适于陆地棉品种身份鉴定的SNP核心位点筛选与评价

Genome-wide Screening and Evaluation of SNP Core Loci for Identification of Upland Cotton Varieties

利用全基因组SNP信息,筛选陆地棉品种特异的核心SNP位点组合,可为陆地棉品种身份鉴定提供准确高效的检测手段。本研究利用棉花CottonSNP80K芯片对326份不同来源的陆地棉种质进行SNP分型。以南京农业大学陆地棉TM-1基因组Gossypium hirsutum (AD1) genome NBI v1.1版本为参考序列,对SNP位点进行注释。结果表明, 93.85%(72 990/77 774)的位点检出率超过99%, 61 595 (79.20%)个SNP位点具有多态性,其中76.32%(47 009)的位点最小等位基因频率(MAF)大于0.1。基于位点检出率大于0.99、位点具多态性、MAF大于0.2、杂合率小于0.05、每条染色体的SNP密度为400 kb/SNP左右等要求,最终获得4857个覆盖全基因组的高质量核心SNP位点组合。这些核心SNP位点组合平均检出率接近100%;平均MAF值为0.34;平均杂合率为0.02; 99%以上的陆地棉材料均能够被准确鉴定。统计分析表明利用核心SNP位点组合与CottonSNP80K的鉴定结果呈极显著相关。本研究提供了包含4857个SNP位点,适于陆地棉品种指纹图谱绘制的核心SNP位点组合,可实现陆地棉品种身份鉴定和品种确权。

Utilizing the genome-wide SNP information to screen the core SNP loci may provide an accurate and efficient method for the identification of upland cotton varieties.Using the CottonSNP80K array,SNP genotyping was performed within 326 upland cotton accessions.Then,the SNP loci were annotated with TM-1 genomic sequence of Gossypium hirsutum(AD1)genome NBI v1.1 Upland cotton of Nanjing Agricultural University as reference sequence.Statistical analysis of all loci in CottonSNP80K showed that the call rate of 93.85%loci(72 990 in 77 774)was more than 99%,and 61 595(79.20%)SNPs were polymorphic loci among the tested upland cotton accessions.Among them,minor allele frequency(MAF)of 76.32%(47 009)loci was greater than 0.1.Based on call frequency for each locus>0.99;loci with polymorphism;MAF>0.2;heterozygosity rate<0.05;SNP density with^400 kb/SNP in each chromosome,we obtained 4857 high-quality core SNP loci.The characteristic statistics of the core SNP loci combination showed that the average call rate was nearly 100%;the average MAF was 0.34;and the average heterozygosity was 0.02.Using these core SNPs,more than 99%of the materials could be identified accurately and effectively.In addition,the identification results of core SNP loci showed extremely significant linear correlation with that of CottonSNP80K.Taken together,a core combination containing 4857 SNP loci for fingerprint identification of upland cotton varieties is constructed,which can accurately identify the purity and reality of modern upland cotton varieties.