遗传学报2024，Vol.51Issue(4) ：394-406.DOI:10.1016/j.jgg.2023.11.005

Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

Xin Li Quan Liu Chong Fu Mengxun Li Changchun Li Xinyun Li Shuhong Zhao Zhuqing Zheng
遗传学报2024，Vol.51Issue(4) ：394-406.DOI:10.1016/j.jgg.2023.11.005
✕
  • NETL
  • NSTL
  • 万方数据

Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

Xin Li 1Quan Liu 1Chong Fu 1Mengxun Li 1Changchun Li 2Xinyun Li 3Shuhong Zhao 3Zhuqing Zheng4
扫码查看

作者信息

  • 1. Key Lab of Agricultural Animal Genetics,Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture,College of Animal Science and Technology,Huazhong Agricultural University,Wuhan,Hubei 430070,China
  • 2. Key Lab of Agricultural Animal Genetics,Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture,College of Animal Science and Technology,Huazhong Agricultural University,Wuhan,Hubei 430070,China;The Cooperative Innovation Center for Sustainable Pig Production,Wuhan,Hubei 430070,China
  • 3. Key Lab of Agricultural Animal Genetics,Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture,College of Animal Science and Technology,Huazhong Agricultural University,Wuhan,Hubei 430070,China;The Cooperative Innovation Center for Sustainable Pig Production,Wuhan,Hubei 430070,China;Hubei Hongshan Laboratory,Wuhan,Hubei 430070,China
  • 4. Key Lab of Agricultural Animal Genetics,Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture,College of Animal Science and Technology,Huazhong Agricultural University,Wuhan,Hubei 430070,China;Institute of Agricultural Biotechnology,Jingchu University of Technology,Jingmen,Hubei 448000,China
  • 折叠

Abstract

Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes.Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation.Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements.We identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101-52,172,397;278-bp DEL,chr18:23,840,143-23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in pigs.Our results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.

Key words

Pigs/Structural variation/Selection signatures/Regulatory elements

引用本文复制引用

基金项目

Creative Research Team Project of the National Natural Science Foundation of China(32221005)

National Natural Science Foundation of China(32202637)

National Natural Science Foundation of China(31972536)

earmarked fund(CARS-35)

China Postdoctoral Science Foundation(2020M682446)

出版年

2024
遗传学报
中国遗传学会 中国科学院遗传与发育生物学研究所

遗传学报

CSTPCDCSCD
影响因子：0.821
ISSN：1673-8527
参考文献量82
段落导航相关论文