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

Jian Hua,Sharon Mitchell,Qi Sun,Zachary Stansell,Jonathan Fresnedo-Ramírez,Katie Hyma,Thomas Björkman

doi:10.1038/s41438-018-0040-3

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.

Highlights

Brassica oleracea is an economically important and outcrossing species domesticated as early as 2000 BCE and has been specialized into many unique botanical types such as broccoli, cauliflower, cabbage, kale, Chinese kale, and Brussels sprouts
Crops is frequently subject to abiotic stressors such as heat stress typically resulting in a reduction in horticultural quality. Improvement efforts for these crop groups are often limited by a lack of knowledge of available diversity or genetic bottlenecks that occurred during domestication or dispersal
Two broccoli landraces, “Cavolo Broccolo Ramoso Calabrese” and “Cavolo Broccolo Verde Calbrese Precoce”, collocated within the clade otherwise comprised of improved broccoli

Summary

Introduction

Brassica oleracea is an economically important and outcrossing species domesticated as early as 2000 BCE and has been specialized into many unique botanical types such as broccoli, cauliflower, cabbage, kale, Chinese kale, and Brussels sprouts. Commercial production of these crops is frequently subject to abiotic stressors such as heat stress typically resulting in a reduction in horticultural quality. Domestication of B. oleracea occurred in the Mediterranean and was spread by trade resulting in a proliferation of locally adapted landraces representing a complex genetic admixture[3,4,5]. It is currently unclear if broccoli and cauliflower were domesticated independently, if one was selected from within the other, or the degree to which mutual introgression has occurred[6,7,8]

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