Journal Article

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

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

2017

Overview

Summary Genomic 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.

• Publisher: John Wiley & Sons, Inc,Wiley,John Wiley and Sons Inc
• Subject: allopolyploidy / Analysis / Artificial chromosomes / Bacteria / Bacterial artificial chromosomes / Biotechnology / Brassica / Brassica napus / Brassica napus - genetics / Chromosome Mapping / Chromosome Pairing / Chromosomes / Chromosomes, Artificial, Bacterial - genetics / Chromosomes, Plant - genetics / Copy number / copy number variation / cytogenetic analysis / Diploidy / DNA Copy Number Variations / DNA probes / DNA, Plant - genetics / Fluorescence / Fluorescence in situ hybridization / Fluorescent indicators / Gene mapping / Gene Rearrangement / Genes / Genetic diversity / Genetic Linkage - genetics / genetic mapping / Genetic research / Genome rearrangements / Genome, Plant / Genomes / Genomics / Genotype / homoeologous exchange / In Situ Hybridization, Fluorescence / Life Sciences / Mapping / Nucleic Acid Hybridization / Phenotype / phenotypic variation / Phenotypic variations / polymerase chain reaction / Polymorphism, Single Nucleotide / Polyploidy / Primers / Quantitative genetics / Quantitative trait loci / Quantitative Trait Loci - genetics / quantitative traits / Rape plants / Recombination, Genetic / seed quality / Seeds - chemistry / Single-nucleotide polymorphism / Whole Genome Sequencing