适于玉米品种鉴定的一套三等位变异SNP新型标记组合OA
A novel set of tri-allelic variant SNP loci suitable for maize variety identification
高通量测序、生物信息学以及基因型分型技术的快速发展,为农作物品种的精准鉴定开辟了新的方法路径.本文基于全基因组水平挖掘的 78 万个初始多等位变异 SNP 位点,利用生物信息、统计分析、靶向测序验证以及最优遗传算法等方法评估确定了一套三等位变异SNP新型标记组合.该组合包含的 40 个位点均匀分布于玉米的 10 对染色体上,每对染色体为 4 个位点.利用 200 个杂交种和 270 个自交系的基因型数据对 40 个 SNP位点进行多角度评估,结果显示:(1)对于杂交种和自交系,所有位点的PIC值均高于二等位变异SNP位点的最高值0.375,平均值为0.470 和 0.480,DP平均值为 0.68 和 0.57.(2)利用 40 个三等位和 96 个二等位变异SNP标记的杂交种数据进行品种的两两成对比较,显示差异位点百分比分别集中在50%～85%和50%～70%;自交系数据分析显示,品种间差异分别集中在 35%～75%和 35%～60%;三等位与二等位变异SNP标记相比,品种间差异位点百分比平均值提高了 10%.(3)对于杂交种和自交系,40个SNP位点的第一等位变异频率平均值分别为0.58和0.57,第二等位变异平均值均为0.31,第三等位变异平均值分别为 0.11 和 0.12.(4)聚类结果显示,40 个位点将 270 个自交系精准划分为 10 个杂种优势类群,与高密度芯片划分结果一致.综上所述,本研究报道了一套高质量、高鉴别力的三等位变异核心SNP标记位点组合,为玉米品种鉴定提供了一种新型标记类型;凭借其更高的变异解析能力,有望与现有标记类型形成互补,推动农作物分子鉴定技术的发展.
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.
田红丽;杨扬;范亚明;易红梅;郭丹丹;王凤格;赵久然
北京市农林科学院玉米研究所/农业农村部农作物DNA指纹创新利用重点实验室(部省共建)/玉米DNA指纹及分子育种北京市重点实验室,北京 100097北京市农林科学院玉米研究所/农业农村部农作物DNA指纹创新利用重点实验室(部省共建)/玉米DNA指纹及分子育种北京市重点实验室,北京 100097北京市农林科学院玉米研究所/农业农村部农作物DNA指纹创新利用重点实验室(部省共建)/玉米DNA指纹及分子育种北京市重点实验室,北京 100097北京市农林科学院玉米研究所/农业农村部农作物DNA指纹创新利用重点实验室(部省共建)/玉米DNA指纹及分子育种北京市重点实验室,北京 100097北京市农林科学院玉米研究所/农业农村部农作物DNA指纹创新利用重点实验室(部省共建)/玉米DNA指纹及分子育种北京市重点实验室,北京 100097北京市农林科学院玉米研究所/农业农村部农作物DNA指纹创新利用重点实验室(部省共建)/玉米DNA指纹及分子育种北京市重点实验室,北京 100097北京市农林科学院玉米研究所/农业农村部农作物DNA指纹创新利用重点实验室(部省共建)/玉米DNA指纹及分子育种北京市重点实验室,北京 100097
玉米品种鉴定SNP位点三等位变异核心位点组合
maizevariety identificationSNP locitri-alleliccore loci set
《作物学报》 2026 (4)
993-1005,13
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).
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