Genome-wide methylation changes are associated with muscle fiber density and drip loss in male three-yellow chickens

Transcriptome-metabolome reveals the molecular changes in meat production and quality in the hybrid populations of Sichuan white goose

Hybrid breeding has proven to enhance meat quality and is extensively utilized in goose breeding. Nevertheless, there is a paucity of research investigating the molecular mechanisms that underlie the meat quality of hybrid geese. In this study, we employed the Sichuan White Goose as the maternal line for hybridization with the Zhedong White Goose and Tianfu Meat Goose P3 line. We assessed the growth and slaughter meat quality performance of 10-wk-old hybrid offspring in comparison to Sichuan white goose purebred offspring. The results indicate that hybrid geese have significantly improved performance in growth and slaughter meat quality. Furthermore, we conducted a comprehensive analysis of the chest muscles of hybrid offspring through transcriptomics and metabolomics to unravel the effects of hybrid breeding on growth and meat quality. A total of 673 differentially expressed genes (DEGs), and 93 differentially expressed metabolites were identified. The joint analysis highlighted the significant enrichment of DEGs AMPD1, AMPD3, RRM2, ENTPD3, and the metabolite UMP in the nucleotide metabolism pathway. These findings underscore the crucial role of these genetic and metabolic factors in regulating muscle growth and meat quality in hybrid populations.

Identification of the Differentially Expressed Genes in the leg muscles of Zhedong White Geese (Anser cygnoides) reared under different photoperiods

Light is a factor affecting muscle development and meat quality in poultry production. However, few studies have reported on the role of light in muscle development and meat quality in geese. In this experiment, 10 healthy 220-day-old Zhedong white geese were reared for 60 d under a long photoperiod (15L:9D, LL) and short photoperiod (9L:15D, SL). The gastrocnemius muscles were collected after slaughter to evaluate muscle fiber characteristics and meat color, and RNA-seq analysis. The results showed that compared to the LL group, the SL group had large muscle fiber diameter and cross-sectional area, few muscle fibers per unit area, high meat color a* value, and low L* value at 24 h postmortem. On comparing the 2 groups, 70 differentially expressed genes (DEGs) were identified. Compared to the SL group, the LL group had 25 upregulated and 45 downregulated genes. Gene Ontology (GO) enrichment analysis showed that these DEGs were mainly involved in cell, cell part, binding, cellular processes, and single-organism processes. Several significantly enriched athways were identified in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, such as the calcium and PI3k-Akt signaling pathways. The expression of five randomly selected DEGs was verified using quantitative real-time PCR, and the results were consistent with the RNA-seq data. This study provides a theoretical basis for studying the molecular mechanisms by which light affects muscle development and meat color in geese.

Whole-genome bisulfite sequencing of abdominal adipose reveals DNA methylation pattern variations in broiler lines divergently selected for fatness

The methylation status of pivotal genes involved in fat deposition in chickens has been extensively studied. However, the whole-genome DNA methylation profiles of broiler abdominal adipose tissue remain poorly understood. Using whole-genome bisulfite sequencing, we generated DNA methylation profiles of chicken abdominal adipose tissue from Northeast Agricultural University broiler lines divergently selected for abdominal fat content. We aimed to explore whether DNA methylation was associated with abdominal fat deposition in broilers. The whole-genome DNA methylation profiles of fat- and lean-line broilers abdominal adipose tissue were constructed. The DNA methylation levels of functional genomic regions in the fat broiler were higher than those in the lean broiler, especially in the 3' untranslated regions (UTRs) and exons in the non-CG contexts. Additionally, we identified 29,631 differentially methylated regions and, subsequently, annotated 6,484 and 2,016 differentially methylated genes (DMGs) in the gene body and promoter regions between the two lines, respectively. Functional annotation showed that the DMGs in promoter regions were significantly enriched mainly in the triglyceride catabolic process, lipid metabolism-related pathways, and extracellular matrix signal pathways. When the DMG in promoter regions and differentially expressed genes were integrated, we identified 30 genes with DNA methylation levels that negatively correlated with their messenger RNA (mRNA) expression, of which CMSS1 reached significant levels (false discovery rate < 0.05). These 30 genes were mainly involved in fatty acid metabolism, peroxisome-proliferator-activated receptor signaling, Wnt signaling pathways, transmembrane transport, RNA degradation, and glycosaminoglycan degradation. Comparing the DNA methylation profiles between fat- and lean-line broilers demonstrated that DNA methylation is involved in regulating broiler abdominal fat deposition. Our study offers a basis for further exploring the underlying mechanisms of abdominal adipose deposition in broilers.

Feeding conditions and breed affect the level of DNA methylation of the mitochondrial uncoupling protein 3 gene in chicken breast muscle

To investigate the effects of feed condition and breed on the level of DNA methylation for the uncoupling protein 3 (UCP3) gene, which is an important candidate gene for regulating intramuscular fat (IMF) content in chicken breast muscle, breast muscle of Daninghe (DNH) and Qingjiaoma (QJM) chickens under scatter-feed and captivity-feed conditions was analyzed. Using RNA sequencing, 47 and 113 candidate genes were determined to be related to feed conditions and breed, respectively, and 7 differentially expressed genes were confirmed by real-time quantitative PCR, including UCP3. The mRNA levels of UCP3 were significantly different between the 2 feed conditions. The DNA region from bp +1700 to +2459 of the UCP3 gene was studied using the bisulfite sequencing method and contained 46 methylation sites and 3 CpG islands. The results showed that the methylation level of this UCP3 region was lower in DNH chickens (0.77% to 0.88%, P = 0.012) and QJM chickens (0.88% to 0.91%, P = 0.20) under scatter-feed conditions than under captivity-feed conditions. The mean methylation level of UCP3 in DNH chickens was lower than that in QJM chickens under scatter-feed conditions (DNH to QJM, 0.77% to 0.88%, P = 0.007), which suggests that breed affects the mean methylation level of UCP3 under scatter-feed conditions. In summary, our findings suggest that feed condition and breed affect the methylation of UCP3 in chicken breast muscle.