基因组分析对猪乳头数相关数量性状基因座鉴定  

Identifying Quantitative Trait Loci Associated with Teat Number of Pig by Genomic Analysis

作　　者：尹彦镇 侯黎明 刘航[1,2] 陶伟 石传宗 刘锴月 张萍 牛培培[2] 李强 李平华 黄瑞华 YIN YanZhen;HOU LiMing;LIU Hang;TAO Wei;SHI ChuanZong;LIU KaiYue;ZHANG Ping;NIU PeiPei;LI Qiang;LI PingHua;HUANG RuiHua(Institute of Swine Science,Nanjing Agricultural University,Nanjing 210095;Huaian Academy,Nanjing Agricultural University,Huai’an 223001,Jiangsu;Huaiyin Xinhuai Pig Breeding Farm of Huai’an City,Huai’an 223322,Jiangsu)

机构地区：[1]南京农业大学养猪研究所,南京210095 [2]南京农业大学淮安研究院,江苏淮安223001 [3]淮安市淮阴新淮种猪场,江苏淮安223322

出　　处：《中国农业科学》2023年第10期1994-2006,共13页Scientia Agricultura Sinica

基　　金：国家自然科学基金-河南联合基金项目(U1904115);江苏现代农业(生猪)产业技术体系建设项目(JATS[2020]399);农业农村部农业品种改良提升专项(19210387);江苏省农业新品种创制重点项目(PZCZ201732)。

摘　　要：【目的】分析乳头数的变异,挖掘与乳头数相关的数量性状基因座(quantitative trait locus,QTL)和候选基因,为猪乳头数的选育研究提供重要分子标记。【方法】准确测定了709头苏淮猪(335头育肥猪和374头种猪)的左、右和总乳头数。对苏淮育肥猪进行80K芯片分型,并使用芯片数据计算左、右、总乳头数的遗传力和基因组估计育种值(genomic estimated breeding value,GEBV)。基于乳头数GEBV和表型排名,选择前10%的个体以及后10%的个体进行群体分化指数分析(fixation Index,FST)检测高度分化的位点。接着,通过全基因组关联分析(genome wide association analysis,GWAS)鉴定与乳头数关联的位点,选择高度分化且与乳头数显著关联的位点作为候选位点,选择位于候选位点附近且功能注释后与乳头数相关的基因作为候选基因。最后,选择每个染色体上最显著的候选位点对709头苏淮猪进行乳头数关联分析,以验证上述位点的显著性。【结果】苏淮育肥猪左、右、总乳头数的变异系数分别为10.20%、9.26%、8.50%,遗传力分别为0.212、0.257、0.312。基于FST和GWAS分析,总共在7、13、16、18号染色体(Sus Scrofa Chromosome,SSC)上鉴定到20个乳头数的候选位点,这些候选位点可解释5.49%—8.03%的表型方差。其中,SSC7上与总乳头数关联的位点rs80894106与文献中报道的影响大白和杜洛克猪总乳头数的候选位点一致,但左乳头的候选位点rs81444134(26.51 Mb,SSC13)和rs81233299(8.13 Mb,SSC18)均为新发现的与乳头数相关的位点。左、右、总乳头的候选位点主要集中在SSC16上的6.36—10.66 Mb区间;连锁不平衡(linkage disequilibrium,LD)分析发现,区间内7.47—8.27 Mb的候选位点拟合成了一个795 kb的单倍型块,且该单倍型块是新发现的影响乳头数的候选区域;单倍型块内的rs337606862(7.47 Mb)与右乳头和总乳头最显著关联,单倍型块内的3个位点均位于cadherin 18(CDH18)基�【Objective】The purposes of this study were to analyze the variation of teat number,to explore the quantitative trait locus(QTL)and candidate genes related to teat number,and to provide important molecular markers for the breeding of pig teat number.【Method】This study accurately measured left,right,total teat number of 709 Suhuai pigs(335 fattening pigs and 374 breeding pigs).Fattening pigs were selected for 80K chip genotyping and the heritability and genomic estimated breeding value(GEBV)of left,right and total teat number were calculated by chip data.Based on the rank of GEBV and phenotype of teat number,the top 10%individuals and the bottom 10%individuals were selected for Fixation Index(FST)analysis to detect highly differentiated loci.Then,the loci associated with teat number were identified by genome wide association analysis(GWAS)and loci which were highly differentiated and significantly associated with teat number were selected as candidate loci.Genes located near candidate loci and related to teat number after functional annotation were selected as candidate genes.Finally,the association analyses between the most significant candidate loci on each chromosome and teat number of 709 Suhuai pigs were performed to verify the significance of the above loci.【Result】The variation coefficients of left,right and total teat number of Suhuai fattening pigs were 10.20%,9.26%and 8.50%,respectively,and the heritability were 0.212,0.257 and 0.312,respectively.Based on FST and GWAS analyses,a total of 20 candidate loci on Sus scorfa chromosomes(SSC)7,13,16 and 18 for teat number were identified and these candidate loci could explain 5.49%-8.03%of the phenotypic variance.Among them,locus rs80894106 on SSC7 associated with total teat number was consistent with the reported candidate locus of total teat number based on Large white and Duroc pig populations,but candidate loci rs81444134(26.51 Mb,SSC13)and rs81233299(8.13 Mb,SSC18)of left teat number were newly discovered loci related to teat number.Interestingl

关 键 词：FST GWAS 数量性状基因座(quantitative trait locus QTL) 苏淮猪 乳头数 候选基因 

分 类 号：S828.2[农业科学—畜牧学]