威宁牛和关岭牛Y染色体基因组遗传多样性研究

Study on genetic diversity of the Y-chromosome genome in Weining cattle and Guanling cattle

为了从全基因组水平上探究威宁牛与关岭牛Y染色体基因组遗传多样性及其父系起源,试验利用生物信息学方法对10头关岭牛公牛与20头威宁牛公牛进行全基因组重测序,并对其Y染色体雄性特异区(MSY区)进行扫描与分析,对获得的Y染色体基因组数据进行单核苷酸多态性(SNPs)位点分析,计算单倍型多样度和核苷酸多样度,利用MEGA 11-64软件中的NJ法构建Y染色体基因组系统发育树,并用Network软件绘制单倍型网络图。结果表明:共获得2 553个Y-SNPs位点。威宁牛和关岭牛的Y染色体基因组单倍型多样度分别为0.947±0.034和0.978±0.054,核苷酸多样度分别为0.322±0.045和0.020±0.004。10头关岭牛共定义7种单倍型,均属Y3单倍型组,具有Y3a和Y3b 2种亚单倍型组,其中Y3a为优势亚单倍型组,占比为90%,Y3b占比为10%。20头威宁牛共定义12种单倍型,属于Y1、Y2和Y3单倍型组,其中Y1占比为10%,Y2a占比为25%,Y3a(优势亚单倍型组)占比为45%,Y3b占比为20%。10头关岭牛与20头威宁牛均主要为瘤牛血统,且优势亚单倍型组一致,但威宁牛父系起源较为复杂。说明两个黄牛品种威宁牛与关岭牛均具有较丰富的父系遗传多样性,父系遗传结构有明显差异。

In order to explore the genetic diversity and paternal origin of the Y chromosome genomes of Weining cattle and Guanling cattle from the whole genome level, the whole genome resequencing of 10 Guanling bulls and 20 Weining bulls was carried out by bioinformatics method,and the MSY region of the Y chromosome was scanned and analyzed. The obtained Y chromosome genomic data were analyzed by single nucleotide polymorphism( SNP) locus, and haplotype diversity and nucleotide diversity were calculated. The phylogenetic tree of Y chromosome was constructed by NJ method in MEG A11-64, and the haplotype Network map was drawn by network software. The results showed that a total of 2 553 Y-SNPs were obtained. The Y chromosome haplotype diversity of Weining cattle and Guanling cattle was 0. 947±0. 034 and 0. 978 ± 0. 054, respectively, and the nucleotide diversity was 0. 322 ± 0. 045 and 0. 020 ± 0. 004, respectively. A total of 7haplotypes were defined in 10 Guanling cattle, all belonging to the Y3 haplotype group, with Y3a and Y3b subhaplotype groups, of which Y3a was the dominant subhaplotype group, accounting for 90% and Y3b accounting for 10%. A total of 12 haplotypes were defined in 20 Weining cattle, belonging to Y1, Y2 and Y3 haplotype groups, of which Y1 accounted for 10%, Y2a accounted for 25%, Y3a was the dominant subhaplotype group, accounting for 45%, and Y3b accounted for 20%. Although the 10 Guanling cattle and the 20 Weining cattle were mainly Bos indicus bloodlines, and the dominant subhaplotype group was the same, the paternal origin of Weining cattle was more complicated. The results indicated that Weining cattle and Guanling cattle both had rich paternal genetic diversity and obvious differences in the paternal genetic structure.