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Open Access Highly Accessed Research article

Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa

Jun Wang14, Derek J Lydiate2, Isobel AP Parkin2, Cyril Falentin3, Régine Delourme3, Pierre WC Carion1 and Graham J King15*

Author affiliations

1 Department of Plant Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK

2 Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada

3 UMR 118 Amélioration des Plantes et Biotechnologies Végétales, INRA, BP 35327, 35653 Le Rheu Cedex, France

4 Centre for Haemato-Oncology, Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Charterhouse Square, London, EC1 M 6BQ, UK

5 Southern Cross Plant Sciences, Southern Cross University, Lismore, NSW 2480, Australia

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Citation and License

BMC Genomics 2011, 12:101  doi:10.1186/1471-2164-12-101

Published: 9 February 2011

Abstract

Background

The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available.

Results

We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa.

Conclusions

Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.