油橄榄(Olea europaea L.)核心SNP位点筛选与评价  

Identification and Evaluation of SNP Core Loci for Olive Germplasm(Olea europaea L.)

作　　者：朱申龙[1] 牛二利 王伟[2] 施爱农[3] Zhu Shenlong;Niu Erli;Wang Wei;Shi Ainong(Institute of Crops and Nuclear Technology Utilization,Zhejiang Academy of Agricultural Sciences,Hangzhou,310021;Institute of Quality Standards for Agricultural Products,Zhejiang Academy of Agricultural Sciences,Hangzhou,310021;Department of Horticulture,University of Arkansas,Fayetteville,AR 72701,USA)

机构地区：[1]浙江省农业科学院作物与核技术利用研究所,杭州310021 [2]浙江省农业科学院农产品质量标准研究所,杭州310021 [3]美国阿肯色大学园艺系,美国费耶特维尔AR 72701

出　　处：《分子植物育种》2020年第5期1548-1557,共10页Molecular Plant Breeding

基　　金：国家国际科技合作专项(2013DFG32780);浙江省农业科学院橄榄油品质营养国际联合实验室共同资助。

摘　　要：本研究基于前期对57份油橄榄种质资源的全基因组GBS-SNP分型结果开展核心SNP位点的筛选。统计分析73482个GPS-SNP位点发现,有68030个(92.58%)SNP位点的检出率达到100%,33979个(46.2%)位点的最小等位基因频率≥0.2,29647个(40.35%)位点的杂合率为0,其中同时符合上述3个条件(检出率=100%,最小等位基因频率≥0.2,杂合率=0)的位点有14125个(19.2%),其位置覆盖全基因组,既分布于基因区也位于基因间区,与73482个SNP位点的分布高度一致(R=0.997),多态信息量平均为0.43(0.33~0.67)。进一步以14125个SNP位点信息为依据,计算57个油橄榄品种间的遗传距离,并与基于全部位点(73482个SNPs)信息获得的对应品种间的遗传距离作比较,结果显示两者呈极显著的相关性(R=0.9),表明这些SNP位点具有多态性好、代表性广、可靠性高的特点,可作为油橄榄的核心SNP位点,适用于油橄榄品种鉴定、种质评价、基因定位和分子辅助育种。本研究对核心SNP位点在油橄榄品种鉴定中的具体应用进行了探讨,并指出至少需要11个核心SNP位点组合才能实现对57个油橄榄品种的完全区分。Based on the genome-wide GBS-SNP genotyping of 57 olive germplasms,we conducted the identification of core SNP loci for olive tree.Statistical analysis of 73482 GPS-SNP loci revealed that 68030(92.58%)SNP loci were with the call rate of 100%;33979(46.2%)loci had their minor allele frequencies(MAF)greater than or equal to 0.2;and 29647(40.35%)loci were homozygosity with 0%heterozygous rate.There were a total of 14125(19.2%)SNP loci satisfying the above three conditions(call rate=100%,MAF≥0.2,and heterozygous rate=0).The subset of 14125 SNPs had the similar distribution as the set of all 73482 SNP loci(R=0.997)locating at the gene and intergenic regions of whole olive genome and its polymorphic information content was 0.43(0.33-0.67)on average.Based on the information of the subset of 14125 SNP loci,the genetic distances among the 57 olive genotypes was calculated and the results showed that there was a significant correlation(R=0.9)compared with the genetic distances between corresponding genotypes obtained based on all locus(73482 SNPs)in-formation.Therefore,the subset of 14125 SNP loci with the characteristics of good polymorphisms,wide repre sentativeness and high reliability,can be used as the core SNP set of oil-olive,and is suitable for identification of olive varieties,germplasm evaluation,genetic mapping and marker-assisted breeding.This study specific applica tion of the core SNP set in the identification of olive varieties was discussed in the paper and it was also pointed out that a set of 11 SNP loci can distinguish the 57 olive genotypes.

关 键 词：油橄榄(Olea europaea) GBS-SNP 核心位点 品种鉴定 

分 类 号：S565.7[农业科学—作物学]