Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds  

作　　者：Jiaxin Liu Liangyu Shi Yang Li Liang Chen Dorian Garrick Lixian Wang Fuping Zhao 

机构地区：[1]Key Laboratory of Animal Genetics,Breeding and Reproduction(Poultry)of Ministry of Agriculture,Institute of Animal Sciences,Chinese Academy of Agricultural Sciences,Beijing 100193,China [2]The Affiliated High School of Peking University,Beijing 100192,China [3]A.L.Rae Centre of Genetics and Breeding,Massey University,Hamilton 3240,New Zealand

出　　处：《Journal of Animal Science and Biotechnology》2022年第1期52-65,共14页畜牧与生物技术杂志（英文版）

基　　金：funded by the Natural Science Foundations of China(No.31572357)to FPZ;Agricultural Science and Technology Innovation Program(ASTIP-IAS02)to LXW.

摘　　要：Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified based on ROH.Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands.We carried out ROH analyses in five Chinese indigenous sheep breeds;Altay sheep(n=50 individuals),Large-tailed Han sheep(n=50),Hulun Buir sheep(n=150),Short-tailed grassland sheep(n=150),and Tibetan sheep(n=50),using genotypes from an Ovine Infinium HD SNP BeadChip.Results:A total of 18,288 ROH were identified.The average number of ROH per individual across the five sheep breeds ranged from 39(Hulun Buir sheep)to 78(Large-tailed Han sheep)and the average length of ROH ranged from 0.929 Mb(Hulun Buir sheep)to 2.544 Mb(Large-tailed Han sheep).The effective population size(Ne)of Altay sheep,Large-tailed Han sheep,Hulun Buir sheep,Short-tailed grassland sheep and Tibetan sheep were estimated to be 81,78,253,238 and 70 five generations ago.The highest ROH-based inbreeding estimate(FROH)was 0.0808 in Large-tailed Han sheep,whereas the lowest F_(ROH)was 0.0148 in Hulun Buir sheep.Furthermore,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent inbreeding.In total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep breeds.Three ROH islands were common to all the five sheep breeds,and were located on OAR2:12.2-12.3 Mb,OAR12:78.4-79.1 Mb and OAR13:53.0-53.6 Mb.Three breed-specific ROH islands were observed in Altay sheep(OAR15:3.4-3.8 Mb),Large-tailed Han sheep(ORA17:53.5-53.8 Mb)and Tibetan sheep(ORA5:19.8-20.2 Mb).Collectively,the ROH islands harbored 78 unique genes,including 19 genes that have been documented as having associations with tail types,adaptation,growth,body size,reproduction or immune response.Conclusion:Different ROH patterns were observed in five Chinese indig

关 键 词：Candidate genes Genomic inbreeding coefficient ROH islands Runs of homozygosity SHEEP 

分 类 号：S826[农业科学—畜牧学]