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

doi:10.1016/j.jgg.2023.11.005

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

J Genet Genomics. 2024 Apr;51(4):394-406. doi: 10.1016/j.jgg.2023.11.005. Epub 2023 Dec 4.

Authors

Xin Li¹, Quan Liu¹, Chong Fu¹, Mengxun Li¹, Changchun Li², Xinyun Li³, Shuhong Zhao⁴, Zhuqing Zheng⁵

Affiliations

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; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China. Electronic address: shzhao@mail.hzau.edu.cn.
⁵ 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. Electronic address: zzq_1207@mail.hzau.edu.cn.

PMID: 38056526
DOI: 10.1016/j.jgg.2023.11.005

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.

Keywords: Pigs; Regulatory elements; Selection signatures; Structural variation.

MeSH terms

Animals
Domestication*
Genome* / genetics
Genomics
Genotype
Phenotype
Swine / genetics