title: Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing.
abstract: Polyploidy complicates genomics-based breeding of many crops, including wheat, potato, cotton, oat and sugarcane. To address this challenge, we sequenced leaf transcriptomes across a mapping population of the polyploid crop oilseed rape (Brassica napus) and representative ancestors of the parents of the population. Analysis of sequence variation and transcript abundance enabled us to construct twin single nucleotide polymorphism linkage maps of B. napus, comprising 23,037 markers. We used these to align the B. napus genome with that of a related species, Arabidopsis thaliana, and to genome sequence assemblies of its progenitor species, Brassica rapa and Brassica oleracea. We also developed methods to detect genome rearrangements and track inheritance of genomic segments, including the outcome of an interspecific cross. By revealing the genetic consequences of breeding, cost-effective, high-resolution dissection of crop genomes by transcriptome sequencing will increase the efficiency of predictive breeding even in the absence of a complete genome sequence.
authors.affiliation: John Innes Centre, Norwich Research Park, Norwich, Norfolk, UK. ian.bancroft@jic.ac.uk
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.forename: Colin
authors.initials: C
authors.lastname: Morgan
authors.forename: Fiona
authors.initials: F
authors.lastname: Fraser
authors.forename: Janet
authors.initials: J
authors.lastname: Higgins
authors.forename: Rachel
authors.initials: R
authors.lastname: Wells
authors.forename: Leah
authors.initials: L
authors.lastname: Clissold
authors.forename: David
authors.initials: D
authors.lastname: Baker
authors.forename: Yan
authors.initials: Y
authors.lastname: Long
authors.forename: Jinling
authors.initials: J
authors.lastname: Meng
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
authors.forename: Shengyi
authors.initials: S
authors.lastname: Liu
authors.forename: Martin
authors.initials: M
authors.lastname: Trick
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029688:Brassica napus / Q000235:genetics; D029741:Brassica rapa / Q000235:genetics*; D002874:Chromosome Mapping; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D011110:Polymorphism, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D059467:Transcriptome