基于全基因组重测序分析大尾寒羊基因组变异特征和群体结构

Analysis on Genomic Variation and Population Structure of Large-tailed Han Sheep Based on Whole Genome Resequencing

旨在了解大尾寒羊基因组遗传变异特征和群体结构,可以为更好地保护和利用大尾寒羊提供指导。本研究对170只(66只公羊,104只母羊)大尾寒羊进行了全基因组重测序,利用GATK、Manta、Plink等软件对大尾寒羊基因组遗传变异、群体结构和连锁不平衡等进行了分析,以期了解大尾寒羊基因组变异特征和群体结构。测序共获得1599.56 G高质量数据(平均9.409 G·只^(-1))。大尾寒羊群体中共发现50276079个SNPs和7240540个InDel,它们多分布于基因间和内含子区域。群体的基因组结构性变异(SV)最多的类型为染色体间的易位(CTX),平均每只羊有415.82个CTX,主要分布在基因间区域;发生拷贝数变异(CNV)最多的区域在外显子,平均每只羊有175个。主成分分析显示,大尾寒羊个体较分散,聚集不集中。结合亲缘关系、系统发育树和群体结构,将大尾寒羊分为6个家系,各家系含量差别较大,体型有差异。群体聚类分析中发现有些个体祖先成分较为单一。群体连锁不平衡(LD)分析显示LD衰减速度快,群体遗传多样性较高。驯化中受选择的基因主要与脂质代谢和产热有关。综上,大尾寒羊群体包含6个家系,遗传多样性较丰富,保种效果良好,建议对小家系进行扩繁,大家系注意减少近交,确保家系结构平衡,同时注重大尾寒羊的开发和利用。

This study aimed to analyze the genomic variations and population structure of Large-tailed Han(LTH)sheep to provide guidance for scientific conservation and sustainable utilization.Whole-genomic sequencing data from 170 LTH sheep(66 rams,104 ewes)was used to investigate the genomic variations,population structure and linkage disequilibrium by GATK,Manta,Plink and other softwares.The 1599.56 G clean data was obtained and on average,9.409 G clean data per sheep.In the LTH sheep population,50276079 SNPs and 7240540 InDel were found,which were mostly distributed in intergenic and intronic region.The interchromosomal translocation(CTX)was the most common type of structural variation(SV)in the genome of LTH sheep,on average,415.82 CTX per sheep,and also mainly distributed in the intergenic region.The copy number variation(CNV)was mostly distributed in exons,175 CNV per sheep on average.The result of principal component analysis showed that individuals were relatively scattered and poorly clustered.According to the genetic relationship,phylogenetic tree and population structure,the 170 LTH sheep were clustered into 6 families,and there was a significant difference in family size and body size.The results of cluster analysis showed that ancestry component of some individuals was single.The linkage disequilibrium analysis showed that LTH sheep population had a relatively fast attenuation rate.The selected genes during domestication were mainly related with lipids metabolism and thermogenesis.In conclusion,LTH sheep population contains 6 families and has rich genetic diversity and remarkable conservation effect.It is suggested to expand the number of small families and to prevent inbreeding in the big families to keep a balanced population size and structure and focus on the utilization of LTH sheep.