title: Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus.
abstract: 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.
authors.affiliation: Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Stein
authors.affiliation: IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Coriton
authors.affiliation: IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Rousseau-Gueutin
authors.affiliation: Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
authors.forename: Birgit
authors.initials: B
authors.lastname: Samans
authors.affiliation: Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
authors.forename: Sarah V
authors.initials: SV
authors.lastname: Schiessl
authors.affiliation: Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Obermeier
authors.affiliation: Agriculture and Agri-Food Canada, Saskatoon, Canada.
authors.forename: Isobel A P
authors.initials: IAP
authors.lastname: Parkin
authors.affiliation: IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Chèvre
authors.affiliation: Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
authors.forename: Rod J
authors.initials: RJ
authors.lastname: Snowdon
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D002874:Chromosome Mapping; D023902:Chromosome Pairing; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D056915:DNA Copy Number Variations; D018744:DNA, Plant / Q000235:genetics; D004171:Diploidy; D015321:Gene Rearrangement; D008040:Genetic Linkage / Q000235:genetics; D018745:Genome, Plant; D005838:Genotype; D017404:In Situ Hybridization, Fluorescence; D009693:Nucleic Acid Hybridization; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D011995:Recombination, Genetic; D012639:Seeds / Q000737:chemistry; D000073336:Whole Genome Sequencing
chemical_list: D018744:DNA, Plant
keywords: Genome rearrangements; genetic mapping; homoeologous exchange; quantitative trait loci; single nucleotide polymorphism