Genetic Diversity, Genome Scan and Morphological Variation in a Leafy Brassica rapa Germplasm Collection

Brassica species comprises a large and diverse group of vegetables, fodder, and oil crops. Chinese cabbage (B. rapa ssp. pekinensis) is an important leafy vegetables with a heading character. Presently, the Korean Brassica Genome Resource Bank collected over 10,000 accessions of Brassicas from different areas in the world. Collected germplasms were analyzed for their morphological traits and functional compounds. The accessions with diverse morphological type and high level of functional compounds were selected to develop inbred lines and double haploid lines by propagation and microspore culture. Finally, a set of 238 leafy vegetables B. rapa fixed lines were developed successfully. Genetic diversity and structure analysis were performed by genome-wide distributed SSR and SNP markers over these fixed lines. Combined SSR and SNP profiling divided them into four subpopulation, corresponding with geographical origin and morphology. Based on the structured result, geographic origin, and morphological type, 96 lines were selected for whole-genome re-sequencing. Candidate genes and a large numbers of SNPs for morphological trait, flowering-related trait and metabolism synthesis were identified from re-sequencing data by NGS (Next-Generation Sequencing) and used for genetic diversity and genome-wide association analysis. This set of structured B. rapa leafy vegetable fixed lines would be useful resources for B. rapa DFFS (Diversity Fixed Foundation Set) development.