玉米低密度育种芯片开发及在种质资源评价中的应用
Journal of Plant Genetic Resources（2022）
Abstract
SNP基因分型芯片是分子育种的重要工具,高密度SNP芯片往往存在标记冗余、价格高、目标性不强等问题,是分子育种走向常规化、规模化的主要限制因素之一.本研究介绍了一款新开发的低密度育种芯片,并就芯片在种质资源评价中的价值进行了分析.首先,对37份玉米自交系进行10×重测序,获得了18.2 Mb的SNP标记,从中挑选2080个SNPs;再从已开发55 K芯片中挑选3390个缺失率低、多态性高、标记类型为高多态分辨率的标记;最后从HapMap3中挑选586个标记,设计的育种芯片共包含6056个SNPs,采用靶向测序基因型检测(GBTS,genotyping by target sequencing)技术对标记进行检测.通过自然群体、双亲群体和多亲本重组自交系(MAGIC,multiparent advanced generation inter-cross)群体验证表明,育种芯片检测到的原始设计位点数为4773～5967个,自然群体中最小等位基因频率(MAF,minor allele frequency) ＞0.4和多态性信息含量(PIC,polymorphism information content) ＞0.4的标记比例分别为57.6％和88.6％,MAGIC群体平均捕获率为70.6％.用该芯片对226份玉米种质资源进行评价,主成分分析可以将其划分为温带和热带两大类群,UPGMA聚类分析进一步将其划分为6个已知类群,分别是瑞德、兰卡斯特、PB、旅大红骨、四平头和热带类群,利用Structure软件进行群体结构分析,没有出现最佳K值,但热带材料都独立成群;类群内和类群间的遗传距离平均值分别为0.394和0.471,其中PB群内的遗传距离最小(0.316),热带类群内的遗传距离最大(0.424);类群间,瑞德与热带之间的遗传距离最大(0.493);类群间的遗传分化系数(FST)表明,PB类群与其他类群间的FST均较大.
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