Genetic Structure,Selection Signal Analysis and ROH Detection of Sunan Yak Population
BAO Qi, BAO Pengjia, MA Xiaoming, WU Xiaoyun, MENG Guangyao, CHU Min, CAO Hongmei, LANG Jianying, AN Yufeng, LIANG Chunnian, YAN Ping
China Animal Husbandry and Veterinary Medicine
2022, 49 (8):
【Objective】 The analysis of population genetic structure,selection signal analysis and ROH detection were performed to Sunan yak to explore the genes related to the germplasm characteristics of Sunan yak.【Method】 A total of 48 yaks were collected from Sunan yak,Bazhou yak,Sibu yak,Jiulong yak and Tianzhu White yak for genome resequencing.Genome Analysis Toolkit (GATK) mutation detection process was used to obtain high-quality single nucleotide polymorphism (SNP) for downstream analysis.Principal component analysis,ancestral component analysis and phylogenetic tree analysis were used to determine the population structure of 5 yak breeds.ROH detection and inbreeding coefficient calculation of 5 yak populations were carried out.A comprehensive haplotype score (iHS) was used to screen selected sites in shared high-frequency ROH regions.【Result】 By analyzing the SNPs identified from 5 yak breeds,a total of 15 092 883 SNPs were identified.The identified SNPs were mainly distributed in the intron regions.The results of kinship calculation showed that all individuals did not have kinship within 3 generations,which met the requirements of subsequent analysis.Principal component analysis showed that the 5 yak breeds could be significantly divided into 5 groups,and the genetic variation within the Sunan yak group was small.The population structure showed that Sunan yak contained other 4 yak ancestors,among which Tianzhu White yak accounted for the largest proportion.ROH analysis showed that a total of 8 426 ROH fragments were detected in 5 yak breeds,of which 421 were in high-frequency ROH regions.Compared with the other 4 yak breeds,Sunan yak had the largest total length and number of ROH regions and had a higher degree of linkage,and its inbreeding coefficient was much larger than that of other yak populations.465 candidate genes were annotated on the high-frequency ROH region of Sunan yak,mainly enriched in pathways related to body development,brain morphogenesis,and fat oxidation,including embryonic skeletal system morphogenesis,anterior and posterior pattern specification,thyroid development pathways and Hippo path.Among them,genes related to embryonic development and tissue differentiation (homeobox A3 (HOXA3),HOXA5,HOXD3),meat quality (arachidonic acid 12B (ALOX12B),ALOX15B,ALOXE3),and midbrain development (fibroblast growth factor 8 (FGF8)) were identified.In addition,3 shared genes (heterogeneous nuclear ribonucleoprotein K (HNRNPK),kinesin family member 27(KIF27),G kinase anchor protein 1 (GKAP1)) were identified in a high-frequency ROH region on chromosome 7 (Chr7:12 661 870-13 045 935),which were related to the plateau adaptation shared by yak.The iHS analysis of loci within the shared high-frequency ROH region identified selected genes that were mainly associated with disease resistance,endoplasmic reticulum-secreted protein processing,and cell cycle regulation,including N-alpha-acetyltransferase 25 (NAA25),endoplasmic reticulum protein 29 (ERP29),transmembrane protein16 (TMEM116),TRAF-type zinc finger domain containing 1 (TRAFD1) and HECT domain E3 ubiquitin protein ligase 4 (HECTD4) genes.【Conclusion】 This study systematically investigated the genetic diversity and identified candidate genes related to traits of Sunan yak at the genome-wide level,providing an important theoretical basis for the development and utilization of Sunan yak germplasm resources.
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