Genome-wide DNA methylation profiles reveal novel candidate genes associated with meat quality at different age stages in hens

Abstract

Poultry meat quality is associated with breed, age, tissue and other factors. Many previous studies have focused on distinct breeds; however, little is known regarding the epigenetic regulatory mechanisms in different age stages, such as DNA methylation. Here, we compared the global DNA methylation profiles between juvenile (20 weeks old) and later laying-period (55 weeks old) hens and identified candidate genes related to the development and meat quality of breast muscle using whole-genome bisulfite sequencing. The results showed that the later laying-period hens, which had a higher intramuscular fat (IMF) deposition capacity and water holding capacity (WHC) and less tenderness, exhibited higher global DNA methylation levels than the juvenile hens. A total of 2,714 differentially methylated regions were identified in the present study, which corresponded to 378 differentially methylated genes, mainly affecting muscle development, lipid metabolism, and the ageing process. Hypermethylation of the promoters of the genes ABCA1, COL6A1 and GSTT1L and the resulting transcriptional down-regulation in the later laying-period hens may be the reason for the significant difference in the meat quality between the juvenile and later laying-period hens. These findings contribute to a better understanding of epigenetic regulation in the skeletal muscle development and meat quality of chicken.

Genome-Wide Epigenetic Studies in Chicken: A Review

“…The authors showed that late-laying hens showed a higher DNA methylation level along the genome compared to the juvenile hens. This increase in methylation was also found at the promoter of genes known to be involved in meat quality [82]. These findings are similar to what Laine et al reported using a passerine bird species [9].…”

“…The non-CpG methylation rate was negatively correlated with transposable element activity in the brain and it was proposed that non-CpG methylation might be involved in the regulation of transposable element silencing in this tissue. The significant presence of non-CpG methylation in brain is in agreement with what was reported in mammals and chicken [78,82,83]. Altogether, these studies suggest that the methylation landscape is likely to be comparable between bird species and other species such as mammals.…”

“…Another recent WGBS study lead to new insights about DNA methylation variations during the lifespan of chicken. Indeed, Zhang et al revealed variation in methylation profiles at different ages in hens breast muscle tissue [82]. The authors showed that late-laying hens showed a higher DNA methylation level along the genome compared to the juvenile hens.…”

Integrated Analysis of MiRNA and Genes Associated with Meat Quality Reveals that Gga-MiR-140-5p Affects Intramuscular Fat Deposition in Chickens

“…Previous studies suggested that miRNAs play crucial roles in animal meat quality [16, 17]. In our previous study, we found a remarkable difference in the meat traits and lipid metabolism levels between juvenile and late-laying-period hens [18]. Furthermore, we identified numerous differentially methylated genes and differentially expressed genes (DEGs) associated with meat quality in breast muscle between the two physiological stages [18].…”

“…In our previous study, we found a remarkable difference in the meat traits and lipid metabolism levels between juvenile and late-laying-period hens [18]. Furthermore, we identified numerous differentially methylated genes and differentially expressed genes (DEGs) associated with meat quality in breast muscle between the two physiological stages [18]. Given that there existed a considerable quantity of DEGs between the juvenile (20 weeks old) and late-laying-period (55 weeks old) hens and tremendous differences in meat quality and lipid metabolism levels, we speculated that miRNAs might serve as important regulators of chicken meat quality between different age stages.…”