利用基因分型测序(GBS)对 60只湘东黑山羊(9只公羊、51只母羊)进行基因组测序,获得湘东黑山羊染色体上的 SNP 数据和连续纯合子片段(ROH)数据.通过 SNP 数据进行基于 G 矩阵的基因组亲缘关系分析和 NJ聚类分析,构建湘东黑山羊的群体家系结构,并通过ROH数据得到群体平均近交系数.结果表明,60只湘东黑山羊的平均测序深度为 9.15X,与参考基因组比对率平均为 99.59%;在SNP检测过程中,3只母羊不符合基因型数据质控标准,将其过滤后获得其他 57只黑山羊 29条染色体上 153 046个SNPs位点和 1 937 个ROH片段;构建的湘东黑山羊8个家系,其中 9只公羊和6只母羊被分为7个家系,另42只母羊被单独分类;基于ROH片段分析的湘东黑山羊群体中每个个体的近交系数均值为0.047,说明湘东黑山羊公羊在繁育过程中有较大的利用空间.
Genetic relationship and inbreeding coefficient among Xiangdong black goats based on GBS sequencing
In this study,60 Xiangdong black goats,including 9 rams and 51 ewes,were sequenced through GBS sequencing,for SNPs and ROH on the chromosomes of Xiangdong black goats.Genetic relationship analysis based on G matrix and NJ cluster analysis were carried out using SNP data to construct pedigree of population structure and inbreeding coefficient was obtained based on ROH data.These results showed that average sequencing depth of 60 Xiangdong black goats was 9.15X,with a mapping rate of 99.59%compared with reference genomes.In the process of SNPs detection,the data of 3 ewes failed to meet the genotype quality control standards thus were excluded to obtain the 153046 SNPs and 1937 ROH fragments on 29 autosomes from 57 Xiangdong black goats,based on which pedigree including 8 families was constructed in which 9 rams and 6 ewes were divided into 7 families and other 42 ewes were classified separately.Based on ROH,the average inbreeding coefficient of individual in the population of Xiangdong black goat was 0.047,indicating that the rams have good potential for breeding.
Xiangdong black goatgenotyping by sequencingsingle nucleotide polymorphism(SNP)runs of homozygosity(ROH)inbreeding coefficientgenetic relationship
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