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

作     者：Xin Li Quan Liu Chong Fu Mengxun Li Changchun Li Xinyun Li Shuhong Zhao Zhuqing Zheng Xin Li;Quan Liu;Chong Fu;Mengxun Li;Changchun Li;Xinyun Li;Shuhong Zhao;Zhuqing Zheng

作者机构：Key Lab of Agricultural Animal GeneticsBreeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China Institute of Agricultural BiotechnologyJingchu University of TechnologyJingmenHubei 448000China The Cooperative Innovation Center for Sustainable Pig ProductionWuhanHubei 430070China Hubei Hongshan LaboratoryWuhanHubei 430070China 

出 版 物：《Journal of Genetics and Genomics》 (遗传学报（英文版）)

年 卷 期：2024年第51卷第4期

页      面：394-406页

核心收录：

学科分类：090504[农学-特种经济动物饲养（含：蚕、蜂等）] 0905[农学-畜牧学] 09[农学] 0902[农学-园艺学] 090201[农学-果树学] 

基　　金：supported by Creative Research Team Project of the National Natural Science Foundation of China(32221005 to S.Zhao) grants from the National Natural Science Foundation of China(32202637 to Z.Zheng and 31972536 to X.Li) the earmarked fund for CARS-35,and China Postdoctoral Science Foundation(2020M682446 to Z.Zheng) 

主　　题：Pigs Structural variation Selection signatures Regulatory elements 

摘      要：Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic *** 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 *** results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local *** characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory *** identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)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 *** 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.