Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification

Abstract

Background Brassica oleracea includes several morphologically diverse, economically important vegetable crops, such as the cauliflower and cabbage. However, genetic variants, especially large structural variants (SVs), that underlie the extreme morphological diversity of B. oleracea remain largely unexplored. Results Here we present high-quality chromosome-scale genome assemblies for two B. oleracea morphotypes, cauliflower and cabbage. Direct comparison of these two assemblies identifies ~ 120 K high-confidence SVs. Population analysis of 271 B. oleracea accessions using these SVs clearly separates different morphotypes, suggesting the association of SVs with B. oleracea intraspecific divergence. Genes affected by SVs selected between cauliflower and cabbage are enriched with functions related to response to stress and stimulus and meristem and flower development. Furthermore, genes affected by selected SVs and involved in the switch from vegetative to generative growth that defines curd initiation, inflorescence meristem proliferation for curd formation, maintenance and enlargement, are identified, providing insights into the regulatory network of curd development. Conclusions This study reveals the important roles of SVs in diversification of different morphotypes of B. oleracea, and the newly assembled genomes and the SVs provide rich resources for future research and breeding.

Whole-genome resequencing reveals genomic footprints of Italian sweet and hot pepper heirlooms giving insight into genes underlying key agronomic and qualitative traits

“…As far as structural variation is concerned, their number and types were in general consistent with what has been reported in other plant species [ 29 , 30 ], although the use of different methods and parameters in different studies make them difficult to compare. Indeed, it is difficult to compare our results with other pepper genomes, since in resequencing projects, SVs were usually not annotated and discussed.…”

Evidence for two domestication lineages supporting a middle-eastern origin forBrassica oleraceacrops from diversified kale populations

“…Both summer/autumn and tropical broccoli and cauliflower also have only a weak vernalization requirement. In the SVD-quartets tree, Chinese kale is closest related to the cauliflowers and broccoli clades (AIL), which share the early flowering phenotype due to FLC mutations [ 18 ] but are characterized by more mutations (e.g. curd proliferation arrested inflorescence meristems).…”

“…Crisp (1982) hypothesized that cauliflowers are evolved from broccoli’s based on crossing experiments. In a recent study by Guo et al (2021), this was also suggested based on their inflorescence phenotypes and causal mutations [ 18 ]. Dale-Champ (1586) writes that cauliflowers have evolved between 400–600 BC and are believed to have diversified in the Eastern Mediterranean, and from there introduced to Italy [ 14 ].…”

Understanding R Gene Evolution in Brassica

“…Large-scale structural variants can be detected using advanced third-generation sequencing methods and read mapping strategies such as high throughput chromosome conformation capture (Hi-C) and BioNano optical mapping technologies, as well as third-generation whole-genome sequencing strategies such as PacBio single-molecule real-time sequencing (SMRT) and Oxford Nanopore (ONT), which produce long reads and have been shown to overcome limitations on short reads to detect various SVs [131,132]. For example, in B. oleracea, large (100 kb or greater) SVs were detected using a combination of PacBio SMRT (DNA sequencing), PacBio Iso-Seq (RNA sequencing), BioNano optical mapping and Hi-C technologies [133], with genes related to stress response found to be related to these SVs. In B. napus, a 700 bp deletion of the V. longisporum resistance gene was identified using PacBio ONT sequencing [58].…”