and the establishment of the map position of high numbers of ESTs are required for a better understanding of the Rosaceae genome and to foster additional research and applications on fruit tree genetics.
Peach fruit: metabolic comparative analysis of two varieties with different resistances to insect attacks by NMR spectroscopy.
Capitani Donatella,Sobolev Anatoly P,Tomassini Alberta,Sciubba Fabio,De Salvador Flavio Roberto,Mannina Luisa,Delfini Maurizio
Journal of agricultural and food chemistry
The metabolite profile of aqueous extracts of two peach varieties, Percoca Romagnola 7 and Flaminia, with different susceptibilities to Ceratitis capitata attack was investigated by means of 1D and 2D high-field NMR spectroscopy. Water-soluble metabolites belonging to different classes such as organic acids (citric, fumaric, malic, quinic, shikimic, and succinic acids), sugars (fucose, fructose, fructose-6-phosphate, glucose, glucose-6-phosphate, rhamnose, sucrose, and xylose), amino acids (alanine, asparagine, isoleucine, threonine, and valine) and other metabolites such as myo-inositol, choline, trigonelline, catechin, chlorogenic and neochlorogenic acids, orthophosphate, and α-l-glycerophosphorylcholine were identified. The metabolite profile together with a suitable statistical analysis was used to make a comparison between the two varieties. The levels of glucose, xylose, myo-inositol, choline, isoleucine, and valine were found to be higher in Flaminia than in Percoca Romagnola 7 samples, whereas the levels of fumaric acid, alanine, quinic acid, sucrose, fucose, and chlorogenic and neochlorogenic acid were found to be higher in Percoca Romagnola 7 than in Flaminia samples.
Simple sequence repeat (SSR) analysis for assessment of genetic variability in apricot germplasm.
Zhebentyayeva T N,Reighard G L,Gorina V M,Abbott A G
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Thirty SSR primer combinations, developed from peach SSR-enriched genomic libraries and BAC libraries of peach [ Prunus persica (L.) Batsch.], were tested for cross amplification with 74 apricot ( Prunus armeniaca L.) germplasm accessions. Twelve primer pairs amplified 14 polymorphic SSR loci useful for discriminating most apricot cultivars, as well as for investigating patterns of variation in apricot germplasm. Levels of polymorphism were higher than the levels described using other codominant marker systems (i.e., isozymes, RFLP markers). Overall, 107 alleles were identified, and all but 11 accessions were unambiguously discriminated. Genetic differentiation of native germplasm into traditional ecogeographical groups was low, with a high level of genetic identity (> 0.75) between the groups. However, neighbor joining cluster analysis of marker distances between cultivars reflected the complex history of apricot domestication, producing groupings not evidently based on the geographical origin of the cultivars. Distant positioning of Chinese cultivars on UPGMA and neighbor joining dendrograms supports the authors' consideration of Chinese apricots as subspecies, Prunus armeniaca var. ansu Maxim., rather than a separate species.
Peach fruit ripening: A proteomic comparative analysis of the mesocarp of two cultivars with different flesh firmness at two ripening stages.
Prinsi Bhakti,Negri Alfredo Simone,Fedeli Chiara,Morgutti Silvia,Negrini Noemi,Cocucci Maurizio,Espen Luca
A proteomic analysis was conducted on peach fruit mesocarp in order to better elucidate the biochemical and physiological events which characterize the transition of fruit from the "unripe" to the "ripe" phase. The first goal of the present work was to set-up a protocol suitable for improving protein extraction from peach mesocarp. The use of freeze-dried powdered tissue, together with the addition of phenol prior to the extraction with an aqueous buffer, significantly increased the protein yield and the quality of 2-DE gels. The proteomic profiles of the mesocarp from peach fruit of a non-melting flesh (NMF; 'Oro A') and a melting flesh (MF; 'Bolero') cultivar, at "unripe" and "ripe" stages as defined by some parameters typical of ripening, were then analyzed. The comparative analysis of the 2-DE gels showed that in NMF and MF peaches the relative volumes of 53 protein spots significantly changed in relation to both the ripening stage ("unripe" versus "ripe") and/or the genetic background of the cultivar ('Oro A' versus 'Bolero'). Thirty out of the 53 differently abundant spots were identified by LC-ESI-MS/MS. The analysis revealed enzymes involved in primary metabolism (e.g. C-compounds, carbohydrates, organic acids and amino acids) and in ethylene biosynthesis as well as proteins involved in secondary metabolism and responses to stress. Among these, 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) appeared to be one of the proteins with the largest change in relative abundance during the fruit transition from the pre-climacteric ("unripe") to the climacteric ("ripe") phase. Other proteins, such as S-adenosylmethionine synthetase and β-cyanoalanine synthase involved in ethylene metabolism, were also identified. Moreover, the changes in the relative abundances of a sucrose synthase and an α-amylase suggested differences between the two cultivars in the carbohydrate import activity of ripe fruit. The different accumulation of a few typical ROS-scavenger enzymes suggested that a higher oxidative stress occurred in MF with respect to NMF fruit. This result, together with data concerning the levels of total proteins and free amino acids and those regarding proteins involved in the maintenance of tissue integrity, was consistent with the hypothesis that the last phase of ripening in MF fruit is characterized by the appearance of a senescence status. The present study appears to define well some of the biochemical and physiological events that characterize the ripening of peach and, at the same time, provides interesting indications that could be employed in future marker assisted selection (MAS) programmes aimed to obtain MF fruits with higher ability to preserve tissue functionality maintaining for a longer time their organoleptic characteristics.
Non-enzymatic browning due to storage is reduced by using clarified lemon juice as acidifier in industrial-scale production of canned peach halves.
Saura Domingo,Vegara Salud,Martí Nuria,Valero Manuel,Laencina José
Journal of food science and technology
Non-enzymatic browning (NEB) in canned peach halves in syrup during storage was investigated. Absorbance at 420 nm (), colorimetric parameters (CIE, TCD and /), fructose, glucose and sucrose, total sugar, organic acids, ascorbic acid (AA), dehydroascorbic acid, and 2,3-diketogulonic acid were used to estimate the extent of NEB during 1 year of storage at 30 °C and the relationships between each of these parameters and were established. The investigation was carried out to explore the possibility of replacing the E330 commonly used as acidifier by turbid or clarified lemon juice (TLJ or CLJ) to obtain a product having good nutrition with better retention of quality. The , /, glucose and fructose were positively correlated with and all proved to be good indicators of browning development. Overall results showed that replacement of acidifier E330 with CLJ for controlling pH in canned peach halves in syrup had some advantages.
Floral traits influence the opportunity for selection among male gametophytes: independent and combined effects of style length and petal area.
Mazer Susan J,Chellew Joseph P,Peach Kristen
American journal of botany
PREMISE:Strong correlations between traits can obscure their independent effects on components of reproduction. Style length (SL) and petal area (PA) vary within species, for example, but their independent effects on the opportunity for selection among pollen genotypes are poorly understood. Previous work in Clarkia detected a positive effect of SL on pollen receipt, potentially intensifying selection. However, this apparent effect of SL may be influenced by a correlated trait, such as PA. Here, we examine the independent effects of these two traits on pollen receipt and performance. METHODS:We collected petals and styles from wild populations of two insect-pollinated Clarkia taxa and estimated the independent and combined effects of SL and PA on pollen receipt and performance. RESULTS:In both taxa, SL and PA are positively correlated. In C. unguiculata, both traits positively and independently affect pollen receipt, but in C. xantiana ssp. xantiana, the two traits act only in combination to affect pollen receipt. In both taxa, pollen receipt positively affects the numbers of pollen tubes entering and penetrating the style, as well as pollen tube attrition. CONCLUSIONS:The effects of SL and PA on pollen receipt and performance are taxon specific. In C. unguiculata, both traits may be independent targets of selection due to their effects on pollen receipt. In C. xantiana ssp. xantiana, by contrast, the combined (but not independent) effects of SL and PA influence pollen receipt. Ecological differences between these taxa require exploration to understand the mechanisms by which these traits affect pollinator behavior.
An integrative "omics" approach identifies new candidate genes to impact aroma volatiles in peach fruit.
Sánchez Gerardo,Venegas-Calerón Mónica,Salas Joaquín J,Monforte Antonio,Badenes María L,Granell Antonio
BACKGROUND:Ever since the recent completion of the peach genome, the focus of genetic research in this area has turned to the identification of genes related to important traits, such as fruit aroma volatiles. Of the over 100 volatile compounds described in peach, lactones most likely have the strongest effect on fruit aroma, while esters, terpenoids, and aldehydes have minor, yet significant effects. The identification of key genes underlying the production of aroma compounds is of interest for any fruit-quality improvement strategy. RESULTS:Volatile (52 compounds) and gene expression (4348 genes) levels were profiled in peach fruit from a maturity time-course series belonging to two peach genotypes that showed considerable differences in maturation characteristics and postharvest ripening. This data set was analyzed by complementary correlation-based approaches to discover the genes related to the main aroma-contributing compounds: lactones, esters, and phenolic volatiles, among others. As a case study, one of the candidate genes was cloned and expressed in yeast to show specificity as an ω-6 Oleate desaturase, which may be involved in the production of a precursor of lactones/esters. CONCLUSIONS:Our approach revealed a set of genes (an alcohol acyl transferase, fatty acid desaturases, transcription factors, protein kinases, cytochromes, etc.) that are highly associated with peach fruit volatiles, and which could prove useful in breeding or for biotechnological purposes.
Peach PpSnRK1 Participates in Sucrose-Mediated Root Growth Through Auxin Signaling.
Zhang Shuhui,Peng Futian,Xiao Yuansong,Wang Wenru,Wu Xuelian
Frontiers in plant science
Sugar signals play a key role in root growth and development. SnRK1, as one of the energy centers, can respond to energy changes in plants and affect the growth and development of plants. However, studies on sugar signals and SnRK1 regulating root growth in fruit trees have not been reported. In this study, we found that 5% exogenous sucrose could increase the total volume and total surface area of the peach root system, enhance the number and growth of lateral roots, and promote the activity of SnRK1. When exogenous trehalose was applied, the growth of roots was poor. Sucrose treatment reversed the inhibitory effects of trehalose on SnRK1 enzyme activity and root growth. We also found that the lateral root number of -overexpressing plants (4-1, 4-2, and 4-3) increased significantly. Therefore, we believe that peach SnRK1 is involved in sucrose-mediated root growth and development. To further clarify this mechanism, we used qRT-PCR analysis to show that exogenous sucrose could promote the expression of auxin-related genes in roots, thereby leading to the accumulation of auxin in the root system. In addition, the genes related to auxin synthesis and auxin transport in the root systems of -overexpressing lines were also significantly up-regulated. Using peach PpSnRK1a as the bait, we obtained two positive clones, PpIAA12 and PpPIN-LIKES6, which play key roles in auxin signaling. The interactions between peach PpSnRK1a and PpIAA12/PpPIN-LIKES6 were verified by yeast two-hybrid assays and bimolecular fluorescence complementation experiments, and the complexes were localized in the nucleus. After exogenous trehalose treatment, the expression of these two genes in peach root system was inhibited, whereas sucrose had a significant stimulatory effect and could alleviate the inhibition of these two genes by trehalose, which was consistent with the trend of sucrose's regulation of SnRK1 activity. In conclusion, peach SnRK1 can respond to sucrose and regulate root growth through the auxin signal pathway. This experiment increases our understanding of the function of fruit tree SnRK1 and provides a new insight to further study sugar hormone crosstalk in the future.
Expression of genes associated with aroma formation derived from the fatty acid pathway during peach fruit ripening.
Zhang Bo,Shen Ji-Yuan,Wei Wen-Wen,Xi Wan-Peng,Xu Chang-Jie,Ferguson Ian,Chen Kunsong
Journal of agricultural and food chemistry
Changes in characteristic aroma volatiles, levels of fatty acids as aroma precursors, and expression patterns of related genes, including lipoxygenase (LOX), hydroperoxide lyase (HPL), alcohol dehydrogenase (ADH), alcohol acyltransferase (AAT), and fatty acid desaturase (FAD), were studied in peach ( Prunus persica L. Batsch., cv. Yulu) fruit during postharvest ripening at 20 degrees C. Concentrations of n-hexanal, (E)-2-hexenal, (E)-2-hexenol, and (Z)-3-hexenol decreased, whereas the production of (Z)-3-hexenyl acetate, gamma-hexalactone, gamma-octalactone, gamma-decalactone, and delta-decalactone increased with fruit ripening. Lactones showed a clear pattern concomitant with the climacteric rise in ethylene production, with gamma-decalactone being the principal volatile compound at the late ripening stage. Of the LOX family genes, PpLOX2 and PpLOX3 had relatively high transcript levels initially followed by a decline with fruit ripening, while levels of PpLOX1 and PpLOX4 transcripts were upregulated by accumulated ethylene production. Expression of PpHPL1, PpADH1, PpADH2, and PpADH3 showed similar decreasing patterns during ripening. Expression levels of PpAAT1 showed a rapid increase during the first 2 days of postharvest ripening followed by a gradual decrease. Contents of polyunsaturated linoleic and linolenic acids increased, and saturated palmitic acid levels tended to decline as the fruit ripened. The increased levels of unsaturated fatty acids closely paralleled increasing expression of PpFAD1 and PpFAD2. The significance of gene expression changes in relation to aroma volatile production is discussed.
ESTree db: a tool for peach functional genomics.
Lazzari Barbara,Caprera Andrea,Vecchietti Alberto,Stella Alessandra,Milanesi Luciano,Pozzi Carlo
BACKGROUND:The ESTree db http://www.itb.cnr.it/estree/ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. RESULTS:The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. CONCLUSION:The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig.
Comparison Between Flat and Round Peaches, Genomic Evidences of Heterozygosity Events.
Tan Qiuping,Liu Xiao,Gao Hongru,Xiao Wei,Chen Xiude,Fu Xiling,Li Ling,Li Dongmei,Gao Dongsheng
Frontiers in plant science
Bud sports occur in many plant species, including fruit trees. Although they are correlated with genetic variance in somatic cells, the mechanisms responsible for bud sports are mostly unknown. In this study, a peach bud sport whose fruit shape was transformed to round from flat was identified by next generation sequencing (NGS), and we provide evidence that a long loss of heterozygosity (LOH) event may be responsible for this alteration in fruit shape. Moreover, compared to the reference genome, we identified 237,476 high quality single nucleotide polymorphisms (SNPs) in the wild-type and bud sport genomes. Using this SNP set, a long LOH event was identified at the distal end of scaffold Pp06 of the bud sport genome. Haplotypes from 155 additional peach accessions were phased, suggesting that the homozygous distal end of scaffold Pp06 of the bud sport was likely derived from only one haplotype of the wild-type flat peach. A genome-wide association study (GWAS) of 127 peach accessions was conducted to associate a SNP found at 26,924,482 bp of scaffold Pp06 to differences in fruit shape. All accessions with round-shaped fruit were found to have an A/A genotype, while those with A/T, or T/T genotypes had flat-shaped fruits. Finally, we also found that 236 peach accessions and 141 Prunus species with round-type fruit were found to have an A/A genotype at this SNP, while 22 flat peach accessions had an A/T genotype. Taken together, our results suggest that genes flanking this A/T polymorphism, and haplotyped carrying the T allele may determine flat fruit shape in this population. Furthermore, the LOH event resulting in the loss of the haplotype carrying the T allele may therefore be responsible for fruit shape alteration in wild-type flat peach.
DNA Methylation Analysis of Dormancy Release in Almond () Flower Buds Using Epi-Genotyping by Sequencing.
Prudencio Ángela S,Werner Olaf,Martínez-García Pedro J,Dicenta Federico,Ros Rosa M,Martínez-Gómez Pedro
International journal of molecular sciences
DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond ( (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.
Determination of Quality Changes in Peaches Wrapped in Active Paper and Stored at Ambient Temperature in Summer.
Du Xiao-Long,Li Hui,Zhou Wei-Hong,Liu Ying,Li Jian-Long
Peaches are known for their palatable flavor and abundant nutrients. However, peaches are perishable, and the existing preservation techniques for peaches are still immature. To further extend the shelf life and prevent nutrient loss of perishable peaches under ambient temperature in summer (approximately 25-32 °C), we conducted experiments wrapping peaches (Prunus persica cv 'Baihua') in single- and composite-treated vegetal fibrous papers that contained calcium carbonate, phytic acid, Na-alginate and vitamin C. The pathogenic fungi that primarily caused peach decay during storage belonged to the genera of Penicillium, Botrytis, Aspergillus, Alternaria, and Rhizopus. After analyzing quality attributes, including weight loss, firmness, soluble sugar content, respiration rate, relative electric conductivity, malonaldehyde content, peroxidase activity and the decay index, we proved that vitamin C within the preservative paper greatly contributes to peach preservation. Combined with phytic acid and Na-alginate, the composite vitamin C preservative papers played significant roles in delaying fruit senescence, and 0.4% (w/v) vitamin C preservative paper with 1% Na-alginate could maintain quality and extend shelf life with the best effect. This preservation technique significantly postponed the respiration peak by 2-3 days and is a significant contribution to contemporary commercial production.
[Peach genomics and genome-wide association study: a review].
Li Xiong-Wei,Jia Hui-Juan,Gao Zhong-Shan
Yi chuan = Hereditas
Peach (Prunus persica (L.) Batsch) is one of the most predominant stone fruits in Rosaceae family. The broad climate adaption, diverse cultivation region and good fruit taste make it one of the favorate fruits by consumers. Improving fruit quality and enhancing disease/pest resistance are always a focus for peach genetists and breeders to follow with interests. This paper reviews the main achievements on linkage map and physical map construction, development of various molecular markers, whole genome sequencing and transcriptome sequencing for peach in recent years, and also elaborates the applications of genome wide association study (GWAS) with high density SNP markers in peach and other plant crops. This review also provides a theoretical basis for GWAS analysis in the future study to identify high efficient markers of targeted traits for peach.
Biometric Characterization and Morphophysiological Quality of Peach Rootstock Seeds Using Images of their Seedling Vigor.
Souza Aline G,Smiderle Oscar J,Bianchi Valmor J
Recent patents on food, nutrition & agriculture
BACKGROUND:This study aimed to evaluate the efficiency of using the computerized imaging Seed Analysis System (SAS) in the biometric and morphophysiological characterization of seeds and the initial growth of seedlings from peach rootstocks. METHODS:The experimental design was completely randomized with five replicates of 20 seeds. The variables analyzed were the seed humidity content, length and width of seeds measured by SAS technology and manual measurements, mean germination time, germination percentage, radicle length and width, taproot length, length of the aerial part and taproot/aerial part ratio. RESULTS:The highest seed length, germination percentage (100%) and lower germination time (11.3), were obtained with the cv. Capdeboscq while, 'Tsukuba 1', 2' and 3' had intermediate seedlings length, varying from 1.55 to 1.65 cm with mean germination times between 14.5 and 18.0 days and average germination percentage of 96%. The computerized analysis of images is fast and efficient for biometric evaluations such as seed width and length, as well as initial growth of peach tree seedlings. The cvs Capdeboscq, Flordaguard and Tsukuba 2 presented greater radicle width, length and a mean taproot/aerial part ratio equal to 2, as well as higher number of adventitious roots, which indicated a strong positive correlation between radicle length, taproot length and initial seedling growth. CONCLUSION:The continuity of the research will certainly allow the development of reliable procedures for other species, besides allowing the identification of wider alternatives for the use of this system for the expansion of knowledge in the areas of physiology and evaluation of the physiological potential of seeds.
Transcriptome analysis of differentially expressed genes relevant to variegation in peach flowers.
Chen Yingnan,Mao Yan,Liu Hailin,Yu Faxin,Li Shuxian,Yin Tongming
BACKGROUND:Variegation in flower color is commonly observed in many plant species and also occurs on ornamental peaches (Prunus persica f. versicolor [Sieb.] Voss). Variegated plants are highly valuable in the floricultural market. To gain a global perspective on genes differentially expressed in variegated peach flowers, we performed large-scale transcriptome sequencing of white and red petals separately collected from a variegated peach tree. RESULTS:A total of 1,556,597 high-quality reads were obtained, with an average read length of 445 bp. The ESTs were assembled into 16,530 contigs and 42,050 singletons. The resulting unigenes covered about 60% of total predicted genes in the peach genome. These unigenes were further subjected to functional annotation and biochemical pathway analysis. Digital expression analysis identified a total of 514 genes differentially expressed between red and white flower petals. Since peach flower coloration is determined by the expression and regulation of structural genes relevant to flavonoid biosynthesis, a detailed examination detected four key structural genes, including C4H, CHS, CHI and F3H, expressed at a significantly higher level in red than in white petal. Except for the structural genes, we also detected 11 differentially expressed regulatory genes relating to flavonoid biosynthesis. Using the differentially expressed structural genes as the test objects, we validated the digital expression results by using quantitative real-time PCR, and the differential expression of C4H, CHS and F3H were confirmed. CONCLUSION:In this study, we generated a large EST collection from flower petals of a variegated peach. By digital expression analysis, we identified an informative list of candidate genes associated with variegation in peach flowers, which offered a unique opportunity to uncover the genetic mechanisms underlying flower color variegation.
Peach genetic resources: diversity, population structure and linkage disequilibrium.
Li Xiong-wei,Meng Xian-qiao,Jia Hui-juan,Yu Ming-liang,Ma Rui-juan,Wang Li-rong,Cao Ke,Shen Zhi-jun,Niu Liang,Tian Jian-bao,Chen Miao-jin,Xie Ming,Arus Pere,Gao Zhong-shan,Aranzana Maria Jose
BACKGROUND:Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among Chinese cultivars, and North American and European cultivars, and the evolution of current peach cultivars. RESULTS:In total, 588 alleles were obtained with 48 SSRs on 653 peach accessions, giving an average of 12.25 alleles per locus. In general, the average value of observed heterozygosity (0.47) was lower than the expected heterozygosity (0.60). The separate analysis of groups of accessions according to their origin or reproductive strategies showed greater variability in Oriental cultivars, mainly due to the high level of heterozygosity in Chinese landraces. Genetic distance analysis clustered the cultivars into two main groups: one included four wild related Prunus, and the other included most of the Oriental and Occidental landraces and breeding cultivars. STRUCTURE analysis assigned 469 accessions to three subpopulations: Oriental (234), Occidental (174), and Landraces (61). Nested STRUCTURE analysis divided the Oriental subpopulation into two different subpopulations: 'Yu Lu' and 'Hakuho'. The Occidental breeding subpopulation was also subdivided into nectarine and peach subpopulations. Linkage disequilibrium (LD) analysis in each of these subpopulations showed that the percentage of linked (r2 > 0.1) intra-chromosome comparisons ranged between 14% and 47%. LD decayed faster in Oriental (1,196 Kbp) than in Occidental (2,687 Kbp) samples. In the 'Yu Lu' subpopulation there was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations. CONCLUSIONS:Our study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach.
Mutation rate analysis via parent-progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids.
Xie Zhengqing,Wang Long,Wang Lirong,Wang Zhiqiang,Lu Zhenhua,Tian Dacheng,Yang Sihai,Hurst Laurence D
Proceedings. Biological sciences
Mutation rates vary between species, between strains within species and between regions within a genome. What are the determinants of these forms of variation? Here, via parent-offspring sequencing of the peach we ask whether (i) woody perennials tend to have lower per unit time mutation rates compared to annuals, and (ii) hybrid strains have high mutation rates. Between a leaf from a low heterozygosity individual, derived from an intraspecific cross, to a leaf of its selfed progeny, the mutation rate is 7.77 × 10 point mutations per bp per generation, similar to Arabidopsis thaliana (7.0-7.4 × 10 point mutations per bp per generation). This suggests a low per unit time mutation rate as the generation time is much longer in peach. This is supported by our estimate of 9.48 × 10 point mutations per bp per generation from a 200-year-old low heterozygosity peach to its progeny. From a more highly heterozygous individual derived from an interspecific cross to its selfed progeny, the mutation rate is 1.38 × 10 mutations per site per generation, consistent with raised rates in hybrids. Our data thus suggest that (i) peach has an approximately order of magnitude lower mutation rate per unit time than Arabidopsis, consistent with reports of low evolutionary rates in woody perennials, and (ii) hybridization may, indeed, be associated with increased mutation rates as considered over a century ago.
High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow.
Vanderzande Stijn,Howard Nicholas P,Cai Lichun,Da Silva Linge Cassia,Antanaviciute Laima,Bink Marco C A M,Kruisselbrink Johannes W,Bassil Nahla,Gasic Ksenija,Iezzoni Amy,Van de Weg Eric,Peace Cameron
High-quality genotypic data is a requirement for many genetic analyses. For any crop, errors in genotype calls, phasing of markers, linkage maps, pedigree records, and unnoticed variation in ploidy levels can lead to spurious marker-locus-trait associations and incorrect origin assignment of alleles to individuals. High-throughput genotyping requires automated scoring, as manual inspection of thousands of scored loci is too time-consuming. However, automated SNP scoring can result in errors that should be corrected to ensure recorded genotypic data are accurate and thereby ensure confidence in downstream genetic analyses. To enable quick identification of errors in a large genotypic data set, we have developed a comprehensive workflow. This multiple-step workflow is based on inheritance principles and on removal of markers and individuals that do not follow these principles, as demonstrated here for apple, peach, and sweet cherry. Genotypic data was obtained on pedigreed germplasm using 6-9K SNP arrays for each crop and a subset of well-performing SNPs was created using ASSIsT. Use of correct (and corrected) pedigree records readily identified violations of simple inheritance principles in the genotypic data, streamlined with FlexQTL software. Retained SNPs were grouped into haploblocks to increase the information content of single alleles and reduce computational power needed in downstream genetic analyses. Haploblock borders were defined by recombination locations detected in ancestral generations of cultivars and selections. Another round of inheritance-checking was conducted, for haploblock alleles (i.e., haplotypes). High-quality genotypic data sets were created using this workflow for pedigreed collections representing the U.S. breeding germplasm of apple, peach, and sweet cherry evaluated within the RosBREED project. These data sets contain 3855, 4005, and 1617 SNPs spread over 932, 103, and 196 haploblocks in apple, peach, and sweet cherry, respectively. The highly curated phased SNP and haplotype data sets, as well as the raw iScan data, of germplasm in the apple, peach, and sweet cherry Crop Reference Sets is available through the Genome Database for Rosaceae.
Mutation rate analysis via parent-progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation.
Wang Long,Zhang Yanchun,Qin Chao,Tian Dacheng,Yang Sihai,Hurst Laurence D
Proceedings. Biological sciences
Mutation rates and recombination rates vary between species and between regions within a genome. What are the determinants of these forms of variation? Prior evidence has suggested that the recombination might be mutagenic with an excess of new mutations in the vicinity of recombination break points. As it is conjectured that domesticated taxa have higher recombination rates than wild ones, we expect domesticated taxa to have raised mutation rates. Here, we use parent-offspring sequencing in domesticated and wild peach to ask (i) whether recombination is mutagenic, and (ii) whether domesticated peach has a higher recombination rate than wild peach. We find no evidence that domesticated peach has an increased recombination rate, nor an increased mutation rate near recombination events. If recombination is mutagenic in this taxa, the effect is too weak to be detected by our analysis. While an absence of recombination-associated mutation might explain an absence of a recombination-heterozygozity correlation in peach, we caution against such an interpretation.
E-Nose and GC-MS Reveal a Difference in the Volatile Profiles of White- and Red-Fleshed Peach Fruit.
Xin Rui,Liu Xiaohong,Wei Chunyan,Yang Chong,Liu Hongru,Cao Xiangmei,Wu Di,Zhang Bo,Chen Kunsong
Sensors (Basel, Switzerland)
First purchases of fruit are mainly dependent on aspects of appearance such as color. However, repeat buys of fruit are determined by internal quality traits such as flavor-related volatiles. Differences in volatile profiles in white- and red-fleshed peach fruit are not well understood. In the present study, peach cultivars with white- and red-fleshed fruit were subjected to sensory analysis using electronic nose (e-nose) to evaluate overview volatile profiles. Approximately 97.3% of the total variation in peach color-volatiles was explained by the first principle component 1 (PC1) and PC2. After analyzing sensory differences between peach fruit samples, 50 volatile compounds were characterized based on GC-MS. Multivariate analysis such as partial least squares discriminant analysis (PLS-DA) was applied to identify volatile compounds that contribute to difference in white- and red-fleshed peach fruit cultivars. A total of 18 volatiles that could separate peach fruit cultivars with different colors in flesh during ripening were identified based on variable importance in projection (VIP) score. Fruity note latone γ-hexalactone had higher contents in red-fleshed cultivars, while grassy note C6 compounds such as hexanal, 2-hexenal, ()-2-hexenal, 1-hexanol, and ()-2-hexen-1-ol showed great accumulation in white-fleshed peach fruit.
Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.
Shen Z J,Ma R J,Cai Z X,Yu M L,Zhang Z
Genetics and molecular research : GMR
The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.
Deletion of the miR172 target site in a TOE-type gene is a strong candidate variant for dominant double-flower trait in Rosaceae.
Gattolin Stefano,Cirilli Marco,Pacheco Igor,Ciacciulli Angelo,Da Silva Linge Cássia,Mauroux Jehan-Baptiste,Lambert Patrick,Cammarata Elia,Bassi Daniele,Pascal Thierry,Rossini Laura
The Plant journal : for cell and molecular biology
Double flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants, including Prunus persica (peach), a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double-flower phenotype in peach, we focused on the dominant Di2 locus. High-resolution linkage mapping in five segregating progenies delimited Di2 to an interval spanning 150 858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic resequencing data from single- and double-flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double-flower trait, and we showed transcript expression for both wild-type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical times for floral development. The indelDi2 molecular marker designed on this sequence variant co-segregated with the phenotype in 621 progenies, accounting for the dominant inheritance of the Di2 locus. Further corroborating the results in peach, we identified a distinct but similar mutation in the ortholog of Prupe.6G242400 in double-flower roses. Phylogenetic analysis showed that these two genes belong to a TARGET OF EAT (TOE)-type clade not represented in Arabidopsis, indicating a divergence of gene functions between AP2-type and TOE-type factors in Arabidopsis and other species. The identification of orthologous candidate genes for the double-flower phenotype in two important Rosaceae species provides valuable information to understand the genetic control of this trait in other major ornamental plants.
Genome-wide association study of 12 agronomic traits in peach.
Cao Ke,Zhou Zhengkui,Wang Qi,Guo Jian,Zhao Pei,Zhu Gengrui,Fang Weichao,Chen Changwen,Wang Xinwei,Wang Xiaoli,Tian Zhixi,Wang Lirong
Peach (Prunus persica L.) is a highly valuable crop species and is recognized by molecular researchers as a model fruit for the Rosaceae family. Using whole-genome sequencing data generated from 129 peach accessions, here we perform a comprehensive genome-wide association study for 12 key agronomic traits. We show that among the 10 qualitative traits investigated, nine exhibit consistent and more precise association signals than previously identified by linkage analysis. For two of the qualitative traits, we describe candidate genes, one potentially involved in cell death and another predicted to encode an auxin-efflux carrier, that are highly associated with fruit shape and non-acidity, respectively. Furthermore, we find that several genomic regions harbouring association signals for fruit weight and soluble solid content overlapped with predicted selective sweeps that occurred during peach domestication and improvement. Our findings contribute to the large-scale characterization of genes controlling agronomic traits in peach.
Transcriptomic and metabolic analyses provide new insights into chilling injury in peach fruit.
Wang Ke,Yin Xue-Ren,Zhang Bo,Grierson Don,Xu Chang-Jie,Chen Kun-Song
Plant, cell & environment
Low temperature conditioning (LTC) alleviates peach fruit chilling injury but the underlying molecular basis is poorly understood. Here, changes in transcriptome, ethylene production, flesh softening, internal browning and membrane lipids were compared in fruit maintained in constant 0 °C and LTC (pre-storage at 8 °C for 5 d before storage at 0 °C). Low temperature conditioning resulted in a higher rate of ethylene production and a more rapid flesh softening as a result of higher expression of ethylene biosynthetic genes and a series of cell wall hydrolases. Reduced internal browning of fruit was observed in LTC, with lower transcript levels of polyphenol oxidase and peroxidase, but higher lipoxygenase. Low temperature conditioning fruit also showed enhanced fatty acid content, increased desaturation, higher levels of phospholipids and a preferential biosynthesis of glucosylceramide. Genes encoding cell wall hydrolases and lipid metabolism enzymes were coexpressed with differentially expressed ethylene response factors (ERFs) and contained ERF binding elements in their promoters. In conclusion, LTC is a special case of cold acclimation which increases ethylene production and, operating through ERFs, promotes both softening and changes in lipid composition and desaturation, which may modulate membrane stability, reducing browning and contributing to alleviation of peach fruit chilling injury.
Two ω-3 FADs Are Associated with Peach Fruit Volatile Formation.
Wang Jiao-Jiao,Liu Hong-Ru,Gao Jie,Huang Yu-Ji,Zhang Bo,Chen Kun-Song
International journal of molecular sciences
Aroma-related volatiles, together with sugars and acids, play an important role in determining fruit flavor quality. Characteristic volatiles of peach fruit are mainly derived from fatty acids such as linoleic acid (18:2) and linolenic acid (18:3). In the present study, six genes encoding fatty acid desaturases (FAD) were cloned, including two ω-6 FAD genes (PpFAD2, PpFAD6) and four ω-3 FAD genes (PpFAD3-1, PpFAD3-2, PpFAD7 and PpFAD8). Heterologous expression of peach FADs in tobacco plants showed that PpFAD3-1, and PpFAD3-2 significantly reduced contents of 18:2, and accumulated significant higher levels of 18:3. In the case of volatiles, transgenic plants produced lower concentrations of hexanal and higher levels of (E)-2-hexenal. Consequently, the ratio of the (E)-2-hexenal and hexanal was about 5- and 3-fold higher than that of wild type (WT) in PpFAD3-1 and PpFAD3-2 transformants, respectively. No significant changes in volatile profiles were observed in transgenic plants overexpressing the four other peach FAD genes. Real-time quantitative polymerase chain reaction (qPCR) analysis showed that ripe fruit had high PpFAD3-1 and low PpFAD3-2 transcript levels. In contrast, high PpFAD3-2 and low PpFAD3-1 transcript levels were observed in young fruit. These results indicate a temporal regulation of these two ω-3 FADs during development and ripening, influencing peach fruit volatile formation.
Cloning and bioinformatic analysis of transcription factor MYB10 from the red-leaf peach.
Wang X Q,Han J,Wen Y,Jiang W B,Fang J G,Zhang B B,Ma R J
Genetics and molecular research : GMR
In higher plants, the transcription factor MYB10 is an important regulator of anthocyanin biosynthesis. In order to study its role in the development of red coloration in peach leaves, the full-length MYB10 complementary DNA sequence of the red-leaf peach cultivar 'Tsukuba No. 5' (Prunus persica f. atropurpurea) was successfully cloned using reverse transcription-polymerase chain reaction. The sequence was assigned the GenBank accession No. KP315904. Bioinformatic analysis identified the complete MYB10 open reading frame, consisting of 678 bp encoding 225 amino acids. The predicted protein has a molecular weight of 26.56 kDa and a theoretical isoelectric point of 8.97. The secondary structure was found to comprise approximately 34.22% alpha helix, 15.11% extended strand, 10.67% beta turn, and 40% random coil. Subcellular analysis indicated that MYB10 may function in the cytoplasm. Assessment of the amino acid sequence suggested the presence of one serine and two threonine phosphorylation sites. Quantitative real-time polymerase chain reaction revealed that MYB10 expression positively correlated with anthocyanin content in red-leaf peach, indicating that this transcription factor plays a role in the biosynthesis of this pigment in peach trees.
Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history.
Li Yong,Cao Ke,Zhu Gengrui,Fang Weichao,Chen Changwen,Wang Xinwei,Zhao Pei,Guo Jian,Ding Tiyu,Guan Liping,Zhang Qian,Guo Wenwu,Fei Zhangjun,Wang Lirong
BACKGROUND:Human selection has a long history of transforming crop genomes. Peach (Prunus persica) has undergone more than 5000 years of domestication that led to remarkable changes in a series of agronomically important traits, but genetic bases underlying these changes and the effects of artificial selection on genomic diversity are not well understood. RESULTS:Here, we report a comprehensive analysis of peach evolution based on genome sequences of 480 wild and cultivated accessions. By focusing on a set of quantitative trait loci (QTLs), we provide evidence supporting that distinct phases of domestication and improvement have led to an increase in fruit size and taste and extended its geographic distribution. Fruit size was predominantly selected during domestication, and selection for large fruits has led to the loss of genetic diversity in several fruit weight QTLs. In contrast, fruit taste-related QTLs were successively selected for by domestication and improvement, with more QTLs selected for during improvement. Genome-wide association studies of 11 agronomic traits suggest a set of candidate genes controlling these traits and potential markers for molecular breeding. Candidate loci for genes that contributed to the adaption to low-chill regions were identified. Furthermore, the genomic bases of divergent selection for fruit texture and local breeding for different flavors between Asian and European/North American cultivars were also determined. CONCLUSIONS:Our results elucidate the genetic basis of peach evolution and provide new resources for future genomics-guided peach breeding.
Metabolic profiling of a range of peach fruit varieties reveals high metabolic diversity and commonalities and differences during ripening.
Monti Laura L,Bustamante Claudia A,Osorio Sonia,Gabilondo Julieta,Borsani Julia,Lauxmann Martin A,Maulión Evangelina,Valentini Gabriel,Budde Claudio O,Fernie Alisdair R,Lara María V,Drincovich María F
Peach (Prunus persica) fruits from different varieties display differential organoleptic and nutritional properties, characteristics related to their chemical composition. Here, chemical biodiversity of peach fruits from fifteen varieties, at harvest and after post-harvest ripening, was explored by gas chromatography-mass spectrometry. Metabolic profiling revealed that metabolites involved in organoleptic properties (sugars, organic and amino acids), stress tolerance (raffinose, galactinol, maltitol), and with nutritional properties (amino, caffeoylquinic and dehydroascorbic acids) displayed variety-dependent levels. Peach varieties clustered into four groups: two groups of early-harvest varieties with higher amino acid levels; two groups of mid- and late-harvest varieties with higher maltose levels. Further separation was mostly dependent on organic acids/raffinose levels. Variety-dependent and independent metabolic changes associated with ripening were detected; which contribute to chemical diversity or can be used as ripening markers, respectively. The great variety-dependent diversity in the content of metabolites that define fruit quality reinforces metabolomics usage as a tool to assist fruit quality improvement in peach.
PpGST1, an anthocyanin-related glutathione S-transferase gene, is essential for fruit coloration in peach.
Zhao Yun,Dong Weiqi,Zhu Yongchao,Allan Andrew C,Lin-Wang Kui,Xu Changjie
Plant biotechnology journal
Anthocyanins have crucial biological functions and affect quality of horticultural produce. Anthocyanins accumulate in ripe peach fruit; differential accumulation is observed in deep coloured cultivar 'Hujingmilu' and lightly pigmented cultivar 'Yulu'. The difference was not fully explained by accumulation of total flavonoids and expression of anthocyanin biosynthetic genes. Expression analysis was conducted on a glutathione S-transferase gene (PpGST1), and it was found that the expression correlated well with anthocyanin accumulation in peach fruit tissues. Functional complementation of the Arabidopsis tt19 mutant indicated that PpGST1 was responsible for transport of anthocyanins but not proanthocyanidins. PpGST1 was localized in nuclei and the tonoplast, including the sites at which anthocyanin vacuolar sequestration occurred. Transient overexpression of PpGST1 together with PpMYB10.1 in tobacco leaves and peach fruit significantly increased anthocyanin accumulation as compared with PpMYB10.1 alone. Furthermore, virus-induced gene silencing of PpGST1 in a blood-fleshed peach not only resulted in a reduction in anthocyanin accumulation but also a decline in expression of anthocyanin biosynthetic and regulatory genes. Cis-element analysis of the PpGST1 promoter revealed the presence of four MYB binding sites (MBSs). Dual-luciferase assays indicated that PpMYB10.1 bound to the promoter and activated the transcription of PpGST1 by recognizing MBS1, the one closest to the ATG start codon, with this trans-activation being stronger against the promoter of deep coloured 'Hujingmilu' compared with lightly coloured cultivar 'Yulu'. Altogether, our data provided molecular evidence supporting coordinative regulatory roles of PpGST1 and PpMYB10.1 in anthocyanin accumulation in peach.
Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach.
Cao Ke,Li Yong,Deng Cecilia H,Gardiner Susan E,Zhu Gengrui,Fang Weichao,Chen Changwen,Wang Xinwei,Wang Lirong
Plant biotechnology journal
Crop evolution is a long-term process involving selection by natural evolutionary forces and anthropogenic influences; however, the genetic mechanisms underlying the domestication and improvement of fruit crops have not been well studied to date. Here, we performed a population structure analysis in peach (Prunus persica) based on the genome-wide resequencing of 418 accessions and confirmed the presence of an obvious domestication event during evolution. We identified 132 and 106 selective sweeps associated with domestication and improvement, respectively. Analysis of their tissue-specific expression patterns indicated that the up-regulation of selection genes during domestication occurred mostly in fruit and seeds as opposed to other organs. However, during the improvement stage, more up-regulated selection genes were identified in leaves and seeds than in the other organs. Genome-wide association studies (GWAS) using 4.24 million single nucleotide polymorphisms (SNPs) revealed 171 loci associated with 26 fruit domestication traits. Among these loci, three candidate genes were highly associated with fruit weight and the sorbitol and catechin content in fruit. We demonstrated that as the allele frequency of the SNPs associated with high polyphenol composition decreased during peach evolution, alleles associated with high sugar content increased significantly. This indicates that there is genetic potential for the breeding of more nutritious fruit with enhanced bioactive polyphenols without disturbing a harmonious sugar and acid balance by crossing with wild species. This study also describes the development of the genomic resources necessary for evolutionary research in peach and provides the large-scale characterization of key agronomic traits in this crop species.
PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data.
Cirilli Marco,Flati Tiziano,Gioiosa Silvia,Tagliaferri Ilario,Ciacciulli Angelo,Gao Zhongshan,Gattolin Stefano,Geuna Filippo,Maggi Francesco,Bottoni Paolo,Rossini Laura,Bassi Daniele,Castrignanò Tiziana,Chillemi Giovanni
Plant & cell physiology
Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalog of genetic variants present in peach (Prunus persica L. Batsch) and wild-related species of Prunus genera, annotated from 146 samples publicly released on the Sequence Read Archive (SRA). We designed a user-friendly web-based interface of the database, providing search tools to retrieve single nucleotide polymorphism (SNP) and InDel variants, along with useful statistics and information. PeachVar-DB results are linked to the Genome Database for Rosaceae (GDR) and the Phytozome database to allow easy access to other external useful plant-oriented resources. In order to extend the genetic diversity covered by the PeachVar-DB further, and to allow increasingly powerful comparative analysis, we will progressively integrate newly released data.
Detection and application of genome-wide variations in peach for association and genetic relationship analysis.
Guan Liping,Cao Ke,Li Yong,Guo Jian,Xu Qiang,Wang Lirong
BACKGROUND:Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. RESULTS:In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. CONCLUSIONS:The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.
Biochemical and proteomic analysis of 'Dixiland' peach fruit (Prunus persica) upon heat treatment.
Lara María V,Borsani Julia,Budde Claudio O,Lauxmann Martin A,Lombardo Verónica A,Murray Ricardo,Andreo Carlos S,Drincovich María F
Journal of experimental botany
Shipping of peaches to distant markets and storage require low temperature; however, cold storage affects fruit quality causing physiological disorders collectively termed 'chilling injury' (CI). In order to ameliorate CI, different strategies have been applied before cold storage; among them heat treatment (HT) has been widely used. In this work, the effect of HT on peach fruit quality as well as on carbon metabolism was evaluated. When fruit were exposed to 39 degrees C for 3 d, ripening was delayed, with softening inhibition and slowing down of ethylene production. Several differences were observed between fruit ripening at ambient temperature versus fruit that had been heat treated. However, the major effects of HT on carbon metabolism and organoleptic characteristics were reversible, since normal fruit ripening was restored after transferring heated peaches to ambient temperature. Positive quality features such as an increment in the fructose content, largely responsible for the sweetness, and reddish coloration were observed. Nevertheless, high amounts of acetaldehyde and low organic acid content were also detected. The differential proteome of heated fruit was characterized, revealing that heat-induced CI tolerance may be acquired by the activation of different molecular mechanisms. Induction of related stress proteins in the heat-exposed fruits such as heat shock proteins, cysteine proteases, and dehydrin, and repression of a polyphenol oxidase provide molecular evidence of candidate proteins that may prevent some of the CI symptoms. This study contributes to a deeper understanding of the cellular events in peach under HT in view of a possible technological use aimed to improve organoleptic and shelf-life features.
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.
Verde Ignazio,Jenkins Jerry,Dondini Luca,Micali Sabrina,Pagliarani Giulia,Vendramin Elisa,Paris Roberta,Aramini Valeria,Gazza Laura,Rossini Laura,Bassi Daniele,Troggio Michela,Shu Shengqiang,Grimwood Jane,Tartarini Stefano,Dettori Maria Teresa,Schmutz Jeremy
BACKGROUND:The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. RESULTS:Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. CONCLUSIONS:The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.
Assessment of Prunus persica fruit softening using a proteomics approach.
P Ricardo Nilo,Campos-Vargas Reinaldo,Orellana Ariel
Journal of proteomics
Fruit ripening in Prunus persica involves a number of physiological changes, being one of the most significant the mesocarp softening in melting varieties. In order to get a better understanding of the molecular processes involved in this phenomenon, the protein accumulation patterns in firm and soft fruit of three peach and two nectarine melting flesh varieties were assessed using 2D gel analysis. A General Linear Model (GLM) two-way analysis of variance determined that 164 of the 621 protein spots analyzed displayed a differential accumulation associated with the softening process. Among them, only 14 proteins changed their accumulation in all the varieties assessed, including proteins mostly involved in carbohydrates and cell wall metabolism as well as fruit senescence. The analysis among varieties showed that 195 and 189 spots changed within the firm and soft fruit conditions, respectively. Despite the changes in relative abundance in the spot proteins, the proteome is conserved among varieties and during the transition from firm to soft fruit. Only two spots proteins exhibited a qualitative change in all the conditions assessed. These results are in agreement with the notion that Prunus persica commercial varieties have a narrow genetic background.
Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies.
Biscarini Filippo,Nazzicari Nelson,Bink Marco,Arús Pere,Aranzana Maria José,Verde Ignazio,Micali Sabrina,Pascal Thierry,Quilot-Turion Benedicte,Lambert Patrick,da Silva Linge Cassia,Pacheco Igor,Bassi Daniele,Stella Alessandra,Rossini Laura
BACKGROUND:Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. RESULTS:A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3-5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted phenotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average). CONCLUSIONS:This study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes.
Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection.
Ahmad Riaz,Parfitt Dan E,Fass Joseph,Ogundiwin Ebenezer,Dhingra Amit,Gradziel Thomas M,Lin Dawei,Joshi Nikhil A,Martinez-Garcia Pedro J,Crisosto Carlos H
BACKGROUND:The application of next generation sequencing technologies and bioinformatic scripts to identify high frequency SNPs distributed throughout the peach genome is described. Three peach genomes were sequenced using Roche 454 and Illumina/Solexa technologies to obtain long contigs for alignment to the draft 'Lovell' peach sequence as well as sufficient depth of coverage for 'in silico' SNP discovery. DESCRIPTION:The sequences were aligned to the 'Lovell' peach genome released April 01, 2010 by the International Peach Genome Initiative (IPGI). 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle' were sequenced to add SNPs segregating in two breeding populations, Pop DF ('Dr. Davis' × 'F8, 1-42') and Pop DG ('Dr. Davis' × 'Georgia Belle'). Roche 454 sequencing produced 980,000 total reads with 236 Mb sequence for 'Dr. Davis' and 735,000 total reads with 172 Mb sequence for 'F8, 1-42'. 84 bp × 84 bp paired end Illumina/Solexa sequences yielded 25.5, 21.4, 25.5 million sequences for 'Dr. Davis', 'F8, 1-42' and 'Georgia Belle', respectively. BWA/SAMtools were used for alignment of raw reads and SNP detection, with custom PERL scripts for SNP filtering. Velvet's Columbus module was used for sequence assembly. Comparison of aligned and overlapping sequences from both Roche 454 and Illumina/Solexa resulted in the selection of 6654 high quality SNPs for 'Dr. Davis' vs. 'F8, 1-42' and 'Georgia Belle', distributed on eight major peach genome scaffolds as defined from the 'Lovell' assembly. CONCLUSION:The eight scaffolds contained about 215-225 Mb of peach genomic sequences with one SNP/~ 40,000 bases. All sequences from Roche 454 and Illumina/Solexa have been submitted to NCBI for public use in the Short Read Archive database. SNPs have been deposited in the NCBI SNP database.
Carotenoids, Phenolic Profile, Mineral Content and Antioxidant Properties in Flesh and Peel of Prunus persica Fruits during Two Maturation Stages.
Dabbou Samia,Maatallah Samira,Castagna Antonella,Guizani Monia,Sghaeir Wala,Hajlaoui Hichem,Ranieri Annamaria
Plant foods for human nutrition (Dordrecht, Netherlands)
Carotenoids and phenolic profile, antioxidant activity as well as concentrations of selected macronutrients (K, N, Mg, Ca and Na) and micronutrients (Zn, Cu and Mn) in flesh and peel of peach fruit were recorded at two harvest dates. Predominant mineral was potassium, followed by calcium, magnesium and sodium. The concentration of most micronutrients was greater in the peel than in the flesh especially in early season. The concentration of most elements in flesh and peel decreased during fruit maturation. Total carotenoids content varied with respect to the cultivar. β-cryptoxanthin and β-carotene were the major carotenoids in both tissues and flesh contain the lowest amounts. Neochlorogenic acid, chlorogenic acid, catechin, epicatechin, gallic acid, rutin, quercetin-3-O-galactoside, cyanidin-3-O-glucoside, cyanidin-3-O-rutinoside, were detected in both peel and flesh, with chlorogenic acid and catechin being the predominant components. Peel extracts showed markedly higher antioxidant activities, when estimated by ABTS or DPPH assays, than the flesh counterparts, consistent with the observed higher phenolic content. Overall, total phenolics levels increased at full ripening stage in both peel and flesh. The results found herein provide important data on carotenoids, phenolic and macro- and micronutrient changes during fruit growth, and emphases peach fruit as a potential functional food.
Changes in biochemical compounds in flesh and peel from Prunus persica fruits grown in Tunisia during two maturation stages.
Dabbou Samia,Lussiana Carola,Maatallah Samira,Gasco Laura,Hajlaoui Hichem,Flamini Guido
Plant physiology and biochemistry : PPB
Plants can synthesize tens to hundreds of thousands of primary and secondary metabolites with diverse biological properties and functions. Fatty acids (FA), phenolic compounds (PC) and volatile compounds (VC) of flesh and peel from three Prunus persica cultivars were evaluated at the Regional Centre of Agricultural Research--Experimental Farm (Sidi Bouzid, Tunisia) during two maturation stages. Palmitic, oleic and linoleic acids are the most abundant FA in Prunus persica cultivars. A genetic effect on FA composition was observed throughout the two sampling periods. Peel was rich in oleic acid with the highest content (31.3% on total FA) in 'O'Henry' cultivar at the commercial ripening date; flesh was rich in linoleic acid with the highest content (44.7% on total FA) in 'Sweet Cap' cultivar at the full ripening date. The monounsaturated/polyunsaturated fatty acids ratios were higher in the commercial ripe than in the full ripe fruits. The analysis of the composition of the VC led to the characterization of 98 different compounds, showing a very high variability among the cultivars. The full ripe fruit (peel and flesh) exhibited the highest total number of terpenoids. Commercial ripe peels were richest in the percentage of hydrocarbons. Comparing cultivars, 'Sweet Cap' cultivar showed the lowest contents of alcohols in peel and flesh of full ripe fruit but highest in peel of commercial ripe fruit, and lowest content of aldehydes in peel and flesh of commercial ripe fruit but highest in peel of ripe ones and the highest ones of lactones. Among PC, the highest contents were observed for o-diphenols and the values showed varietal influence. Total phenols contents decreased during ripening process (p < 0.05) in both peel and flesh tissues, except found for 'Sweet Cap' cultivar. In conclusion, to achieve better FA composition and greater VC and PC production of the peach fruit, P. persica cultivars should be harvested at the commercial ripening date.
Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops.
Cao Ke,Zheng Zhijun,Wang Lirong,Liu Xin,Zhu Gengrui,Fang Weichao,Cheng Shifeng,Zeng Peng,Chen Changwen,Wang Xinwei,Xie Min,Zhong Xiao,Wang Xiaoli,Zhao Pei,Bian Chao,Zhu Yinling,Zhang Jiahui,Ma Guosheng,Chen Chengxuan,Li Yanjun,Hao Fengge,Li Yong,Huang Guodong,Li Yuxiang,Li Haiyan,Guo Jian,Xu Xun,Wang Jun
BACKGROUND:Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution. RESULTS:We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis. CONCLUSIONS:Our analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics.
Self-compatibility in peach [ (L.) Batsch]: patterns of diversity surrounding the -locus and analysis of SFB alleles.
Abdallah Donia,Baraket Ghada,Perez Veronica,Salhi Hannachi Amel,Hormaza Jose I
Self-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and prevalent evolutionary shifts in flowering plants. L. (Rosaceae) is a genus of over 200 species most of which exhibit a Gametophytic SI system. Peach [ (L.) Batsch; 2 = 16] is one of the few exceptions in the genus known to be a fully self-compatible species. However, the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and, in order to fill that gap, in this study 24 peach accessions were analyzed. Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes. The linkage disequilibrium association between alleles at the -locus and linked markers at the end of the sixth linkage group was not significant ( > 0.05), except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the -locus. Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additional α-helices at the C-termini. Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2, while the SFB1 seemed to evolve neutrally. Thus, our results show that the SFB2 allele diversified after and (almond) divergence, a period which is characterized by an important bottleneck, while SFB1 diversified at a transition time between the bottleneck and population expansion.
Phenolic composition and antioxidant properties of different peach [Prunus persica (L.) Batsch] cultivars in China.
Zhao Xiaoyong,Zhang Wenna,Yin Xueren,Su Mingshen,Sun Chongde,Li Xian,Chen Kunsong
International journal of molecular sciences
China is an important centre of diversity for Prunus persica. In the present study, 17 Chinese peach cultivars were evaluated for phenolic content and antioxidant activity. Neochlorogenic acid (NCHA), chlorogenic acid (CHA), procyanidin B1 (B1), catechin (CAT), cyanidin-3-O-glucoside (C3G), quercetin-3-O-galactoside (Q3GAL), quercetin-3-O-glucoside (Q3GLU), quercetin-3-O-rutinoside (Q3R), and kaempferol-3-O-rutinoside (K3R) were identified and quantified. CHA and CAT were the predominant components in both the peel and pulp of this fruit. In general, peel extracts showed higher antioxidant activities than the pulp counterparts, consistent with the observed higher phenolic content. The melting peach cultivar "Xinyu" showed the highest antioxidant potency composite (APC) index. The principal component analysis (PCA) of peel phenolics showed a clear distinction between the melting peach and nectarine. Overall, peach cultivars rich in hydroxycinnamates and flavan-3-ols showed relatively higher antioxidant activities and might be excellent sources of phytochemicals and natural antioxidants.
Comparison of Phytochemical Differences of the Pulp of Different Peach [ (L.) Batsch] Cultivars with Alpha-Glucosidase Inhibitory Activity Variations in China Using UPLC-Q-TOF/MS.
Zhang Xianan,Su Mingshen,Du Jihong,Zhou Huijuan,Li Xiongwei,Li Xin,Ye Zhengwen
Molecules (Basel, Switzerland)
In order to fully understand the variation of the fruit alpha-glucosidase inhibitory activity-related phytochemical basis in the Chinese peach [ (L.) Batsch], mature fruit from 33 cultivars was used for the investigation of fruit phenolic phytochemical attributes, including total phenolics, flavonoids, anthocyanins, and procyanidins, as well as the alpha-glucosidase inhibitory activity in vitro. Alpha-glucosidase inhibitory activity varied significantly among tested peach cultivars and was strongly correlated with total phenolics, total procyanidins, and total flavonoids. Untargeted UPLC-Q-TOF/MS-based metabolomics were used to comprehensively discriminate between peaches with different inhibitory activity on alpha-glucosidase. Principal component analysis (PCA) and orthogonal partial least squares discrimination analysis (OPLS-DA) were used for this process. Twenty-three differential compounds were identified between peach cultivars with high and low alpha-glucosidase inhibitory activity, and nine, including procyanidin C1, procyanidin trimer isomer 1, procyanidin trimer isomer 2, procyanidin B1, procyanidin dimer, epicatechin-epicatechin-epicatechin, phloridzin, kaempferol 3-(2'',6''-di-(E)-p-coumarylglucoside), and luteolin 3'-methyl ether 7-malonylglucoside, were identified as marker compounds responsible for the discrimination. Overall, variations in metabolites in peach pulp reflect the diversity in peach germplasm, and these nine compounds are good candidate markers for future genetic breeding of peach fruit with high alpha-glucosidase inhibitory activity.
Breeding in peach, cherry and plum: from a tissue culture, genetic, transcriptomic and genomic perspective.
Carrasco Basilio,Meisel Lee,Gebauer Marlene,Garcia-Gonzales Rolando,Silva Herman
This review is an overview of traditional and modern breeding methodologies being used to develop new Prunus cultivars (stone fruits) with major emphasis on peach, sweet cherry and Japanese plum. To this end, common breeding tools used to produce seedlings, including in vitro culture tools, are discussed. Additionally, the mechanisms of inheritance of many important agronomical traits are described. Recent advances in stone fruit transcriptomics and genomic resources are providing an understanding of the molecular basis of phenotypic variability as well as the identification of allelic variants and molecular markers. These have potential applications for understanding the genetic diversity of the Prunus species, molecular marker-assisted selection and transgenesis. Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNPs) molecular markers are described as useful tools to describe genetic diversity in peach, sweet cherry and Japanese plum. Additionally, the recently sequenced peach genome and the public release of the sweet cherry genome are discussed in terms of their applicability to breeding programs.
The peach volatilome modularity is reflected at the genetic and environmental response levels in a QTL mapping population.
Sánchez Gerardo,Martínez José,Romeu José,García Jesús,Monforte Antonio J,Badenes María L,Granell Antonio
BMC plant biology
BACKGROUND:The improvement of fruit aroma is currently one of the most sought-after objectives in peach breeding programs. To better characterize and assess the genetic potential for increasing aroma quality by breeding, a quantity trait locus (QTL) analysis approach was carried out in an F1 population segregating largely for fruit traits. RESULTS:Linkage maps were constructed using the IPSC peach 9 K Infinium ® II array, rendering dense genetic maps, except in the case of certain chromosomes, probably due to identity-by-descent of those chromosomes in the parental genotypes. The variability in compounds associated with aroma was analyzed by a metabolomic approach based on GC-MS to profile 81 volatiles across the population from two locations. Quality-related traits were also studied to assess possible pleiotropic effects. Correlation-based analysis of the volatile dataset revealed that the peach volatilome is organized into modules formed by compounds from the same biosynthetic origin or which share similar chemical structures. QTL mapping showed clustering of volatile QTL included in the same volatile modules, indicating that some are subjected to joint genetic control. The monoterpene module is controlled by a unique locus at the top of LG4, a locus previously shown to affect the levels of two terpenoid compounds. At the bottom of LG4, a locus controlling several volatiles but also melting/non-melting and maturity-related traits was found, suggesting putative pleiotropic effects. In addition, two novel loci controlling lactones and esters in linkage groups 5 and 6 were discovered. CONCLUSIONS:The results presented here give light on the mode of inheritance of the peach volatilome confirming previously loci controlling the aroma of peach but also identifying novel ones.
Development of microsatellite markers in peach [ Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry ( Prunus avium L.).
Dirlewanger E.,Cosson P.,Tavaud M.,Aranzana J.,Poizat C.,Zanetto A.,Arús P.,Laigret F.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
We report the sequence of 41 primer pairs of microsatellites from a CT-enriched genomic library of the peach cultivar 'Merrill O'Henry'. Ten microsatellite-containing clones had sequences similar to plant coding sequences in databases and could be used as markers for known functions. For microsatellites segregating at least in one of the two Prunus F(2) progenies analyzed, it was possible to demonstrate Mendelian inheritance. Microsatellite polymorphism was evaluated in 27 peach and 21 sweet cherry cultivars. All primer pairs gave PCR-amplification products on peach and 33 on cherry (80.5%). Six PCR-amplifications revealed several loci (14.6%) in peach and eight (19.5%) in sweet cherry. Among the 33 single-locus microsatellites amplified in peach and sweet cherry, 13 revealed polymorphism both in peach and cherry, 19 were polymorphic only on peach and one was polymorphic only on cherry. The number of alleles per locus ranged from 1 to 9 for peach and from 1 to 6 on sweet cherry with an average of 4.2 and 2.8 in peach and sweet cherry, respectively. Cross-species amplification was tested within the Prunus species: Prunus avium L. (sweet cherry and mazzard), Prunus cerasus L. (sour cherry), Prunus domestica L. (European plum), Prunus amygdalus Batsch. (almond), Prunus armeniaca L. (apricot), Prunus cerasifera Ehrh. (Myrobalan plum). Plants from other genera of the Rosaceae were also tested: Malus (apple) and Fragaria (strawberry), as well as species not belonging to the Rosaceae: Castanea (chestnut tree), Juglans (walnut tree) and Vitis (grapevine). Six microsatellites gave amplification on all the tested species. Among them, one had an amplified region homologous to sequences encoding a MADS-box protein in Malus x domestica. Twelve microsatellites (29.3%) were amplified in all the Rosaceae species tested and 31 (75.6%) were amplified in all the six Prunus species tested. Thirty three (80.5%), 18 (43.9%) and 13 (31.7%) gave amplification on chestnut tree, grapevine and walnut tree, respectively.
Integrated QTL detection for key breeding traits in multiple peach progenies.
Hernández Mora José R,Micheletti Diego,Bink Marco,Van de Weg Eric,Cantín Celia,Nazzicari Nelson,Caprera Andrea,Dettori Maria Teresa,Micali Sabrina,Banchi Elisa,Campoy José Antonio,Dirlewanger Elisabeth,Lambert Patrick,Pascal Thierry,Troggio Michela,Bassi Daniele,Rossini Laura,Verde Ignazio,Quilot-Turion Bénédicte,Laurens François,Arús Pere,Aranzana Maria José
BACKGROUND:Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. RESULTS:Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value. CONCLUSIONS:The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality.
Evaluation of the antioxidant capacity, phenolic compounds, and vitamin C content of different peach and nectarine [ Prunus persica (L.) Batsch] breeding progenies.
Cantín Celia M,Moreno María A,Gogorcena Yolanda
Journal of agricultural and food chemistry
Antioxidant capacity and contents of total phenolics, anthocyanins, flavonoids, and vitamin C were evaluated in 218 genotypes from 15 peach and nectarine breeding progenies. Significant differences were found among progenies on the fruit antioxidant profile, corroborated by the high contribution showed by cross to the phenotypic variance of each phytochemical trait analyzed (16-45%). Phytochemical profile varied depending on peach/nectarine and yellow/white flesh color qualitative traits. On the other hand, no significant effect of year was found on the bioactive profile of peaches and nectarines. Antioxidant capacity was linearly correlated to total phenolic content, but correlation varied depending on the progeny. No correlation was found for vitamin C versus any other phytochemical trait. The results suggest the importance of genetic background on the antioxidant profile of peaches and nectarines and stress its relevance for the ultimate objective of this work: selecting new peach and nectarine genotypes rich in bioactive compounds to benefit consumer's health.
Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch].
Bielenberg Douglas Gary,Rauh Bradley,Fan Shenghua,Gasic Ksenija,Abbott Albert Glenn,Reighard Gregory Lynn,Okie William R,Wells Christina Elizabeth
Low-cost, high throughput genotyping methods are crucial to marker discovery and marker-assisted breeding efforts, but have not been available for many 'specialty crops' such as fruit and nut trees. Here we apply the Genotyping-By-Sequencing (GBS) method developed for cereals to the discovery of single nucleotide polymorphisms (SNPs) in a peach F2 mapping population. Peach is a genetic and genomic model within the Rosaceae and will provide a template for the use of this method with other members of this family. Our F2 mapping population of 57 genotypes segregates for bloom time (BD) and chilling requirement (CR) and we have extensively phenotyped this population. The population derives from a selfed F1 progeny of a cross between 'Hakuho' (high CR) and 'UFGold' (low CR). We were able to successfully employ GBS and the TASSEL GBS pipeline without modification of the original methodology using the ApeKI restriction enzyme and multiplexing at an equivalent of 96 samples per Illumina HiSeq 2000 lane. We obtained hundreds of SNP markers which were then used to construct a genetic linkage map and identify quantitative trait loci (QTL) for BD and CR.
Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development.
Desnoues Elsa,Baldazzi Valentina,Génard Michel,Mauroux Jehan-Baptiste,Lambert Patrick,Confolent Carole,Quilot-Turion Bénédicte
Journal of experimental botany
Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and promote fruit consumption. The sugar content and composition of fruits varies with species, cultivar and stage of development, and is controlled by multiple enzymes. A QTL (quantitative trait locus) study was performed on peach fruit [Prunus persica (L.) Batsch], the model species for Prunus Progeny derived from an interspecific cross between P. persica cultivars and P. davidiana was used. Dynamic QTLs for fresh weight, sugars, acids, and enzyme activities related to sugar metabolism were detected at different stages during fruit development. Changing effects of alleles during fruit growth were observed, including inversions close to maturity. This QTL analysis was supplemented by the identification of genes annotated on the peach genome as enzymes linked to sugar metabolism or sugar transporters. Several cases of co-locations between annotated genes, QTLs for enzyme activities and QTLs controlling metabolite concentrations were observed and discussed. These co-locations raise hypotheses regarding the functional regulation of sugar metabolism and pave the way for further analyses to enable the identification of the underlying genes. In conclusion, we identified the potential impact on fruit breeding of the modification of QTL effect close to maturity.