title: Targeted deep sequencing of flowering regulators in Brassica napus reveals extensive copy number variation.
abstract: Gene copy number variation (CNV) is increasingly implicated in control of complex trait networks, particularly in polyploid plants like rapeseed (Brassica napus L.) with an evolutionary history of genome restructuring. Here we performed sequence capture to assay nucleotide variation and CNV in a panel of central flowering time regulatory genes across a species-wide diversity set of 280 B. napus accessions. The genes were chosen based on prior knowledge from Arabidopsis thaliana and related Brassica species. Target enrichment was performed using the Agilent SureSelect technology, followed by Illumina sequencing. A bait (probe) pool was developed based on results of a preliminary experiment with representatives from different B. napus morphotypes. A very high mean target coverage of ~670x allowed reliable calling of CNV, single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) polymorphisms. No accession exhibited no CNV, and at least one homolog of every gene we investigated showed CNV in some accessions. Some CNV appear more often in specific morphotypes, indicating a role in diversification.
authors.affiliation: Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Schiessl
authors.affiliation: Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
authors.forename: Bruno
authors.initials: B
authors.lastname: Huettel
authors.affiliation: Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
authors.forename: Diana
authors.initials: D
authors.lastname: Kuehn
authors.affiliation: Max Planck Institute for Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.affiliation: Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
authors.forename: Rod J
authors.initials: RJ
authors.lastname: Snowdon
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029688:Brassica napus / Q000235:genetics*; D056915:DNA Copy Number Variations; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA