Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

Anna Stein,Sarah V Schiessl,Christian Obermeier,Birgit Samans,Olivier Coriton,Anne‐Marie Chèvre,Mathieu Rousseau‐Gueutin,Rod J Snowdon,Isobel A.P Parkin

doi:10.1111/pbi.12732

Abstract

SummaryGenomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B. napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies. Here, we demonstrate how high‐density genetic mapping with codominant, physically anchored SNP markers can detect segmental homoeologous exchanges (HE) as well as deletions and accurately link these to QTL. We validated rearrangements detected in genetic mapping data by whole‐genome resequencing of parental lines along with cytogenetic analysis using fluorescence in situ hybridization with bacterial artificial chromosome probes (BAC‐FISH) coupled with PCR using primers specific to the rearranged region. Using a well‐known QTL region influencing seed quality traits as an example, we confirmed that HE underlies the trait variation in a DH population involving a synthetic B. napus trait donor, and succeeded in narrowing the QTL to a small defined interval that enables delineation of key candidate genes.

Highlights

Brassica napus is a very recent allopolyploid species that since its origin has become one of the world’s most important crops
Other than the assumption that resynthesized rapeseed displays some kind of accelerated oilseed rape evolution, it is unknown whether different mechanisms take place in natural and resynthesized oilseed rape
As expected, the natural B. napus accession Express 617 showed the lowest degree of segmentation (685 deleted or duplicated segments), whereas the two synthetic B. napus parents exhibited a considerably higher segmentation degree (821 and 1,630 deletions or duplications, for 1012-98 and R53, respectively)

Summary

Introduction

Brassica napus (rapeseed, oilseed rape, canola) is a very recent allopolyploid species that since its origin has become one of the world’s most important crops. The species was formed by hybridization and genome doubling from the diploid donor genomes of Brassica oleracea and Brassica rapa, respectively. Because this cross can be readily reproduced with the help of embryo rescue techniques, B. napus has become a popular model for studying the genetic and genomic consequences of de novo allopolyploidization and how these have shaped natural and agricultural selection in a modern crop (Mason and Chevre, 2016). Numerous smallscale homoeologous exchanges (HE) are observed throughout the genomes of natural B. napus accessions, whereas large-scale HE are common in synthetic accessions (Chalhoub et al, 2014; Rousseau-Gueutin et al, 2017). Other than the assumption that resynthesized rapeseed displays some kind of accelerated oilseed rape evolution, it is unknown whether different mechanisms take place in natural and resynthesized oilseed rape

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Discussion

Conclusion