Background

Perilla frutescens (Lamiaceae) is distributed in East Asia and is classified into var. frutescens and crispa. P. frutescens is multipurpose crop for human health because of a variety of secondary metabolites such as phenolic compound and essential oil. However, a lack of genetic information has hindered the development and utilization of Perilla genotypes.

Methods and results

This study was performed to develop expressed sequence tag—simple sequence repeat (EST-SSR) markers from P. frutescens var. crispa (wild type) and Antisperill (a mutant cultivar) and used them to assess the genetic diversity of, and relationships among, 94 P. frutescens genotypes. We obtained 65 Gb of sequence data comprising 632,970 transcripts by de novo RNA-sequencing. Of the 14,780 common SSRs, 102 polymorphic EST-SSRs were selected using in silico polymerase chain reaction (PCR). Overall, successful amplification from 58 EST-SSRs markers revealed remarkable genetic diversity and relationships among 94 P. frutescens genotypes. In total, 268 alleles were identified, with an average of 4.62 alleles per locus (range 2–11 alleles/locus). The average polymorphism information content (PIC) value was 0.50 (range 0.04–0.86). In phylogenetic and population structure analyses, the genotypes formed two major groups: Group I (var. crispa) and Group II (var. frutescens).

Conclusion

This results suggest that 58 novel EST-SSR markers derived from wild-type cultivar (var. crispa) and its mutant cultivar (Antisperill) have potential uses for population genetics and recombinant inbred line mapping analyses, which will provide comprehensive insights into the genetic diversity and relationship of P. frutescens.

中文翻译：

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使用源自野生型和突变紫苏转录组的新型 EST-SSR 标记分析紫苏的遗传多样性和关系

背景

紫苏（唇形科）分布于东亚，分为变种。frutescens和crispa。P. frutescens是一种对人类健康有益的多用途作物，因为它含有多种次生代谢物，如酚类化合物和精油。然而，遗传信息的缺乏阻碍了紫苏基因型的开发和利用。

方法和结果

进行这项研究是为了从P. frutescens var.中开发表达序列标签 - 简单序列重复 (EST-SSR) 标记。Krispa （野生型）和 Antisperill（突变品种）并用它们来评估 94 种P. frutescens基因型的遗传多样性和相互关系。我们通过从头 RNA 测序获得了 65 Gb 的序列数据，包括 632,970 个转录本。在 14,780 个常见的 SSR 中，使用计算机聚合酶链式反应 (PCR) 选择了 102 个多态性 EST-SSR。总体而言，58 个 EST-SSRs 标记的成功扩增揭示了 94 个P. frutescens之间显着的遗传多样性和关系基因型。总共鉴定了 268 个等位基因，每个基因座平均有 4.62 个等位基因（范围 2-11 个等位基因/基因座）。平均多态性信息含量（PIC）值为0.50（范围0.04-0.86）。在系统发育和种群结构分析中，基因型形成了两个主要群体：第一组（var.crispa）和第二组（var. frutescens）。

结论

这一结果表明，来自野生型品种（var.crispa）及其突变品种（Antisperill）的 58 个新 EST-SSR 标记具有用于群体遗传学和重组近交系作图分析的潜在用途，这将为了解遗传多样性提供全面的见解。和P. frutescens的关系。