Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs  

作　　者：Wencheng Zong Jinbu Wang Runze Zhao Naiqi Niu Yanfang Su Ziping Hu Xin Liu Xinhua Hou Ligang Wang Lixian Wang Longchao Zhang 

机构地区：[1]State Key Laboratory of Animal Biotech Breeding,Institute of Animal Sciences,Chinese Academy of Agricultural Sciences,Beijing 100193,China [2]College of Animal Science,Shanxi Agricultural University,Jinzhong 030801,China [3]College of Animal Science and Technology,Qingdao Agricultural University,Qingdao 266109,China

出　　处：《Journal of Animal Science and Biotechnology》2024年第1期68-87,共20页畜牧与生物技术杂志（英文版）

基　　金：supported by the National Key R&D Program of China(2021YFD1301101);National Swine Industry Technology System(CARS-35);Agricultural Science and Technology Innovation Program(ASTIP-IAS02)。

摘　　要：Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

关 键 词：Body size GWAS PIG SKELETON Structural variations 

分 类 号：S828[农业科学—畜牧学]