Construction of Bovine Whole-genome Radiation Hybrid and Linkage Maps Using High-throughput Genotyping

Overview

Journal Anim Genet

Specialties Biology
Genetics

Date 2007 Feb 17

PMID 17302794

Citations 24

Authors

S D McKay

R D Schnabel

B M Murdoch

J Aerts

C A Gill

C Gao

C Li

L K Matukumalli

P Stothard

Z Wang

C P Van Tassell

J L Williams

J F Taylor

S S Moore

Affiliations

Soon will be listed here.

Abstract

High-density whole-genome maps are essential for ordering genes or markers and aid in the assembly of genome sequence. To increase the density of markers on the bovine radiation hybrid map, and hence contribute to the assembly of the bovine genome sequence, an Illumina BeadStation was used to simultaneously type large numbers of markers on the Roslin-Cambridge 3000 rad bovine-hamster whole-genome radiation hybrid panel (WGRH3000). In five multiplex reactions, 6738 sequence tagged site (STS) markers were successfully typed on the WGRH3000 panel DNA. These STSs harboured SNPs that were developed as a result of the bovine genome sequencing initiative. Typically, the most time consuming and expensive part of creating high-density radiation hybrid (RH) maps is genotyping the markers on the RH panel with conventional approaches. Using the method described in this article, we have developed a high-density whole-genome RH map with 4690 loci and a linkage map with 2701 loci, with direct comparison to the bovine whole-genome sequence assembly (Btau_2.0) in a fraction of the time it would have taken with conventional typing and genotyping methods.

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References

Mellersh C, Hitte C, Richman M, Vignaux F, Priat C, Jouquand S . An integrated linkage-radiation hybrid map of the canine genome. Mamm Genome. 2000; 11(2):120-30. DOI: 10.1007/s003350010024. View

Rexroad 3rd C, Owens E, Johnson J, Womack J . A 12,000 rad whole genome radiation hybrid panel for high resolution mapping in cattle: characterization of the centromeric end of chromosome 1. Anim Genet. 2000; 31(4):262-5. DOI: 10.1046/j.1365-2052.2000.00641.x. View

Oliphant A, Barker D, Stuelpnagel J, Chee M . BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques. 2002; Suppl:56-8, 60-1. View

Williams J, Eggen A, Ferretti L, Farr C, Gautier M, Amati G . A bovine whole-genome radiation hybrid panel and outline map. Mamm Genome. 2002; 13(8):469-74. DOI: 10.1007/s00335-002-3001-x. View

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

Morsci N, Schnabel R, Taylor J . Association analysis of adiponectin and somatostatin polymorphisms on BTA1 with growth and carcass traits in Angus cattle. Anim Genet. 2006; 37(6):554-62. DOI: 10.1111/j.1365-2052.2006.01528.x. View

Schiex T, Gaspin C . CARTHAGENE: constructing and joining maximum likelihood genetic maps. Proc Int Conf Intell Syst Mol Biol. 1997; 5:258-67. View

Womack J, Johnson J, Owens E, Rexroad 3rd C, Schlapfer J, Yang Y . A whole-genome radiation hybrid panel for bovine gene mapping. Mamm Genome. 1997; 8(11):854-6. DOI: 10.1007/s003359900593. View

Itoh T, Watanabe T, Ihara N, Mariani P, Beattie C, Sugimoto Y . A comprehensive radiation hybrid map of the bovine genome comprising 5593 loci. Genomics. 2005; 85(4):413-24. DOI: 10.1016/j.ygeno.2004.12.007. View

10.

Murphy W, Larkin D, Everts-van der Wind A, Bourque G, Tesler G, Auvil L . Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science. 2005; 309(5734):613-7. DOI: 10.1126/science.1111387. View

11.

Margulies M, Egholm M, Altman W, Attiya S, Bader J, Bemben L . Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005; 437(7057):376-80. PMC: 1464427. DOI: 10.1038/nature03959. View

12.

Lange K, Boehnke M, Cox D, Lunetta K . Statistical methods for polyploid radiation hybrid mapping. Genome Res. 1995; 5(2):136-50. DOI: 10.1101/gr.5.2.136. View