Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes
In this study, we aimed to identified CpG sites at which DNA methylation levels are associated with meat quality traits in 140 Yorkshire pigs, including pH at 45 min (pH45min), pH at 24 h (pH24h), drip loss (DL), meat redness value (a*), yellowness (b*) and lightness (L*). Genome-wide methylation le...
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| Format: | Article |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1028711/full |
| _version_ | 1797961945540722688 |
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| author | Kai Wang Shujie Wang Xiang Ji Dong Chen Qi Shen Yang Yu Pingxian Wu Pingxian Wu Xuewei Li Guoqing Tang |
| author_facet | Kai Wang Shujie Wang Xiang Ji Dong Chen Qi Shen Yang Yu Pingxian Wu Pingxian Wu Xuewei Li Guoqing Tang |
| author_sort | Kai Wang |
| collection | DOAJ |
| description | In this study, we aimed to identified CpG sites at which DNA methylation levels are associated with meat quality traits in 140 Yorkshire pigs, including pH at 45 min (pH45min), pH at 24 h (pH24h), drip loss (DL), meat redness value (a*), yellowness (b*) and lightness (L*). Genome-wide methylation levels were measured in muscular tissue using reduced representation bisulfite sequencing (RRBS). Associations between DNA methylation levels and meat quality traits were examined using linear mixed-effect models that were adjusted for gender, year, month and body weight. A Bonferroni-corrected p-value lower than 7.79×10−8 was considered statistically significant threshold. Eight CpG sites were associated with DL, including CpG sites annotated to RBM4 gene (cpg301054, cpg301055, cpg301058, cpg301059, cpg301066, cpg301072 and cpg301073) and NCAM1 gene (cpg1802985). Two CpG sites were associated with b*, including RNFT1 and MED13 (cpg2272837) and TRIM37 gene (cpg2270611). Five CpG sites were associated with L*, including GSDMA and LRRC3C gene (cpg2252750) and ENSSSCG00000043539 and IRX1 gene (cpg2820178, cpg2820179, cpg2820181 and cpg2820182). No significant associations were observed with pH45min, pH24h or a*. We reported associations of meat quality traits with DNA methylation and identified some candidate genes associated with these traits, such as NCAM1, MED13 and TRIM37 gene. These results provide new insight into the epigenetic molecular mechanisms of meat quality traits in pigs. |
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| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-11T01:06:52Z |
| publishDate | 2023-01-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-c8c72ec2c6244b8f8de69eef5a21ada02023-01-04T12:41:09ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011310.3389/fgene.2022.10287111028711Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genesKai Wang0Shujie Wang1Xiang Ji2Dong Chen3Qi Shen4Yang Yu5Pingxian Wu6Pingxian Wu7Xuewei Li8Guoqing Tang9Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaChongqing Academy of Animal Science, Chongqing, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, ChinaIn this study, we aimed to identified CpG sites at which DNA methylation levels are associated with meat quality traits in 140 Yorkshire pigs, including pH at 45 min (pH45min), pH at 24 h (pH24h), drip loss (DL), meat redness value (a*), yellowness (b*) and lightness (L*). Genome-wide methylation levels were measured in muscular tissue using reduced representation bisulfite sequencing (RRBS). Associations between DNA methylation levels and meat quality traits were examined using linear mixed-effect models that were adjusted for gender, year, month and body weight. A Bonferroni-corrected p-value lower than 7.79×10−8 was considered statistically significant threshold. Eight CpG sites were associated with DL, including CpG sites annotated to RBM4 gene (cpg301054, cpg301055, cpg301058, cpg301059, cpg301066, cpg301072 and cpg301073) and NCAM1 gene (cpg1802985). Two CpG sites were associated with b*, including RNFT1 and MED13 (cpg2272837) and TRIM37 gene (cpg2270611). Five CpG sites were associated with L*, including GSDMA and LRRC3C gene (cpg2252750) and ENSSSCG00000043539 and IRX1 gene (cpg2820178, cpg2820179, cpg2820181 and cpg2820182). No significant associations were observed with pH45min, pH24h or a*. We reported associations of meat quality traits with DNA methylation and identified some candidate genes associated with these traits, such as NCAM1, MED13 and TRIM37 gene. These results provide new insight into the epigenetic molecular mechanisms of meat quality traits in pigs.https://www.frontiersin.org/articles/10.3389/fgene.2022.1028711/fullDNA methylationEWASCPGspiggene |
| spellingShingle | Kai Wang Shujie Wang Xiang Ji Dong Chen Qi Shen Yang Yu Pingxian Wu Pingxian Wu Xuewei Li Guoqing Tang Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes Frontiers in Genetics DNA methylation EWAS CPGs pig gene |
| title | Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes |
| title_full | Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes |
| title_fullStr | Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes |
| title_full_unstemmed | Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes |
| title_short | Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes |
| title_sort | epigenome wide association studies of meat traits in chinese yorkshire pigs highlights several dna methylation loci and genes |
| topic | DNA methylation EWAS CPGs pig gene |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1028711/full |
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