Resequencing Analysis of the Radish (Raphanus sativus L.) Genome Identifies Patterns of Genetic Selection during Domestication

Radish (Raphanus sativus L.) is an important root vegetable crop that has a long history of domestication, but the origins of cultivated radishes remain controversial. Repeated selection on specific traits during domestication reduces genetic variation around domestication-related genes (DRG), which are known as a selective sweep. Finding genetic bottlenecks in crop species is a key for elucidating history of domestication as well as identification of DRG. In this study, we present comprehensive whole-genome resequencing analysis of radish to explore genomic variation in the radish population. Multi-sample genotyping analysis of 17 cultivated and wild accessions obtained 9.5 million homozygous single-nucleotide polymorphisms (SNPs)/insertions or deletions (InDels). Phylogenetic and population structure analysis revealed close relationships between Asian cultivated and wild radishes, suggesting that Asian cultivars were domesticated from wild Asian species. Comparison of genetic variation between Asian genotypes identified 512 DRG candidates that are related to root architecture, cell wall, and sugar metabolism. Expression analysis of DRGs during root development suggested that selective traits included a taproot architecture, reduced cell wall rigidity, and favorable taste. This study provides evolutionary insight into radish domestication as well as the potential trait-related markers for background selection in molecular breeding.