基于黄麻转录组序列SNP位点的CAPS标记开发与验证

Development and verification of CAPS markers based on SNPs from transcriptome of jute(Corchorus L.)

黄麻CAPS分子标记的开发,可以为黄麻遗传多样性分析、种质资源鉴定和分子标记辅助选择等研究提供有效方法。本试验以黄麻179和爱店野生种为材料,采用IlluminaHiSeq4000测序技术进行转录组测序,对其SNP位点进行分析,设计了与木质素合成基因4CL、COMT及转录因子MYB相兲的SNP引物,在此基础上,应用dCAPS Finder2.0软件开发了CAPS标记,并对其有效性进行了验证。结果表明:(1)组装后的黄麻unigene序列共72,674条,序列总长度为29,705,997 bp,检测到的SNP位点总数为67,567个,平均每440 bp有1个SNP。(2)获得了39对分别与4CL、COMT和MYB相兲的SNP引物,从中筛选获得26对CAPS标记引物,开发成功率为66.7%,其中11对CAPS标记具有多态性,多态性比例为43.2%。(3)开发的CAPS标记能较好地将12份不同类型的黄麻种质区分开来,表明CAPS是适用于黄麻研究的较理想的分子标记方法,为黄麻遗传基础研究提供了可靠工具。

Developing CAPS markers can provide a new and effective tool for genetic diversity analysis,germplasm identification and marker-assistant selection of jute.The transcriptional sequence analysis was carried out by Illumina HiSeq 4000 with jute 179 and the wild species in Aidian.Furthermore,the SNP loci were screened and primers related to lignin synthesis genes 4CL,COMT and transcription factor MYB were developed.CAPS markers were screened based on above SNP primers using dCAPS Finder2.0 and their polymorphism was verified.A total of 72,674 unigene sequences were got in jute transcriptome by assembly,with a length of 29,705,997 bp,a number of SNP loci of 67,567,and an average of 1 SNP per 440 bp.Thirty-nine pairs of SNP primers related to 4CL,COMT,and MYB were designed by Oligo8,of which 26 pairs of CAPS primers were screened,with a developing rate of 66.7%.Among the 26 pairs of CAPS markers,11 pairs were polymorphic,with a polymorphic ratio of 43.2%.The screened CAPS markers could effectively distinguish 12 different accessions of jute germplasm,indicating CAPS is an ideal molecular marker which can lie a reliable tool used in genetic research of jute.