BMC Genomics (Dec 2008)

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

  • Tantia Madhu S,
  • Galvão Stephan R,
  • Caetano Alexandre R,
  • Mariani Paola,
  • Miziara Melissa N,
  • Kumar M Aravind,
  • Mathew Boby,
  • Saradhi G Pardha,
  • Kumar Satish,
  • Prasad Aparna,
  • Lin Guohui,
  • Cai Zhipeng,
  • Jeong Jooha,
  • Greco Anthony J,
  • Kochan Kelli J,
  • Brunner Ronald M,
  • Weikard Rosemarie,
  • Goldammer Tom,
  • Filho Edson,
  • Stafuzza Nedenia B,
  • Riggs Penny K,
  • Grant Jason R,
  • Amaral M Elisabete J,
  • Vijh Ramesh K,
  • Mishra Bina,
  • Kumar ST Bharani,
  • Pelai Vanderlei A,
  • Santana Andre M,
  • Fornitano Larissa C,
  • Jones Brittany C,
  • Tonhati Humberto,
  • Moore Stephen,
  • Stothard Paul,
  • Womack James E

DOI
https://doi.org/10.1186/1471-2164-9-631
Journal volume & issue
Vol. 9, no. 1
p. 631

Abstract

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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.