Journal Article

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

Cowling, W.A, Long, Y, Aslam, M.N, Nelson, M.N, Raman, H, Zou, J, Batley, J, Lydiate, D, Detering, F, Meng, J, Raman, R, Edwards, D, Sharpe, A.G, Larkan, N, Kilian, A, Parkin, I.A.P

2013

Overview

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. © 2013 Raman et al.; licensee BioMed Central Ltd.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Agriculture / Animal Genetics and Genomics / Biomedical and Life Sciences / Boron / Brassica / Brassica napus / Brassica napus - genetics / Brassica oleracea / Brassica rapa / chromosome map / Chromosome Mapping / Chromosome Mapping - methods / Chromosomes / Cloning / Consensus / consensus sequence / Councils / diversity array technology / Fatty acids / gene locus / Gene mapping / Genes / Genetic aspects / Genetic diversity / Genetic improvement / Genetic Linkage / Genetic markers / genetic procedures / Genetic testing / genetic trait / genetic variability / Genetic Variation / Genome, Plant / Genomes / Genomics / genotype / Genotyping Techniques / Genotyping Techniques - methods / Life Sciences / Male sterility / microarray analysis / Microarrays / Microbial Genetics and Genomics / molecular cloning / Molecular genetics / plant genetics / Plant Genetics and Genomics / Plant genomics / Population / Proteomics / qualitative analysis / quantitative genetics / Quantitative Trait Loci / quantitative trait locus / quantitative trait locus mapping / R&D / Rape (Plant) / rapeseed / Research & development / Research Article / sequence homology / single nucleotide polymorphism