基于SNP芯片的贵州香禾糯遗传多样性分析及核心种质构建

Genetic Diversity Analysis and Core Germplasm Construction of Guizhou Kam Sweet Rice Based on SNP Chip

以317份贵州香禾糯种质资源为试验材料,10份籼稻材料为对照,采用1 K mGPS SNP芯片对供试材料的遗传多样性和遗传结构进行分析,在此基础上构建贵州香禾糯核心种质并进行评价。结果表明,1 K mGPS SNP芯片在317份香禾糯材料中共获得731个良好多态性SNP位点,多态性标记比例为17.89%,最小等位基因频率为0.0505~0.5000,观测杂合度为0~0.6940,期望杂合度为0.0959~0.5000,多态性信息含量为0.0913~0.5736。基于IBS遗传距离的NJ聚类分析将327份水稻材料分为籼、粳两个亚群,其中317份贵州香禾糯划分为粳稻亚群。利用Core Hunter 3对香禾糯原种质设置5%、10%、15%、20%、25%、30%等6种抽样比例,遗传多样性参数的t检验表明,15%的抽样比例即可保持遗传多样性参数的最大化,同时剔除了许多冗余材料,最终确定47份香禾糯资源为构建的核心种质。

The genetic diversity and genetic structure of 317 Guizhou Kam Sweet Rice germplasm resources and 10 indica rice materials as the control were analyzed by 1 K mGPS SNP chip, and the core germplasm of Guizhou Kam Sweet Rice was constructed and evaluated. The results showed that the 1 K mGPS SNP chip obtained 731 polymorphic SNP loci in 317 samples, the proportion of polymorphic markers was 17.89%, the frequency of minimum alleles was from 0.050 5 to 0.500 0, and the observed heterozygosity was from 0 to 0.694 0. The expected heterozygosity ranged from 0.095 9 to 0.500 0, and the polymorphism information content ranged from 0.091 3 to 0.573 6. NJ cluster analysis based on IBS genetic distance divided 327 rice materials into indica and japonica subgroups, among which 317 Guizhou Kam Sweet Rice were divided into japonica subgroups. Core Hunter 3 was used to set 6 sampling ratios of 5%, 10%, 15%, 20%, 25% and 30% for the original germplasm of Kam Sweet Rice. The t-test of genetic diversity parameters showed that 15% sampling ratio could maintain the maximum genetic diversity parameters, and at the same time, many redundant materials were eliminated. Finally, 47 Kam Sweet Rice resources were identified as the core germplasm of the construction.