基于GBS-seq的青藏扁蓿豆SNP标记开发

Development of SNP Markers in Medicago archiducis-nicolai Based on GBS-seq

开发青藏扁蓿豆(Medicago archiducis-nicolai)单核苷酸多态性标记(single nucleotide polymorphism,SNP),并开展遗传多样性初步分析,为青藏扁蓿豆种质资源的评价与利用提供理论支持。以5个青藏扁蓿豆群体共80份材料进行GBS(genotyping-by-sequencing)测序,采用GATK软件开发SNP标记,并以此进行遗传结构和遗传多样性的初步分析。测序产生的序列数据量为60.79 Gb,过滤后共获得12796个SNP位点,且SNP突变类型存在明显的转换型偏差现象。不同地理来源青藏扁蓿豆群体观测杂合度(H_(O))为0.18768-0.30436,期望杂合度(H_(E))为0.20197-0.36434,遗传多样性指数(Pi)为0.17832-0.24134;祁连(QLCD)群体具有相对最高的遗传多样性水平。遗传结构分析表明5个群体分为2组,且群体遗传距离与地理距离之间存在极显著的正相关性。SNP标记适用于青藏扁蓿豆遗传多样性分析。

In order to provide theoretical support for evaluating and exploiting the genetic resources in Medicago archiducis-nicolai,the SNPs were developed and the preliminary analysis of genetic diversity was carried out.A total of 80 individuals of M.archiducis-nicolai from 5 populations were selected to conduct GBS-seq and SNP markers were developed by using GATK software,and then preliminary analysis of genetic structure and genetic diversity was conducted.A total of 60.79 Gb sequence data was obtained,and 12796 SNP sites were retained after screening,and SNP mutation types demonstrated obvious transition bias.The observed heterozygosity(H_(o))for different geographic sources of M.archiducis-nicolai population was 0.18768-0.30436.The expected heterozygosity(H_(e))was 0.20197-0.36434.The nucleotide diversity index(Pi)was 0.17832-0.24134,the population in Qilian of Qinhai province presented a relatively highest genetic diversity.The results of the genetic structure indicated that 5 populations could be divided into 2 groups,and there was highly significant positive correlation between geographical distance and genetic distance among populations of M.archiducis-nicolai.The SNP markers are suitable for analyzing the genetic diversity of M.archiducis-nicolai.