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

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）是一种广泛种植的多用途植物，在医药领域的应用尤为突出。然而，由于白芷频繁被引种至新区域，其品种间的区分难度大幅提升。基于转录组分析开发的简单序列重复（Simple Sequence Repeats, SSR）分子标记，在构建遗传图谱、分析遗传多样性方面极具应用价值，同时也可用于白芷的分子标记辅助育种。本研究基于转录组测序数据，共鉴定出33724个基因内SSR位点。针对这些SSR位点共设计了114对引物，并对其特异性与多样性进行了验证。最终筛选出10个位于非翻译区的SSR位点。随后，本研究对采自不同区域的56份白芷生态型开展了遗传分析。结果显示，这些SSR位点包含2~8个等位基因，平均每个位点含5.2个等位基因；多态性信息含量（Polymorphic Information Content, PIC）值范围为0.2702~0.6274，平均值为0.4091；香农信息指数（Shannon’s Information Index）范围为0.5618~1.3040，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-温伯格平衡（Hardy-Weinberg Equilibrium），可有效用于白芷遗传关系的分析。本研究结果证实了转录组数据库在开发新型SSR分子标记方面的应用潜力。