Genotyping-by-sequencing of Brassica oleracea vegetables reveals unique phylogenetic patterns, population structure and domestication footprints. Issue 1 (1st July 2018)

• Record Type: Journal Article
• Authors: Stansell, Zachary; Hyma, Katie; Fresnedo-Ramírez, Jonathan; Sun, Qi; Mitchell, Sharon; Björkman, Thomas; Hua, Jian
• Is Part Of: Horticulture research. Volume 5:Issue 1(2018)
• Publication Date: 2018-07-01
• Subjects: Bioinformatics -- Plant domestication; Horticulture -- Research -- Periodicals; 635.072
• DOI: 10.1038/s41438-018-0040-3
• Languages: English
• ISSNs: 2052-7276

Abstract

Abstract: Brassica oleracea 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 B. oleracea 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 B. oleracea 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 B. oleracea 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. Which came first: the broccoli or the cauliflower?: A comparison of gene variations in modern-day offspring of wild cabbage shows that broccoli may have preceded the appearance of cauliflower in domesticated crops. Jian Hua, Thomas Bjorkman, and colleagues from Cornell University in the US examined the DNA sequences of 85 traditional "landrace" and improved broccoli, cauliflower, and Chinese kale plants, all of which descend from the species Brassica oleracea, or wild cabbage. They found 21, 680 sequence variations among them all, which they used to look for patterns of relatedness between the plants. Their results support the possible domestication of cauliflower after or in parallel with broccoli. The study identifies a large pool of genetic diversity within broccoli landraces that could be used to improve future breeding efforts.