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Open Access Research article

A first generation whole genome RH map of the river buffalo with comparison to domestic cattle

M Elisabete J Amaral111*, Jason R Grant2, Penny K Riggs3, Nedenia B Stafuzza1, Edson A Rodrigues Filho1, Tom Goldammer4, Rosemarie Weikard4, Ronald M Brunner4, Kelli J Kochan3, Anthony J Greco3, Jooha Jeong3, Zhipeng Cai5, Guohui Lin5, Aparna Prasad2, Satish Kumar6, G Pardha Saradhi6, Boby Mathew6, M Aravind Kumar6, Melissa N Miziara6, Paola Mariani7, Alexandre R Caetano89, Stephan R Galvão89, Madhu S Tantia10, Ramesh K Vijh10, Bina Mishra10, ST Bharani Kumar10, Vanderlei A Pelai1, Andre M Santana1, Larissa C Fornitano1, Brittany C Jones11, Humberto Tonhati12, Stephen Moore2, Paul Stothard2 and James E Womack11

Author Affiliations

1 Department of Biologia, UNESP – São Paulo State University, IBILCE, São Jose Rio Preto, SP, Brazil

2 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada

3 Department of Animal Science, Texas A&M University, College Station, TX, USA

4 Forschungsbereich Molekularbiologie, Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere (FBN), Dummerstorf, Germany

5 Departament of Computing Science, University of Alberta, Edmonton, AB, Canada

6 Centre for Cellular and Molecular Biology, Hyderabad, India

7 Parco Tecnologico Padano, Via Einstein, Polo Universitario, Lodi, Italy

8 Embrapa Recursos Geneticos e Biotecnologia, Parque Estacao Biologica, Brasilia, DF, Brazil

9 Programa de Pos Graduacao em Ciencias Animais, Universidade de Brasilia, Brasilia, DF, Brazil

10 National Bureau of Animal Genetic Resources, Karnal, India

11 Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA

12 Department of Animal Sciences, UNESP – São Paulo State University, FCAV, Jaboticabal, SP, Brazil

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BMC Genomics 2008, 9:631  doi:10.1186/1471-2164-9-631

Published: 24 December 2008

Abstract

Background

The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species.

Results

A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD ≥ 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score ≥ 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0).

Conclusion

We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.