作物学报2024，Vol.50Issue(5)：1115-1123,9.DOI:10.3724/SP.J.1006.2024.33052
用于玉米品种真实性鉴定的最优核心SNP位点集的研发
Development of an optimal core SNP loci set for maize variety genuineness identification
摘要
Abstract
Variety genuineness is an important indicator for seed quality monitoring.In order to establish accurate,reliable,fast,simple,high-throughput,and low-cost maize variety genuineness identification technology,we evaluated and determined a set of high discriminative power core SNP loci set including 96 SNPs based on SNP fingerprint data of 5816 maize hybrids and 3274 inbred lines using the genetic algorithm and variety recognition rate.All 96 SNPs were located in the intra-gene region,generally distributed evenly on 10 pairs of chromosomes.The evaluation results using the above hybrid and inbred line data showed that 96 SNPs set had high polymorphism and variety discrimination power.The average values of PIC,MAF,and DP were 0.36,0.40,0.60,and 0.36,0.39,0.48 for hybrids and inbred lines,respectively.The variety discrimination power for hybrids and inbred lines reached 99.14%and 99.24%,respectively.Pairwise comparison between varieties showed that 99.99%of the comparisons had at least three differential loci.About 96.74%of hybrids and 95.67%of inbred lines mostly had the 30-65 and 30-60 differential loci between varieties,respectively.Compared with the 40 SSRs genotype dataset using 221 hybrids,the 96-SNPs set had high con-sistency in the identification results of the two marker sets.In summary,the optimal core SNPs set reported in this study had the advantage of the minimum number of loci,the highest discrimination power,the strongest differentiation platforms,and the auto-matic genotyping.It is expected that the extensive application of this core SNP loci set will be widely used in maize variety genu-ineness monitor and seed quality control for maintaining seed market order,so as to defend the breeders'rights and protecting interests of farmers.关键词
玉米品种/真实性鉴定/SNP位点集/高鉴别力Key words
maize variety/genuineness identification/SNP loci set/high discrimination power引用本文复制引用
田红丽,王凤格,赵久然,杨扬,范亚明,易红梅,王蕊,金石桥,晋芳,张云龙,刘亚维..用于玉米品种真实性鉴定的最优核心SNP位点集的研发[J].作物学报,2024,50(5):1115-1123,9.基金项目
本研究由国家科技创新重大项目(2022ZD04019)和北京市农林科学院财政项目(KJCX20230301,CZZJ202206)资助.This study was supported by the National Scientific and Technological Innovation-Major Projects(2022ZD04019)and the Financial Project of Beijing Academy of Agriculture and Forestry Sciences(KJCX20230301,CZZJ202206). （2022ZD04019）
