Lei Liu, Guoqiang Yi, Yilong Yao, Yuwen Liu, Jiang Li, Yalan Yang, Mei Liu, Lingzhao Fang, Delin Mo, Longchao Zhang, Yonggang Liu, Yongchao Niu, Liyuan Wang, Xiaolu Qu, Zhangyuan Pan, Lei Wang, Muya Chen, Xinhao Fan, Yun Chen, Yongsheng Zhang, Xingzheng Li, Zhen Wang, Yijie Tang, Hetian Huang, Pengxiang Yuan, Yuying Liao, Xinjian Li, Zongjun Yin, Di Liu, Dongjie Zhang, Quanyong Zhou, Wangjun Wu, Jicai Jiang, Yahui Gao, George E. Liu, Lixian Wang, Yaosheng Chen, Kui Li, Martien A. M. Groenen, Zhonglin Tang
{"title":"多组学分析揭示了猪的选择特征和与复杂性状相关的位点","authors":"Lei Liu, Guoqiang Yi, Yilong Yao, Yuwen Liu, Jiang Li, Yalan Yang, Mei Liu, Lingzhao Fang, Delin Mo, Longchao Zhang, Yonggang Liu, Yongchao Niu, Liyuan Wang, Xiaolu Qu, Zhangyuan Pan, Lei Wang, Muya Chen, Xinhao Fan, Yun Chen, Yongsheng Zhang, Xingzheng Li, Zhen Wang, Yijie Tang, Hetian Huang, Pengxiang Yuan, Yuying Liao, Xinjian Li, Zongjun Yin, Di Liu, Dongjie Zhang, Quanyong Zhou, Wangjun Wu, Jicai Jiang, Yahui Gao, George E. Liu, Lixian Wang, Yaosheng Chen, Kui Li, Martien A. M. Groenen, Zhonglin Tang","doi":"10.1002/imt2.250","DOIUrl":null,"url":null,"abstract":"<p>The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Using nine genomes—seven of which were newly generated, high-quality de novo assembled genomes—and 1081 resequencing genomes, we built a pan-genome and identified 134.24 Mb nonredundant nonreference sequences, 1099 novel protein-coding genes, 187,927 structural variations (SVs) and 30,143,962 single-nucleotide polymorphisms (SNPs). Analysis of selective domestication revealed <i>BRCA1</i> associated with enhanced adipocyte growth and fat deposition, and <i>ABCA3</i> linked to an alleviated immune response and reduced lung injury. Integrating 162 transcriptomes and 162 methylomes of skeletal muscle across 27 developmental stages revealed the regulatory mechanism of phenotypic differentiation between Eastern and Western breeds. Artificial selection reshaped local DNA methylation status and imparted regulatory effects on the progression patterns of heterochronic genes such as <i>GHSR</i> and <i>BDH1</i>, particularly during embryonic development. Altogether, our work provides valuable resources for understanding molecular mechanisms behind phenotypic variations and enhancing the genetic improvement programs in pigs.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7000,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.250","citationCount":"0","resultStr":"{\"title\":\"Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs\",\"authors\":\"Lei Liu, Guoqiang Yi, Yilong Yao, Yuwen Liu, Jiang Li, Yalan Yang, Mei Liu, Lingzhao Fang, Delin Mo, Longchao Zhang, Yonggang Liu, Yongchao Niu, Liyuan Wang, Xiaolu Qu, Zhangyuan Pan, Lei Wang, Muya Chen, Xinhao Fan, Yun Chen, Yongsheng Zhang, Xingzheng Li, Zhen Wang, Yijie Tang, Hetian Huang, Pengxiang Yuan, Yuying Liao, Xinjian Li, Zongjun Yin, Di Liu, Dongjie Zhang, Quanyong Zhou, Wangjun Wu, Jicai Jiang, Yahui Gao, George E. Liu, Lixian Wang, Yaosheng Chen, Kui Li, Martien A. M. Groenen, Zhonglin Tang\",\"doi\":\"10.1002/imt2.250\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Using nine genomes—seven of which were newly generated, high-quality de novo assembled genomes—and 1081 resequencing genomes, we built a pan-genome and identified 134.24 Mb nonredundant nonreference sequences, 1099 novel protein-coding genes, 187,927 structural variations (SVs) and 30,143,962 single-nucleotide polymorphisms (SNPs). Analysis of selective domestication revealed <i>BRCA1</i> associated with enhanced adipocyte growth and fat deposition, and <i>ABCA3</i> linked to an alleviated immune response and reduced lung injury. Integrating 162 transcriptomes and 162 methylomes of skeletal muscle across 27 developmental stages revealed the regulatory mechanism of phenotypic differentiation between Eastern and Western breeds. Artificial selection reshaped local DNA methylation status and imparted regulatory effects on the progression patterns of heterochronic genes such as <i>GHSR</i> and <i>BDH1</i>, particularly during embryonic development. Altogether, our work provides valuable resources for understanding molecular mechanisms behind phenotypic variations and enhancing the genetic improvement programs in pigs.</p>\",\"PeriodicalId\":73342,\"journal\":{\"name\":\"iMeta\",\"volume\":\"3 6\",\"pages\":\"\"},\"PeriodicalIF\":23.7000,\"publicationDate\":\"2024-12-15\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.250\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"iMeta\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/imt2.250\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"iMeta","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/imt2.250","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs
The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Using nine genomes—seven of which were newly generated, high-quality de novo assembled genomes—and 1081 resequencing genomes, we built a pan-genome and identified 134.24 Mb nonredundant nonreference sequences, 1099 novel protein-coding genes, 187,927 structural variations (SVs) and 30,143,962 single-nucleotide polymorphisms (SNPs). Analysis of selective domestication revealed BRCA1 associated with enhanced adipocyte growth and fat deposition, and ABCA3 linked to an alleviated immune response and reduced lung injury. Integrating 162 transcriptomes and 162 methylomes of skeletal muscle across 27 developmental stages revealed the regulatory mechanism of phenotypic differentiation between Eastern and Western breeds. Artificial selection reshaped local DNA methylation status and imparted regulatory effects on the progression patterns of heterochronic genes such as GHSR and BDH1, particularly during embryonic development. Altogether, our work provides valuable resources for understanding molecular mechanisms behind phenotypic variations and enhancing the genetic improvement programs in pigs.
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