Zhang Jian, Yang Chenglong, Yang Xiaoyu, Lei Jing, Long Peiling
GuiZhou Institute of Subtropical Crops Guizhou Academy of Agricultural Sciences Guiyang China.
Ministry of Agriculture and Rural Affairs Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Region Guiyang China.
Ecol Evol. 2025 Sep 10;15(9):e72128. doi: 10.1002/ece3.72128. eCollection 2025 Sep.
, the underground rhizome of Siebold et Zucc., serves as a traditional medicinal resource among the Miao ethnic group in Guizhou, China. This study aimed to develop SSR molecular markers from the transcriptome to assess the genetic diversity of its germplasm across diverse regions. A transcriptome database was constructed using high-throughput sequencing, followed by the extraction of SSR loci with MISA software. Polymorphic SSR markers were identified and utilized to evaluate the genetic diversity of 45 germplasm resources. In total, 38,806 Unigenes were obtained, with an average length of 993.00 bp. Comparative annotation against the GO, KEGG, EggNOG, NR, Swiss-prot, and Pfam databases yielded 23,558, 12,412, 25,448, 28,101, 20,056, and 18,460 annotated Unigenes, respectively. A total of 7501 SSR loci were identified, with trinucleotide repeats constituting the predominant class (44.03%), and ACC/GGT being the most frequent motif. Ten pairs of polymorphic primers were developed, all exhibiting a PIC value greater than 0.5. The 45 spp. accessions were classified into three distinct groups using the UPGMA method. The transcriptome harbors abundant polymorphic SSRs. The developed primers enable rapid molecular identification of germplasm and provide insights into its genetic diversity, which may underlie variations in medicinal properties and environmental adaptation. These findings support applications in germplasm conservation, marker-assisted breeding, and quality control of medicinal resources.
，作为中国贵州苗族的传统药用资源。本研究旨在从转录组中开发SSR分子标记，以评估其在不同地区种质的遗传多样性。利用高通量测序构建转录组数据库，随后用MISA软件提取SSR位点。鉴定出多态性SSR标记并用于评估45份种质资源的遗传多样性。共获得38,806个单基因，平均长度为993.00bp。与GO、KEGG、EggNOG、NR、Swiss-prot和Pfam数据库进行比较注释，分别得到23,558、12,412、25,448、28,101、20,056和18,460个注释单基因。共鉴定出7501个SSR位点，其中三核苷酸重复为主导类型（44.03%），ACC/GGT为最常见基序。开发了10对多态性引物，所有引物的PIC值均大于0.5。采用UPGMA方法将45份种源分为三个不同的组。该转录组含有丰富的多态性SSR。开发的引物能够快速对种质进行分子鉴定，并为其遗传多样性提供见解，这可能是药用特性和环境适应性变异的基础。这些发现支持在种质保护、标记辅助育种和药用资源质量控制中的应用。
