作物学报2026，Vol.52Issue(4)：993-1005,13.DOI:10.3724/SP.J.1006.2026.53084
适于玉米品种鉴定的一套三等位变异SNP新型标记组合
A novel set of tri-allelic variant SNP loci suitable for maize variety identification
摘要
Abstract
The rapid development of high-throughput sequencing,bioinformatics,and genotyping technologies has opened new avenues for the precise identification of crop varieties.In this study,based on 780,000 initially mined multi-allelic variant SNPs from the maize whole genome,a novel set of 40 tri-allelic SNP markers was evaluated and identified using bioinformatics ap-proaches,statistical analysis,targeted sequencing validation,and optimal genetic algorithms.These 40 SNPs are evenly distrib-uted across the 10 maize chromosome pairs,with four markers per chromosome.A comprehensive evaluation and comparison of the 40 SNPs were conducted using genotype data from 200 hybrids and 270 inbred lines.The results showed that:(1)For both hybrids and inbred lines,the PIC values of all loci exceeded the maximum value of 0.375 typical for bi-allelic SNP loci,with average values of 0.470 and 0.480,and average discrimination power(DP)values of 0.68 and 0.57,respectively.(2)Pairwise comparisons using the 40 tri-allelic and 96 bi-allelic SNP markers revealed that the percentage of differential loci among hybrids mainly ranged from 50%to 85%and 50%to 70%,respectively;for inbred lines,the ranges were 35%to 75%and 35%to 60%,respectively.The average percentage of differential loci among varieties increased by 10%for tri-allelic SNPs compared to bi-allelic SNPs.(3)For both hybrids and inbred lines,the average frequencies of the first,second,and third alleles at the 40 tri-allelic loci were 0.58 and 0.57,0.31,and 0.11 and 0.12,respectively.(4)Clustering analysis showed that the 40 loci effectively classified the 270 inbred lines into 10 heterotic groups,consistent with classifications based on high-density SNP chip data.In summary,this study reports a high-quality,highly discriminative core set of tri-allelic SNP markers,providing a novel marker type for maize variety identification.With their enhanced ability to resolve genetic variation,these markers are expected to com-plement existing marker systems and contribute to the advancement of molecular identification technologies in crop breeding.关键词
玉米/品种鉴定/SNP位点/三等位变异/核心位点组合Key words
maize/variety identification/SNP loci/tri-allelic/core loci set引用本文复制引用
田红丽,杨扬,范亚明,易红梅,郭丹丹,王凤格,赵久然..适于玉米品种鉴定的一套三等位变异SNP新型标记组合[J].作物学报,2026,52(4):993-1005,13.基金项目
本研究由国家科技重大专项(2022ZD04019)和北京市农林科学院科技创新能力建设专项(KJCX20230303)资助.This study was supported by the National Scientific and Technological Innovation-Major Projects(2022ZD04019)and the Science and Technology Innovation Capacity Building Project of BAAFS(KJCX20230303). （2022ZD04019）
