From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection

Zachary Stansell,Thomas Björkman

doi:10.1038/s41438-020-00375-0

Abstract

Worldwide, broccoli (Brassica oleracea var. italica) is among the most economically important, nutritionally rich, and widely-grown vegetable crops. To explore the genomic basis of the dramatic changes in broccoli morphology in the last century, we evaluated 109 broccoli or broccoli/cauliflower intermediates for 24 horticultural traits. Genotype-by-sequencing markers were used to determine four subpopulations within italica: Calabrese broccoli landraces and hybrids, sprouting broccoli, and violet cauliflower, and to evaluate between and within group relatedness and diversity. While overall horticultural quality and harvest index of improved hybrid broccoli germplasm has increased by year of cultivar release, this improvement has been accompanied by a considerable reduction in allelic diversity when compared to the larger pool of germplasm. Two landraces are the most likely founding source of modern broccoli hybrids, and within these modern hybrids, we identified 13 reduction-in-diversity genomic regions, 53 selective sweeps, and 30 (>1 Mbp) runs of homozygosity. Landrace accessions collected in southern Italy contained 4.8-fold greater unique alleles per accessions compared to modern hybrids and provide a valuable resource in subsequent improvement efforts. This work broadens the understanding of broccoli germplasm, informs conservation efforts, and enables breeding for complex quality traits and regionally adapted cultivars.

Highlights

Broccoli (Brassica oleracea var. italica) and cauliflower (B. oleracea var. botrytis) are the most widely-grown brassica vegetable crops internationally, with a cumulative production area of 1.4 million Ha1
We build on previous work by clarifying the relationship of elite broccoli germplasm within a larger pool of italica germplasm, and characterize the genomic and phenotypic changes that occurred during this improvement process[16]
We evaluated critical genomic regions and targets of selection in modern F1 Calabrese broccoli by evaluating genome-wide population differentiation, reduced or enriched nucleotide diversity, selectivesweeps, and runs of homozygosity (Figs. 2–4)

Summary

Introduction

Broccoli (Brassica oleracea var. italica) and cauliflower (B. oleracea var. botrytis) are the most widely-grown brassica vegetable crops internationally, with a cumulative production area of 1.4 million Ha1. Botrytis) are the most widely-grown brassica vegetable crops internationally, with a cumulative production area of 1.4 million Ha1. F1 hybrid broccoli is the most economically important brassica vegetable crop in the United States with a farm-gate value of ~1 billion USD2. While modern broccoli cultivars are distinct from their landrace precursors in heading induction requirement, time to maturity, crown size and architecture, and secondary metabolic profile[14,17,36,37,38,39,40,41,42,43,44], the basis for these dramatic changes remains largely unexplored using genomics era tools, such as genotype-by-sequencing. We build on previous work by clarifying the relationship of elite broccoli germplasm within a larger pool of italica germplasm, and characterize the genomic and phenotypic changes that occurred during this improvement process[16]

Methods

Results

Conclusion