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    Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality. Sibut Vonick,Hennequet-Antier Christelle,Le Bihan-Duval Elisabeth,Marthey Sylvain,Duclos Michel J,Berri Cécile BMC genomics BACKGROUND:The processing ability of poultry meat is highly related to its ultimate pH, the latter being mainly determined by the amount of glycogen in the muscle at death. The genetic determinism of glycogen and related meat quality traits has been established in the chicken but the molecular mechanisms involved in variations in these traits remain to be fully described. In this study, Chicken Genome Arrays (20 K) were used to compare muscle gene expression profiles of chickens from Fat (F) and Lean (L) lines that exhibited high and low muscle glycogen content, respectively, and of individuals exhibiting extremely high (G+) or low (G-) muscle glycogen content originating from the F2 cross between the Fat and Lean lines. Real-time RT-PCR was subsequently performed to validate the differential expression of genes either selected from the microarray analysis or whose function in regulating glycogen metabolism was well known. RESULTS:Among the genes found to be expressed in chicken P. major muscle, 197 and 254 transcripts appeared to be differentially expressed on microarrays for the F vs. L and the G+ vs. G- comparisons, respectively. Some involved particularly in lipid and carbohydrate metabolism were selected for further validation studies by real-time RT-PCR. We confirmed that, as in mammals, the down-regulation of CEBPB and RGS2 coincides with a decrease in peripheral adiposity in the chicken, but these genes are also suggested to affect muscle glycogen turnover through their role in the cAMP-dependent signalling pathway. Several other genes were suggested to have roles in the regulation of glycogen storage in chicken muscle. PDK4 may act as a glycogen sensor in muscle, UGDH may compete for glycogen synthesis by using UDP-glucose for glucoronidation, and PRKAB1, PRKAG2, and PHKD may impact on glycogen turnover in muscle, through AMP-activated signalling pathways. CONCLUSIONS:This study is the first stage in the understanding of molecular mechanisms underlying variations in poultry meat quality. Large scale analyses are now required to validate the role of the genes identified and ultimately to find molecular markers that can be used for selection or to optimize rearing practices. 10.1186/1471-2164-12-112
    Genome-wide association study of meat quality traits in chicken. Zhang T,Fan Q C,Wang J Y,Zhang G X,Gu Y P,Tang Y Genetics and molecular research : GMR Meat quality traits are very important in the poultry industry. To identify single nucleotide polymorphisms (SNPs) and candidate genes affecting meat quality traits, a genome-wide association study was performed using the Illumina chicken 60K SNP beadchip in Jinghai yellow chicken. Four meat quality traits were measured. Two SNPs reached 5% Bonferroni genome-wide significance (P < 1.8E-6) and 7 SNPs reached "suggestive" genome-wide significance (P < 3.59E-6) with meat quality. These SNPs were located nearby or in 7 candidate genes, including CBLN2, HPGDS, SETD2, and ANKRD46, among others. A total of 5650 haplotpyes were established and only 1 was found to be associated with fat content in leg muscle. These results indicate that the 9 SNPs and 7 genes are important candidate markers and may influence meat quality traits in chicken. 10.4238/2015.September.8.6
    Integrated Analysis of MiRNA and Genes Associated with Meat Quality Reveals that Gga-MiR-140-5p Affects Intramuscular Fat Deposition in Chickens. Zhang Meng,Li Dong-Hua,Li Fang,Sun Jun-Wei,Jiang Rui-Rui,Li Zhuan-Jian,Han Rui-Li,Li Guo-Xi,Liu Xiao-Jun,Kang Xiang-Tao,Sun Gui-Rong Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology BACKGROUND/AIMS:Poultry meat quality is affected by many factors, among which intramuscular fat (IMF) is predominant. IMF content affects the tenderness, juiciness, and favor of chicken. An increasing number of studies are focusing on the functions of microRNAs (miRNAs) during the adipogenic process. However, little is known about miRNAs associated with poultry IMF deposition, especially intramuscular adipocyte differentiation. METHODS:The IMF content of two physiological stages was measured, and miRNA-Seq and RNA-Seq data were integrated and analyzed. A chicken intramuscular adipocyte cell differentiation model was constructed. A luciferase reporter assay, miRNA overexpression, and Oil Red O staining were used to confirm the targets of gga-miR-140-5p. RESULTS:Our results showed that late-laying-period hens, which had a higher IMF content, exhibited lower global expression levels of miRNAs than juvenile hens. A total of 104 differentially expressed (DE) miRNAs were identified between the two groups. Integrated analysis of differentially expressed genes and DE miRNAs identified a total of 378 miRNA-mRNA pairs. Functional enrichment analysis revealed that these intersecting genes are involved in ubiquitin-mediated proteolysis, the peroxisome proliferator-activated receptor signaling pathway, glycerophospholipid metabolism, and fatty acid elongation and degradation pathways. Furthermore, we demonstrated that gga-miR-140-5p promoted intramuscular adipocyte differentiation via targeting retinoid X receptor gamma. CONCLUSION:Our findings may contribute to a more thorough understanding of chicken IMF deposition and the improvement of poultry meat quality. 10.1159/000489649