Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs
Single-nucleotide polymorphisms (SNPs) that are located near CpG sites have the potential to influence DNA methylation levels, leading to distinct patterns of DNA methylation. These methylation quantitative trait loci (meQTLs) can influence methylation levels across the entire genome, thereby impact...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2023-12-01
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| Series: | Italian Journal of Animal Science |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/1828051X.2023.2247003 |
| _version_ | 1797198472591441920 |
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| author | Qi Shen Kai Wang Shujie Wang Zhenjian Zhao Xiang Ji Dong Chen Yang Yu Shengdi Cui Junge Wang Ziyang Chen Yiren Gu Guoqing Tang |
| author_facet | Qi Shen Kai Wang Shujie Wang Zhenjian Zhao Xiang Ji Dong Chen Yang Yu Shengdi Cui Junge Wang Ziyang Chen Yiren Gu Guoqing Tang |
| author_sort | Qi Shen |
| collection | DOAJ |
| description | Single-nucleotide polymorphisms (SNPs) that are located near CpG sites have the potential to influence DNA methylation levels, leading to distinct patterns of DNA methylation. These methylation quantitative trait loci (meQTLs) can influence methylation levels across the entire genome, thereby impacting phenotypic traits. In this study, we utilised reduced representation bisulphite sequencing (RRBS) to analyse DNA methylation in muscle tissue samples collected from 140 Yorkshire pigs. Additionally, we assessed SNPs using the Porcine 50K chip, examined 17 fatty acid traits, and conducted epigenome-wide association studies (EWAS) and genome-wide association studies (GWAS). Our investigation revealed numerous associations between DNA methylation and fatty acid traits, including C16:0, C18:0, C20:3n-3, and C22:6n-3. Notably, a substantial portion of these associations was specifically identified by EWAS and not GWAS. Subsequently, we performed GWAS to identify meQTLs using methylation levels of significant CpGs from the EWAS as traits. The results revealed the predominance of trans-meQTLs; however, we also discovered a cis-meQTL on SSC12. Finally, we reported a crucial CpG site (SSC12:3735523) and its cis-meQTL on SSC12, which are located in close proximity to the FASN gene. Our findings contribute to the identification of CpG sites and their cis-meQTLs associated with fatty acid traits, utilising comprehensive genome and methylome data. Moreover, our study provides novel insights into the molecular mechanisms underlying fatty acid traits in pigs. |
| first_indexed | 2024-03-08T16:59:27Z |
| format | Article |
| id | doaj.art-f499b992efee44629757a543c1631085 |
| institution | Directory Open Access Journal |
| issn | 1594-4077 1828-051X |
| language | English |
| last_indexed | 2024-04-24T07:00:24Z |
| publishDate | 2023-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Italian Journal of Animal Science |
| spelling | doaj.art-f499b992efee44629757a543c16310852024-04-22T08:52:28ZengTaylor & Francis GroupItalian Journal of Animal Science1594-40771828-051X2023-12-0122182984010.1080/1828051X.2023.22470032247003Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigsQi Shen0Kai Wang1Shujie Wang2Zhenjian Zhao3Xiang Ji4Dong Chen5Yang Yu6Shengdi Cui7Junge Wang8Ziyang Chen9Yiren Gu10Guoqing Tang11Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityNew Hope Liuhe CO., LTDFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityAnimal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science AcademyFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversitySingle-nucleotide polymorphisms (SNPs) that are located near CpG sites have the potential to influence DNA methylation levels, leading to distinct patterns of DNA methylation. These methylation quantitative trait loci (meQTLs) can influence methylation levels across the entire genome, thereby impacting phenotypic traits. In this study, we utilised reduced representation bisulphite sequencing (RRBS) to analyse DNA methylation in muscle tissue samples collected from 140 Yorkshire pigs. Additionally, we assessed SNPs using the Porcine 50K chip, examined 17 fatty acid traits, and conducted epigenome-wide association studies (EWAS) and genome-wide association studies (GWAS). Our investigation revealed numerous associations between DNA methylation and fatty acid traits, including C16:0, C18:0, C20:3n-3, and C22:6n-3. Notably, a substantial portion of these associations was specifically identified by EWAS and not GWAS. Subsequently, we performed GWAS to identify meQTLs using methylation levels of significant CpGs from the EWAS as traits. The results revealed the predominance of trans-meQTLs; however, we also discovered a cis-meQTL on SSC12. Finally, we reported a crucial CpG site (SSC12:3735523) and its cis-meQTL on SSC12, which are located in close proximity to the FASN gene. Our findings contribute to the identification of CpG sites and their cis-meQTLs associated with fatty acid traits, utilising comprehensive genome and methylome data. Moreover, our study provides novel insights into the molecular mechanisms underlying fatty acid traits in pigs.http://dx.doi.org/10.1080/1828051X.2023.2247003pigdna methylationewasgwasmeqtl |
| spellingShingle | Qi Shen Kai Wang Shujie Wang Zhenjian Zhao Xiang Ji Dong Chen Yang Yu Shengdi Cui Junge Wang Ziyang Chen Yiren Gu Guoqing Tang Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs Italian Journal of Animal Science pig dna methylation ewas gwas meqtl |
| title | Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs |
| title_full | Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs |
| title_fullStr | Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs |
| title_full_unstemmed | Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs |
| title_short | Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs |
| title_sort | identifying key dna methylation sites and their cis methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in yorkshire pigs |
| topic | pig dna methylation ewas gwas meqtl |
| url | http://dx.doi.org/10.1080/1828051X.2023.2247003 |
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