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

被引：75

作者：

Amaral, M. Elisabete J. ^{[1
,5
]}

Grant, Jason R. ^{[3
]}

Riggs, Penny K. ^{[4
]}

Stafuzza, Nedenia B. ^{[1
]}

Rodrigues Filho, Edson A. ^{[1
]}

Goldammer, Tom ^{[8
]}

Weikard, Rosemarie ^{[8
]}

Brunner, Ronald M. ^{[8
]}

Kochan, Kelli J. ^{[4
]}

Greco, Anthony J. ^{[4
]}

Jeong, Jooha ^{[4
]}

Cai, Zhipeng ^{[6
]}

Lin, Guohui ^{[6
]}

Prasad, Aparna ^{[3
]}

Kumar, Satish ^{[9
]}

Saradhi, G. Pardha ^{[9
]}

Mathew, Boby ^{[9
]}

Kumar, M. Aravind ^{[9
]}

Miziara, Melissa N. ^{[9
]}

Mariani, Paola ^{[12
]}

Caetano, Alexandre R. ^{[10
,11
]}

Galvao, Stephan R. ^{[10
,11
]}

Tantia, Madhu S. ^{[7
]}

Vijh, Ramesh K. ^{[7
]}

Mishra, Bina ^{[7
]}

Kumar, S. T. Bharani ^{[7
]}

Pelai, Vanderlei A. ^{[1
]}

Santana, Andre M. ^{[1
]}

Fornitano, Larissa C. ^{[1
]}

Jones, Brittany C. ^{[5
]}

Tonhati, Humberto ^{[2
]}

Moore, Stephen ^{[3
]}

Stothard, Paul ^{[3
]}

Womack, James E. ^{[5
]}

机构：

[1] UNESP Sao Paulo State Univ, Dept Biol, IBILCE, Sao Jose Do Rio Preto, SP, Brazil

[2] UNESP Sao Paulo State Univ, Dept Anim Sci, FCAV, Jaboticabal, SP, Brazil

[3] Univ Alberta, Dept Agr Food & Nutr Sci, Edmonton, AB, Canada

[4] Texas A&M Univ, Dept Anim Sci, College Stn, TX 77843 USA

[5] Texas A&M Univ, Dept Vet Pathobiol, College Stn, TX 77843 USA

[6] Univ Alberta, Dept Comp Sci, Edmonton, AB, Canada

[7] Natl Bur Anim Genet Resources, Karnal, Haryana, India

[8] Forschungsinst Biol Landwirtschaftlicher Nutztier, Forsch Bereich Mol Biol, Dummerstorf, Germany

[9] Ctr Cellular & Mol Biol, Hyderabad 500007, Andhra Pradesh, India

[10] Univ Brasilia, Programa Pos Grad Ciencias Animais, Brasilia, DF, Brazil

[11] Embrapa Recursos Genet & Biotecnol, Brasilia, DF, Brazil

[12] Polo Univ, Lodi, Italy

来源：

BMC GENOMICS | 2008年 / 9卷 / 1期

基金：

巴西圣保罗研究基金会;

关键词：

D O I：

10.1186/1471-2164-9-631

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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 cR(5000). 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.

引用

页数：11

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