The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of simple sequence repeat (SSR) markers for nonmodel crop. In the Perilla crop, analysis of the distribution of different repeat motifs showed that the most abundant type was dinucleotide repeats (62.0%), followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. In total, 130 alleles were detected segregating in nine Perilla accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of Perilla crop, 40 individuals from an F₂ population of Perilla were selected for association analysis based on their leaf- and plant-related characteristics. An association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F₂ population was conducted. From the analysis, we identified 12 SSR markers associated with leaf-related traits and 11 SSR markers associated with plant-related traits. Therefore, the new Perilla SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for Perilla crop breeding programs, and allowing Perilla breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs.

转录组测序方法 RNA-seq 是一种强大的工具，可用于非模型作物的简单序列重复 (SSR) 标记的转录分析和开发。在紫苏作物中，对不同重复基序分布的分析表明，最丰富的类型是二核苷酸重复（62.0%），其次是三核苷酸重复（35.3%），两者合计占 eSSR 重复的 97.3%。在这项研究中，我们通过转录组测序方法 RNA-sEq 开发了 39 个新的 SSR 引物组。总共在九个紫苏中检测到 130 个等位基因每个基因座平均有 3.3 个等位基因，范围从 125 到 360 bp。每个基因座的等位基因数从 2 到 6 不等。为了检测与紫苏作物形态特征相关的 SSR 标记，从 F ₂紫苏种群中选取40 个个体进行基于其叶和植物相关特征的关联分析。对 F ₂种群的 40 个个体中的 37 个 SSR 标记和 9 个叶和植物相关性状进行了关联分析。从分析中，我们确定了 12 个与叶相关性状相关的 SSR 标记和 11 个与植物相关性状相关的 SSR 标记。因此，新紫苏本研究中描述的 SSR 引物有助于识别遗传多样性和遗传作图，为紫苏作物育种计划指定重要的基因/QTL ，并允许紫苏育种者通过标记辅助选择 (MAS) 育种计划提高叶片和植物质量。