Abstract
We have investigated the use of AFLP® technology as a tool for the high throughput enrichment of Radiation Hybrid (RH) maps. The 3000 rad TM112 bovine RH panel was assayed with 37 EcoRI/TaqI AFLP primer combinations. The number of selective nucleotides used during PCR was increased to seven, to reduce the complexity of the AFLP profile and minimise the overlap between hamster and bovine bands co-amplified from hybrid cell clones. Seven-hundred-forty-seven bovine AFLP bands were amplified that could be distinguished following electrophoresis. Repeatability was tested within and between laboratories on independent template preparations and an error rate of 1.3% found. Two-point linkage analysis clustered 428 AFLP fragments in 39 linkage groups of at least 4 markers. Multi-point maps were constructed for 5 sample linkage groups. The study demonstrated that the AFLP approach could be used to rapidly screen for the most informative clones during panel construction and to increase the number of markers on RH maps, which could be useful for joining linkage groups formed by other markers. The use of AFLP markers as anchor points between existing RH maps and other physical maps, such as BAC contigs, is also discussed.
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References
Ajmone-Marsan P, Valentini A, Cassandro M, Vecchiotti-Antaldi G, Bertoni G, Kuiper M (1997) AFLP markers for DNA fingerprinting in cattle. Anim Genet 28: 418-426.
Chowdhary BP, Raudsepp T, Honeycutt D et al. (2002) Construction of a 5000(rad) whole-genome radiation hybrid panel in the horse and generation of a comprehensive and comparative map for ECA11. Mamm Genome 13: 89-94.
Geisler R, Rauch GJ, Baier H et al. (1999) A radiation hybrid map of the zebrafish genome. Nat Genet 23: 86-89.
Gort G (2003) Statistical properties of AFLP. Theme Conference of the Royal Statistical Society, Statistical genetics and bioinformatics, Limburgs Universitair Centrum, Hasselt-Diepenbeek, Belgium.
Gyapay G, Schmit TK, Fizames C et al. (1996) A radiation hybrid map of the human genome. Hum Mol Genet 5: 339-346.
Hudson TJ, Stein LD, Gerety SS et al. (1995) An STS-based map of the human genome. Science 270: 1945-1954.
Klein PE, Klein RR, Cartinhour SW et al. (2000) A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map. Genome Res 10: 789-807.
McCarthy LC, Terrett J, Davis ME et al. (1997) A first-generation whole genome-radiation hybrid map spanning the mouse genome. Genome Res 7: 1153-1161.
Morisson M, Lemiere A, Bosc S et al. (2002) ChickRH6: a chicken whole-genome radiation hybrid panel. Genet Sel Evol 34: 521-533.
Priat C, Hitte C, Vignaux F et al. (1998) A whole-genome radiation hybrid map of the dog genome. Genomics 54: 361-378.
Rexroad CE 3rd, Owens EK, Johnson JS, Womack JE (2000) 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 31: 262-265.
Schiex T, Chabrier P, Bouchez M, Milan D (2001) Boosting EM for Radiation Hybrid and Genetic mapping. Proceedings of WABI (First Workshop on Algorithms in Bioinformatics), LNCS 2149.
Schlapfer J, Stahlberger-Saitbekova N, Comincini S et al. (2002) A higher resolution radiation hybrid map of bovine chromosome 13. Genet Sel Evol 34: 255-267.
Vos P, Hogers R, Bleeker M et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414.
Walter MA, Spillett DJ, Thomas P, Weissenbach J, Goodfellow PN (1994) A method for constructing radiation hybrid maps of whole genomes. Nat Genet 7: 22-28.
Watanabe TK, Bihoreau MT, McCarthy LC et al. (1999) A radiation hybrid map of the rat genome containing 5255 markers. Nat Genet 22: 27-36.
Weikard R, Kuhn C, Goldammer T, Laurent P, Womack JE, Schwerin M (2002) Targeted construction of a high-resolution, integrated, comprehensive, and comparative map for a region specific to bovine chromosome 6 based on radiation hybrid mapping. Genomics 79: 768-776.
Williams JL, Eggen A, Ferretti L et al. (2000) Development of a bovine whole genome radiation hybrid panel map for comparative mapping across species and the identification of positional candidate genes for genetically mapped traits. ISAG congress, abstract #A017.
Williams JL, Eggen A, Ferretti L et al. (2002) A bovine whole-genome radiation hybrid panel and outline map. Mamm Genome 13: 469-474.
Womack JE, Johnson JS, Owens EK, Rexroad CE 3rd, Schlapfer J, Yang YP (1997) A whole-genome radiation hybrid panel for bovine gene mapping. Mamm Genome 8: 854-856.
Yerle M, Pinton P, Robic A et al. (1998) Construction of a whole-genome radiation hybrid panel for high-resolution gene mapping in pigs. Cytogenet Cell Genet 82: 182-188.
Zabeau M, Vos P (1993) Selective restriction amplification: A general method for DNA fingerprinting. European Patent 0 534 858.
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Gorni, C., Williams, J.L., Heuven, H.C.M. et al. Application of AFLP® technology to radiation hybrid mapping. Chromosome Res 12, 285–297 (2004). https://doi.org/10.1023/B:CHRO.0000021912.22552.ff
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DOI: https://doi.org/10.1023/B:CHRO.0000021912.22552.ff