Genome-wide detection for runs of homozygosity analysis in three pig breeds from Chinese Taihu Basin and Landrace pigs by SLAF-seq data  

作　　者：TONG Shi-feng ZHU Mo XIE Rui LI Dong-feng ZHANG Li-fan LIU Yang 

机构地区：[1]Department of Animal Genetics,Breeding and Reproduction,College of Animal Science and Technology,Nanjing Agricultural University,Nanjing 210095,P.R.China [2]Key Laboratory of Urban Agriculture,Ministry of Agriculture and Rural Affairs,Shanghai 200240,P.R.China

出　　处：《Journal of Integrative Agriculture》2022年第11期3293-3301,共9页农业科学学报（英文版）

基　　金：supported by the Jiangsu Agricultural Science and Technology Innovation Found,China(SCX(20)3290);the Open Foundation of Key Laboratory of Urban Agriculture,Ministry of Agriculture and Rural Affairs of China(201906);the Joint Research Project on Pig Breeding in Anhui Province,China(340000211260001000431)。

摘　　要：Erhualian(E),Meishan(MS)and Mi(MI)pigs are excellent indigenous pig breeds in Chinese Taihu Basin,which have made great contributions to the genetic improvement of commercial pigs.Investigation of the genetic structure and inbreeding level of the 3 pig breeds is of great significance for the sustainable breeding of commercial pigs.The length and number of runs of homozygosity(ROH)as well as the frequency of genomes covered by ROH can be used as indicators to evaluate the level of inbreeding and the origin of the population.In this study,the ROH characteristics of E,MS,MI and Landrace(L)pigs were analyzed by SLAF-seq data,and the inbreeding coefficient based on ROH(F_(ROH))was calculated.In addition,we have identified candidate genes in the genomic regions associated with ROH.A total of10568 ROH were detected in 116 individuals of 4 pig breeds.The analysis showed that there were significant differences in genetic structure between 3 Taihu Basin pig breeds and L,and the genetic structure of E and MI was similar.The results of F_(ROH)showed that the inbreeding level of MS was the highest(0.25±0.07),while E and MI were lower than L.Compared with the other 3 pig populations,MS showed a higher frequency of long ROH(>5 Mb),indicating higher inbreeding in MS in recent generations.A large number of candidate genes related to reproductive traits are located in the genomic regions with a high frequency of ROH,and these genes are expected to be used as candidate genes in marker-assisted selection(MAS)breeding programs.Our findings can provide theoretical support for genetic conservation and genetic improvement of 3 pig breeds in Chinese Taihu Basin.

关 键 词：runs of homozygosity inbreeding coefficient PIG candidate gene 

分 类 号：S828[农业科学—畜牧学]