山东小毛驴全基因组选择信号检测

Detection of Selection Signatures of Population-Specific Whole-Genomic Regions Selected in Shandong Little Donkey

为研究不同驴品种间的群体分化程度,检测全基因组选择信号,以挖掘山东小毛驴(SDL)重要性状相关的候选基因,基于山东小毛驴和德州驴的三粉类群(DZS)、德州驴的乌头类群(DZW)、广灵驴(GL)以及华北驴(NC)等5个驴群体共计60个个体全基因组重测序数据,利用群体遗传分化系数(Fst)和核苷酸多样性比值(πratio)方法检测山东小毛驴与其他驴群体间的选择信号,共找到39个落入选择信号区域的候选基因。与DZS群体相比,检测出强选择信号候选基因5个,分别是Fsip1、AHNAK2、CTAGE2、CYP3A12、LOC106830441;与DZW群体相比,检测出强选择信号候选基因5个,分别是NKG2DL1、KLK1E2、CTAGE2、FAM170A、LOC106823932;与GL群体相比,检测出强选择信号候选基因6个,分别是NKG2DL1、AHNAK2、CTAGE2、FAM170A、LOC106823932、LOC106848008;与NC群体相比,检测出强选择信号候选基因2个,分别是CTAGE2、FAM170A。这些候选基因主要在免疫、生殖、细胞作用等通路中发挥重要的作用,说明山东小毛驴在免疫力和生殖能力等性状上经历了人工选择。

This experiment was conducted to study genetic differentiation among different donkey populations by genome-wide detection of selection signatures and search the candidate genes related to important traits of Shandong little donkey(SDL).This study was based on the whole genome re-sequencing data of 60 donkeys from 5 donkey populations including SDL,Dezhou Sanfen donkey(DZS),Dezhou Wutou donkey(DZW),Guangling donkey(GL)and North China donkey(NC).The selection signals between SDL and other donkey populations were detected by population genetic differentiation index(Fst)and ratio of nucleotide diversity(πratio)method.As a result,39 candidate genes were detected in the positive selection signal regions.Compared with DZS,five candidate genes with strong selection signals were detected,including Fsip1,AHNAK2,CTAGE2,CYP3A12 and LOC106830441.Compared with DZW,five candidate genes with strong selection signals were detected,including NKG2DL1,KLK1E2,CTAGE2,FAM170A and LOC106823932.Compared with GL,six candidate genes within strong selection signals were detected,including NKG2DL1,AHNAK2,CTAGE2,FAM170A,LOC106823932 and LOC106848008.Compared with NC,only two candidate genes with strong selection signals were detected,including CTAGE2 and FAM170A.These candidate genes mainly played important roles in the immune,reproductive,cellular and other pathways,revealing that SDL experienced artificial selection in the traits of immunity and reproductive traits.