Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica

Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A. dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are very useful for constructing genetic maps and analyzing genetic diversity. They are also relevant for the molecular marker-assisted breeding of A. dahurica. We identified 33,724 genic SSR loci based on transcriptome sequencing data. A total of 114 primer pairs were designed for the SSR loci and were tested for their specificity and diversity. Ten SSR loci in untranslated regions were ultimately selected. Subsequently, 56 A. dahurica ecotypes collected from different regions were analyzed. The SSR loci comprised 2–8 alleles, with a mean of 5.2 alleles per locus. The polymorphic information content value and Shannon’s information index were 0.6274–0.2702 (average of 0.4091) and 1.3040–0.5618 (average of 0.8475), respectively. Thus, the 10 novel SSRs identified in this study were almost in accordance with Harvey-Weinberg equilibrium and will be useful for analyzing A. dahurica genetic relationships. The results of this study confirm the potential value of transcriptome databases for the development of new SSR markers.白芷（Angelica dahurica）是一种广泛种植、用途多样的植物，尤其在医药领域具备重要应用价值。但由于该物种频繁被引种至新区域，其品种鉴别工作已变得十分困难。基于转录组分析开发的简单序列重复（Simple sequence repeats，SSRs）标记，在构建遗传图谱、分析遗传多样性以及开展白芷的分子标记辅助育种中均具有显著应用潜力。本研究依托转录组测序数据，共鉴定得到33724个基因内SSR位点。针对这些位点设计了114对引物，并对其特异性与多态性进行了检测。最终筛选出10个位于非翻译区的SSR位点。随后，对采集自不同区域的56份白芷生态型开展遗传分析，结果显示：这些SSR位点的等位基因数为2~8，平均每个位点含5.2个等位基因；多态信息含量值介于0.2702~0.6274之间，平均值为0.4091；香农信息指数介于0.5618~1.3040之间，平均值为0.8475。综上，本研究开发的10个新型SSR标记基本符合哈迪-温伯格（Harvey-Weinberg）平衡，可用于解析白芷的遗传亲缘关系。本研究结果证实，转录组数据库在新型SSR标记开发方面具备可观的应用价值。