Genotyping-by-sequencing of Brassica oleracea vegetables reveals unique phylogenetic patterns, population structure and domestication footprints

Abstract

<i>Brassica oleracea</i> forms a diverse and economically significant crop group. Improvement efforts are often hindered by limited knowledge of diversity contained within available germplasm. Here, we employ genotyping-by-sequencing to investigate a diverse panel of 85 landrace and improved <i>B. oleracea</i> broccoli, cauliflower, and Chinese kale entries. Ultimately, 21,680 high-quality SNPs were used to reveal a complex and admixed population structure and clarify phylogenetic relationships among <i>B. oleracea</i> groups. Each broccoli landrace contained, on average, 8.4 times as many unique alleles as an improved broccoli and landraces collectively represented 81% of all broccoli-specific alleles. Commercial broccoli hybrids were largely represented by a single subpopulation identified within a complex population structure. Greater allelic diversity in landrace broccoli and 96.1% of SNPs differentiating improved cauliflower from landrace cauliflower were common to the larger pool of broccoli germplasm, supporting a parallel or later development of cauliflower due to introgression events from broccoli. Chinese kale was readily distinguished by principal coordinate analysis. Genotyping was accomplished with and without reliance upon a reference genome producing 141,317 and 20,815 filtered SNPs, respectively, supporting robust SNP discovery methods in neglected or unimproved crop groups that lack a reference genome. This work clarifies the population structure, phylogeny, and domestication footprints of landrace and improved <i>B. oleracea</i> broccoli using many genotyping-by-sequencing markers. Additionally, a large pool of genetic diversity contained in broccoli landraces is described which may enhance future breeding efforts.