基于单拷贝SNP标记的棉花杂交种纯度高通量检测技术

利用有代表性的材料进行SNP位点的全基因组扫描分析与综合评估,基于KASP技术开发1套适用于我国棉花杂交种纯度高通量检测的核心SNP组合。从63K的棉花全基因组芯片中筛选获得具有单拷贝特性的SNP标记分别为5474个(中棉所TM-1基因组版本)和1850个(南京农大TM-1基因组版本)。根据芯片扫描分析结果,权衡考虑位点多态性、分型效果、纯合率与杂合率等因素,最终从每条染色体上优选1个杂交种杂合率高且分型效果理想的核心SNP位点,合计26个。采用KrakenTM软件将SNP位点转化成KASP标记,利用SNPline平台进行SNP分型检测,实现了对大量样品的高通量基因分型,尤其适用于品种纯度快速检测,为SNP标记技术在棉花品种鉴定及指纹数据库构建等方面的应用奠定基础。

High-throughput Genotyping Assay Technology for Cotton Hybrid Purity Based on Single-copy SNP Markers

Cotton whole genome SNP (Single nucleotide polymorphism) markers were evaluated and screened across representative cotton materials, with the aim of obtaining an appropriate set of core SNP markers suitable for high-throughput identification of cotton hybrid purity based on KASP (Kompetitive allele specific PCR) technology. 5474 and 1850 single-copy SNP markers were screened out of a 63K SNP array with reference to two TM-1 genome versions (Institute of Cotton Research of the Chinese Academy of Agricultural Sciences version; Nanjing Agriculture University version), respectively. A set of 26 pairs of core SNP markers (one marker per chromosome) was achieved in view of polymorphism, genotyping quality, and homozygous and heterozygosis rates. The set of core SNP loci were then converted to KASP markers using Kraken^TM software. Genotyping assays of the KASP markers set were then performed on the SNPline platform. High-throughput genotyping assays of large numbers of samples were achieved, especially for the rapid purity tests.