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. 2020 Feb 1;27(1):dsaa001.
doi: 10.1093/dnares/dsaa001.

Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions

Hiroto Kobayashi  1 , Kenta Shirasawa  2 , Nobuko Fukino  3 , Hideki Hirakawa  2 , Takashi Akanuma  1 , Hiroyasu Kitashiba  1
Affiliations

Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions

Hiroto Kobayashi et al. DNA Res. .

Abstract

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.

Keywords: ddRAD-Seq; genome-wide SNPs; radish accessions.

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Figures

Figure 1
Figure 1
PCoA of radish accessions using common SNPs. PCoA of 510 accessions (a) and 372 Asian accessions (b).
Figure 2
Figure 2
Phylogenetic tree of 81 representative radish accessions constructed using the maximum likelihood method.
Figure 3
Figure 3
Possible migration route of cultivated Raphnanus species from the West to East Asia. (a) Conventional hypothesis, based on previous studies. (b) Proposed hypothesis, based on the results of this study. Arrow means direction of the migration.
See this image and copyright information in PMC

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