Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan.
Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
DNA Res. 2020 Feb 1;27(1). doi: 10.1093/dnares/dsaa001.
Radish (Raphanus sativus L.) is cultivated around the world as a vegetable crop and exhibits diverse morphological and physiological features. DNA polymorphisms are responsible for differences in traits among cultivars. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse radish accessions using the double-digest restriction site-associated DNA sequencing (ddRAD-Seq) method. A total of 52,559 SNPs was identified in a collection of over 500 radish accessions (cultivated and wild) from East Asia, South and Southeast Asia, and the Occident and Near East. In addition, 2,624 SNP sites without missing data (referred to as common SNP sites) were identified among 510 accessions. Genetic diversity analyses, based on the common SNP sites, divided the cultivated radish accessions into four main groups, each derived from four geographical areas (Japan, East Asia, South and Southeast Asia, and the Occident and Near East). Furthermore, we discuss the origin of cultivated radish and its migration from the West to East Asia. SNP data generated in this work will facilitate further genetic studies on the radish breeding and production of DNA markers.
萝卜（Raphanus sativus L.）作为一种蔬菜作物在世界各地广泛种植，具有多种形态和生理特征。DNA 多态性是造成品种间表型差异的原因。本研究采用双酶切相关 DNA 测序（ddRAD-Seq）方法，对来自东亚、南亚和东南亚以及西亚和近东的 500 多个萝卜品种（包括栽培品种和野生品种）进行了全基因组单核苷酸多态性（SNP）分析。在一个包含超过 500 个萝卜品种的样本中，共鉴定出 52559 个 SNP。此外，在 510 个样本中还鉴定出了 2624 个没有缺失数据的 SNP 位点（称为常见 SNP 位点）。基于常见 SNP 位点的遗传多样性分析将栽培萝卜品种分为四个主要组，每组都源自四个地理区域（日本、东亚、南亚和东南亚以及西亚和近东）。此外，我们还讨论了栽培萝卜的起源及其从西方到东亚的迁移。本研究生成的 SNP 数据将有助于进一步开展萝卜遗传育种和 DNA 标记开发的相关研究。
