A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: Applications in genetic dissection of qualitative and quantitative traits

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DOIResolve DOI: http://doi.org/10.1186/1471-2164-14-277
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TypeArticle
Journal titleBMC Genomics
ISSN1471-2164
Volume14
Issue1
Article number277
Subjectarticle; chromosome map; consensus sequence; controlled study; diversity array technology; gene locus; gene mapping; genetic linkage; genetic procedures; genetic trait; genetic variability; genotype; microarray analysis; molecular cloning; nonhuman; plant genetics; qualitative analysis; quantitative genetics; quantitative trait locus; quantitative trait locus mapping; rapeseed; sequence homology; single nucleotide polymorphism; Agriculture; Brassica napus; Chromosome Mapping; Consensus; Genetic Linkage; Genetic Variation; Genome, Plant; Genotyping Techniques; Quantitative Trait Loci; Brassica; Brassica napus; Brassica oleracea; Brassica rapa
AbstractBackground: 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. © 2013 Raman et al.; licensee BioMed Central Ltd.
Publication date
LanguageEnglish
AffiliationNational Research Council Canada (NRC-CNRC)
Peer reviewedYes
NPARC number21270635
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Record identifier7ea39726-14bf-4d21-b2c0-9dcd3b0cae8e
Record created2014-02-17
Record modified2016-05-09
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