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Open Access Highly Accessed Research article

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

Harsh Raman1*, Rosy Raman1, Andrzej Kilian2, Frank Detering2, Yan Long3, David Edwards4, Isobel AP Parkin5, Andrew G Sharpe6, Matthew N Nelson78, Nick Larkan5, Jun Zou3, Jinling Meng3, M Naveed Aslam7, Jacqueline Batley4, Wallace A Cowling8 and Derek Lydiate5

Author Affiliations

1 EH Graham Centre for Agricultural Innovation (an alliance between NSWDPI and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia

2 Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, Yarralumla, Canberra, ACT 2600, Australia

3 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China

4 School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia

5 Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada

6 DNA Technologies Laboratory, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0X2, Canada

7 School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia

8 The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia

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BMC Genomics 2013, 14:277  doi:10.1186/1471-2164-14-277

Published: 23 April 2013

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.