title: A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits.
abstract: BACKGROUND
  Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning. This report describes the construction of the first B. napus consensus map consisting of a 1,359 anchored array based genotyping platform; Diversity Arrays Technology (DArT), and non-DArT markers from six populations originating from Australia, Canada, China and Europe. We aligned the B. napus DArT sequences with genomic scaffolds from Brassica rapa and Brassica oleracea, and identified DArT loci that showed linkage with qualitative and quantitative loci associated with agronomic traits.
  
  
  RESULTS
  The integrated consensus map covered a total of 1,987.2 cM and represented all 19 chromosomes of the A and C genomes, with an average map density of one marker per 1.46 cM, corresponding to approximately 0.88 Mbp of the haploid genome. Through in silico physical mapping 2,457 out of 3,072 (80%) DArT clones were assigned to the genomic scaffolds of B. rapa (A genome) and B. oleracea (C genome). These were used to orientate the genetic consensus map with the chromosomal sequences. The DArT markers showed linkage with previously identified non-DArT markers associated with qualitative and quantitative trait loci for plant architecture, phenological components, seed and oil quality attributes, boron efficiency, sucrose transport, male sterility, and race-specific resistance to blackleg disease.
  
  
  CONCLUSIONS
  The DArT markers provide increased marker density across the B. napus genome. Most of the DArT markers represented on the current array were sequenced and aligned with the B. rapa and B. oleracea genomes, providing insight into the Brassica A and C genomes. This information can be utilised for comparative genomics and genomic evolution studies. In summary, this consensus map can be used to (i) integrate new generation markers such as SNP arrays and next generation sequencing data; (ii) anchor physical maps to facilitate assembly of B. napus genome sequences; and (iii) identify candidate genes underlying natural genetic variation for traits of interest.
authors.affiliation: EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia.
authors.forename: Harsh
authors.initials: H
authors.lastname: Raman
authors.forename: Rosy
authors.initials: R
authors.lastname: Raman
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kilian
authors.forename: Frank
authors.initials: F
authors.lastname: Detering
authors.forename: Yan
authors.initials: Y
authors.lastname: Long
authors.forename: David
authors.initials: D
authors.lastname: Edwards
authors.forename: Isobel A P
authors.initials: IA
authors.lastname: Parkin
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Sharpe
authors.forename: Matthew N
authors.initials: MN
authors.lastname: Nelson
authors.forename: Nick
authors.initials: N
authors.lastname: Larkan
authors.forename: Jun
authors.initials: J
authors.lastname: Zou
authors.forename: Jinling
authors.initials: J
authors.lastname: Meng
authors.forename: M Naveed
authors.initials: MN
authors.lastname: Aslam
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.forename: Wallace A
authors.initials: WA
authors.lastname: Cowling
authors.forename: Derek
authors.initials: D
authors.lastname: Lydiate
mesh_terms: D000383:Agriculture; D029688:Brassica napus / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D032921:Consensus; D008040:Genetic Linkage; D014644:Genetic Variation; D018745:Genome, Plant; D060005:Genotyping Techniques / Q000379:methods*; D040641:Quantitative Trait Loci