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

Published: 9 February 2011

Additional files

Additional file 1:

Comparison of marker orders between the three population-specific consolidated maps, generated by MapChart 2.1.

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Additional file 2:

The BnaWAIT_01_2010a integrated map (by JoinMap) generated by MapChart 2.1.

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Additional file 3:

All the information of high-scoring segement pairs (HSP) of canonical markers against Arabidopsis gene models, Arabidopsis chromosomes and B. rapa sequenced BACs. The information of the BnaWAIT_10_2010a BnaWAIT map and markers aligned with Arabidopsis genes and chromosomes are also shown, so are the skeleton maps of each population.

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Additional file 4:

Dot-plots between the BnaWAIT map and all three population-specific maps for the remainder of all 19 LGs. The marker order of the vertical axis is from the BnaWAIT_01_2010a integrated map, and three marker orders of the horizontal axis are for the three population-specific maps.

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Additional file 5:

Integrated skeleton maps of representative markers generated by JoinMap 4.0 Round 1 and Round 2 under the algorithm of regression. The number of excluded representative markers from the map integration in these two rounds is reported. Spearman's rank correlation coefficients (r) between the two integrated maps (map1 and map2) and the three population-specific maps (BnaSNDH, BnaSGDH and BnaDYDH) are also shown.

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Additional file 6:

Number of different sets of canonical marker assays using in the B. napus mapping, number of marker assays that show homology with Arabidopsis and number of homology regions in Arabidopsis with similarity to Brassica canonical marker assays.

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Additional file 7:

Summary of conserved collinearity blocks between the B. napus integrated map BnaWAIT_01_2010a and the Arabidopsis genome sequence.

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Additional file 8:

Description of mapping populations and genetic markers used in the map integration study, which are maintained in CropStoreDB. Corresponding references are also shown if available.

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Additional file 9:

Diagram of database interaction facilitating the map integration process and establishing links between genetic maps to DNA sequence information (e.g., TAIR9 genome or B. rapa BACs) via sequence-tagged marker sequences. CropStoreDB is used to manage data relating to Brassica genetics, including populations, genetic maps, genetic markers and their positions. SeqStoreDB is used to manage all publicly available Brassica sequences together with sequence data from private sources. AlignStoreDB is used to manage all the homology alignments between query Brassica sequences and target genomic or BAC sequences.

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