基于转录组测序的鬼针草SSR标记开发及其应用

Development and Application of SSR Markers in Bidens bipinnata L. Based on Transcriptome Sequencing

鬼针草(Bidens bipinnata L.)作为一种重要的药用植物,在属内鉴别和临床用药安全上存在较大问题。本研究利用Trinity软件对鬼针草转录组数据进行组装,共得到总长为106 457 436 bp的120 122条unigenes。利用MISA软件寻找到17 140个含有SSR的重复基元。SSR位点中主要重复序列为单核苷酸和三核苷酸,分别占总SSR位点的38.73%和38.06%,其次是二核苷酸,占20.73%。利用Primer 3.0设计引物,从中随机选择50对引物进行PCR扩增。其中有28对扩增出清晰条带,多态性好,重复性好。鬼针草转录组的SSR分子标记将会对鬼针草属植物种质资源鉴定、遗传多样性、重要性状基因定位及分子标记辅助选择育种等起重要推动作用。

Bidens bipinnata L. is one of the important medicinal plant, but there are major problems in the internal identification and clinical medication. In this research, a total of 120 122 unigenes were obtained in the whole length of 106 457 436 bp by the assemble of transcriptome sequencing data in Bidens bipinnata using Trinity software, and 17 140 repeat contigs containing SSR were found by MISA software. Mononucleotide and trinucleotide were the dominant repetitive sequences in SSR loci, which accounted for 38.73% and 38.06%,respectively, followed by the dinucleotide with 20.73%. Using Primer 3.0 to design primers, 50 pairs of primers were randomly selected for PCR amplification. Among them, 28 pairs of primers were amplified with clear bands,which had good polymorphism and repeatability. The SSR markers in the transcriptome of Bidens bipinnata would benefit the identification of germplasm resources, the genetic diversity analysis, locus of candidate trait genes and molecular marker-assisted breeding of Bidens plants.