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

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Journal of Animal Science and Biotechnology 2022年第1期13卷 52-65页

作者： Jiaxin Liu Liangyu Shi Yang Li Liang Chen Dorian Garrick Lixian Wang Fuping Zhao Key Laboratory of Animal Genetics Breeding and Reproduction(Poultry)of Ministry of AgricultureInstitute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China The Affiliated High School of Peking University Beijing 100192China A.L.Rae Centre of Genetics and Breeding Massey UniversityHamilton 3240New Zealand

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 *** inbreeding can be quantified based on *** regions enriched with ROH may be indicative of selection sweeps and are known as ROH *** 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 ***:A total of 18,288 ROH were *** 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 *** 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 ***,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent *** total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep *** 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 *** 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 ***:Different

关键词： Candidate genes genomic inbreeding coefficient ROH islands Runs of homozygosity Sheep

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