全基因组选择信号揭示绒山羊绒毛性状相关的候选基因

Genome-wide Selection Signals Reveal Candidate Genes Associated with the Cashmere Traits of Cashmere Goats

旨在对辽宁绒山羊和内蒙古绒山羊的基因组选择信号进行筛选。本研究利用Illumina 50K的山羊芯片,对内蒙古绒山羊、辽宁绒山羊和黄淮山羊进行基因型检测,质控后获得50010个共同SNPs位点。通过群体分化系数Fst和XP-EHH,以黄淮山羊为参考群体分别对内蒙古绒山羊和辽宁绒山羊进行选择信号检测,Fst和XP-EHH值的top 5%作为阈值。结果,利用Fst在绒山羊基因组中筛选到501个候选基因,利用XP-EHH在绒山羊基因组中筛选到145个候选基因。其中有12个SNPs在绒山羊基因组中受到较强选择。通过基因注释筛选到21个候选基因,包括EXOC 4、ASIC 2、PCDH 9、RHBDD 1、IRS 1和PDE 10A等。这些基因主要富集在PI3K-Akt信号通路、蛋白质消化吸收和松弛素信号通路等。研究结果发现,绒山羊在驯化过程中其基因组很多与毛囊相关的基因受到了强烈的选择。这些发现也有助于更好地了解绒山羊的选择进展,为中国绒山羊品种的种质资源保护和利用提供重要参考。

The purpose of this study was to screen the genome-wide selection signals of Liaoning cashmere goat and Inner Mongolia cashmere goat.Based on the Illumina Caprine 50K SNP chip,Liaoning cashmere goat,Inner Mongolia cashmere goat and Huanghuai goat were genotyped,and the common 50010 SNPs were obtained after quality control.Using population differentiation coefficients Fst and XP-EHH,Huanghuai goats were used as reference populations to detect selection signals for Inner Mongolia cashmere goats and Liaoning cashmere goats.The top 5%of Fst and XP-EHH values was used as the threshold.The result showed that 501 candidate genes were selected by Fst and 145 candidate genes were selected by XP-EHH in cashmere goats.Based on these SNPs,we detected 12 SNPs under strong selection by Fst and XP-EHH.After gene annotation,21 candidate genes were identified,such as EXOC 4,ASIC 2,PCDH 9,RHBDD 1,IRS 1 and PDE 10A.These genes were found to be mainly enriched in PI3K-Akt signaling pathway,protein digestion and absorption and relaxin signaling pathways.The study indicated that genes associated with cashmere traits were subjected to strong artificial selection pressure during domestication of the cashmere goats.These findings also help us better understand the selection progress of cashmere goats and provide a new theoretical basis for the protection and utilization of germplasm resources of Chinese cashmere goat breeds.