Abstract: The aim of this study is to identify candidate genomic regions and genes associated with cattle reproductive traits. Blood samples were collected from 97 Jiaxian Red cows and 32 Chinese Holstein cows.Genomic DNA was isolated from each blood sample.SLAF-seq was used to obtain genome-wide SNP markers and genotypes of each SNP for every individual. Fst value and π ratio value were calculated for each SNP,and used to identify diverged genomic regions across two breeds using selective sweep method.Then the identified regions were compared with the cattle reproductive QTLs in the animal QTL database.Overlapping regions were considered as candidate regions for reproductive traits.Expression status of genes within candidate regions in tissues related to cattle reproduction was checked in the animal omics database.The highly expressed genes(FPKM>10) were prioritized as candidate genes. Based on the Fst and π ratio values which were greater than 99th percentile of genome-wide values,42 highly diverged regions were identified.Eleven regions were overlapped with QTLs for reproductive traits.In these 11 regions,9 genes were expressed in the ovary,ampula and corpus luteum(FPKM>1).CFDP1,CFDP2 and FAM204A genes were highly expressed in the three tissues(FPKM>10).Thus,CFDP1,CFDP2 and FAM204A genes are prioritized as potential candidate genes for cattle reproductive traits.

Key words: Jiaxian Red cattle, Chinese Holstein cattle, Reproductive trait, Selective sweep, Fst value

摘要： 为探究与牛繁殖性状相关的候选基因组区域和候选基因，采集97头郏县红牛和32头中国荷斯坦奶牛母牛血样并提取基因组DNA，利用简化基因组测序(SLAF-seq)技术获得了其全基因组SNP标记及个体基因型。通过计算各SNP位点的遗传分化系数（Fst）和核苷酸多态性（π ratio），利用选择性清除方法筛选2个品种间差异的基因组区域，并与动物QTL数据库中牛繁殖性状相关QTLs进行比对，将重合区域作为候选区域。在Animal Omics Database数据库中查看候选区域内基因在母牛繁殖相关组织中的表达情况，将表达量高（FPKM>10）的基因优先作为候选基因。结果显示，根据Fst值和π ratio值的99%分位数（Fst>0.390,π ratio>1.49）筛选得到了42个品种间高度差异的基因组区域，其中11个基因组区域与繁殖性状QTL重合。其中，9个基因在卵巢、输卵管壶腹部或黄体中表达（FPKM>1）。CFDP1、CFDP2和FAM204A基因在各组织中均高表达（FPKM>10）。以上结果提示，CFDP1、CFDP2和FAM204A基因可优先作为牛繁殖性状相关候选基因。

关键词: 郏县红牛, 中国荷斯坦奶牛, 繁殖性状, 选择性清除, 遗传分化系数