Characterization of agronomic traits and genomic diversity in a newly assembled radish core collection

Crop breeding programs are reliant on the genetic diversity of varieties and germplasm collections. Raphanus sativus L. is a root crop species of the Brassicaceae family that accounts for similar to 2% of global vegetable production. We recently reported the assembly of a new radish core collection consisting of 125 accessions obtained from worldwide germplasm banks. To develop a comprehensive plant resource for radish research and breeding, we characterized the agronomic traits of 83 accessions and analyzed their genome-wide DNA variations along with 17 previously analyzed accessions. A total of 14 agronomically important root, leaf, and flower phenotypic traits were examined according to the guidelines of the International Union for the Protection of New Plant Varieties. Chemical diversity in radish roots was investigated by measuring their sugar, glucosinolate, and anthocyanin contents. Through high-depth whole-genome resequencing of 100 accessions and multi-sample genotyping analysis using the Rs2.0 genome assembly as a reference, we identified a total of 796,294 homozygous high-quality single-nucleotide polymorphisms. Genetic structural analysis using a neighbor-joining algorithm and multi-dimensional scaling analysis of the variations were applied to classify the accessions into three major groups, including 37 and 55 accessions of European and Asian cultivated radishes, respectively, and eight wild radish accessions. For each accession, the mitochondria-encoded Ogura cytoplasmic male-sterility determinant orf138 and nuclear fertility restorer PPR-B genes were reconstructed by reference-guided assembly. It is anticipated that these genetic diversity and agronomic properties of the radish core collection will facilitate breeding programs to develop new radish cultivars with desirable profiles. This study provides important agronomic phenotypic and phytochemical trait data for a new radish core collection.Whole-genome resequencing and multi-sample genotyping analyses identified 796,294 high-quality single-nucleotide polymorphisms.High-depth variation data from 100 radish accessions classified the accessions into three main groups.These resources will enhance research on the trait genetic system, breeding, and diversity conservation of radishes.