Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley

Buetow KH, Edmonson MN, and Cassidy AB (1999) Reliable identification of large numbers of candidate SNPs from public EST data. Nat Genet 21: 323–325. Chen X, Levine L, and Kwok PY (1999) Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res 9: 492–498. Ching ADA, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, and Rafalski A (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3: 19. Clemson University Genomics Institute. Barley EST Project. 18 June 2003 <http://www. genome.clemson.edu/projects/barley>. Douabin-Gicquel V, Soriano N, Ferran H, Wojcik F, Palierne E, Tamin S, Jovelin T, McKei AT, Le Gall JY, David V, and Mosser J (2001) Identification of 96 single nucleotide polymorphisms in eight genes involved in iron metabolism: efficiency of bioinformatic extraction compared with a systematic sequencing approach. Human Genet 109: 393–401. Giesendorf BA, Tyagi VS, Mensink EJ, Trijbels FJ, and Bloom HJ (1998) Molecular beacons: a new approach for semi-automated mutation analysis. Clin Chem 44: 482–486. Grossman PD, Bloch W, Brinson E, Chang CC, Eggerding FA, Fung S, Iovannisci DM, Woo S, Winn-Deen ES, and Iovannisci DA. (1994) High-density multiplex detection of nucleic acid sequences: oligonucleotide ligation assay and sequence-coded separation. Nucl Acids Res 22: 4527–4534. Halushka MK, Fan JB, Bently K, Hsie L, Shen N, Weder A, Cooper R, Lipshutz R, and Chakravarti, A (1999) Patterns of single nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 22: 239–247. Hamajima N (2001) PCR-CTPP: a new genotyping technique in the era of genetic epidemiology. Expert Rev Mol Diagn 1: 119–123. Holliday R and Grigg WG (1993) DNA methylation mutation. Mutation Res 285: 61–67. Karhukorpi J and Karttunen R (2001) Genotyping interleukin-10 high and low producers with single-tube bi-directional allele-specific amplification. Exp Clin Immunogenet 18: 67–70. Lindblad-Toh K, Winchester E, Daly MJ, Wang DG, Hirschhorn JN, Laviolette J-P, Ardlie K, Reich DE, Robinson E, Sklar P, and others (2000) Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat Genet 24: 381–386. Liu Q, Thorland EC, Heit JA, and Sommers SS (1997) Overlapping PCR for bidirectional PCR amplification of specific alleles: A rapid one-tube method for simultaneously differentiating homozygotes and heterozygotes. Genome Res 7: 389–398. Montana State University. Barley SNP Markers by Chromosome Web site. 18 June 2003 <http://hordeum.oscs.montana.edu/locus/index.html>. National Centre for Biotechnology Information. Expressed Sequence Tags Database Web site. 18 June 2003 <http://www.ncbi.nlm.nih.gov/dbEST/index.html>. Richard I and Beckman JS (1995) How neutral are synonymous codon mutations? Nat Genet 10: 259. Ross P, Hall L, Smirnov I, and Haff L (1998) High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat Biotechnol 16: 1347–1351. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, and others (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928–933. Sanger F, Nicklen S, and Coulson AR (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74: 5463–5467 Soleimani VD, Baum BR, and Johnson DA (2002) Identification of Canadian durum wheat [Triticum turgidum L. subsp. durum (Desf) Husn.] cultivars using AFLP and their STS markers. Can J Plant Sci 82: 35–41. Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, and Bork P (1999) Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes. J Mol Med 77: 754–760. Ye S, Humphries S, and Green F (1992) Allele specific amplification by tetra-primer PCR. Nucl Acids Res 20: 1152.