Assembly of a radish core collection for evaluation and preservation of genetic diversity

The radish is both an agronomically important root vegetable crop and a wild species of genus Raphanus in the Brassicaceae family. To date, at least four independent draft genome assemblies, marker development studies, and an analysis of radish evolution have been performed; however, there is no core collection of germplasm representing the genetic diversity in radish with minimum genetic redundancy. We report the assembly of a radish core collection consisting of 125 accessions. These accessions were selected by using 25 sequence-tagged site insertion/deletion markers to genotype 70 alleles in 886 accessions obtained from three germplasm banks in Korea, Japan, and Germany. An unweighted pair-group method with arithmetic mean (UPGMA) analysis of the genotyping data classified the accessions into 125 groups based on a Jaccard’s similarity coefficient of 0.72. One representative accession from each group was selected for a core collection that included 125 accessions, corresponding to 14.1% of the whole collection and including all 70 alleles. Principal coordinates analysis demonstrated that the genetic distribution within the core collection was similar to that of the whole collection, and 94% of the total variance within the whole collection could be explained using the analysis of molecular variance from the core collection. The UPGMA and STRUCTURE software analyses identified three major groups of accessions within the core collection, which were the Asian cultivated radish, the European cultivated radish, and the wild radish. The radish core collection developed in this study will be an important plant resource in future research and radish breeding.