Information de reference pour ce titreAccession Number: | 01041750-200306000-00011.
|
Author: | Somers, Daryl J; Kirkpatrick, Robert; Moniwa, Mariko; Walsh, Andrew
|
Title: | Mining single-nucleotide polymorphisms from hexaploid wheat ESTs.[Article]
|
Source: | Genome. 46(3):431-437, June 2003.
|
Abstract: | Single-nucleotide polymorphisms (SNPs) represent a new form of functional marker, particularly when they are derived from expressed sequence tags (ESTs). A bioinformatics strategy was developed to discover SNPs within a large wheat EST database and to demonstrate the utility of SNPs in genetic mapping and genetic diversity applications. A collection of >90 000 wheat ESTs was assembled into contiguous sequences (contigs), and 45 random contigs were then visually inspected to identify primer pairs capable of amplifying specific alleles. We estimate that homoeologue sequence variants occurred 1 in 24 bp and the frequency of SNPs between wheat genotypes was 1 SNP/540 bp ([theta] = 0.0069). Furthermore, we estimate that one diagnostic SNP test can be developed from every contig with 10-60 EST members. Thus, EST databases are an abundant source of SNP markers. Polymorphism information content for SNPs ranged from 0.04 to 0.50 and ESTs could be mapped into a framework of microsatellite markers using segregating populations. The results showed that SNPs in wheat can be discovered in ESTs, validated, and be applied to conventional genetic studies.
(C) 2003 National Research Council Canada
|
Author Keywords: | SNP; bioinformatics; EST; genetic mapping; SNP; bio-informatique; EST; cartographie genetique.
|
References: | Bhattramakki, D., Dolan, M., Hanafey, M., Wineland, R., Vaske, D., Register, J.C., Tingey, S.V., and Rafalski, A. 2002. Insertion-deletion polymorphisms in 3' regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol. Biol. 48: 539-547.
Chao, S., Sharp, P.J., Worland, A.J., Warham, E.J., Koebner, R.M.D., and Gale, M.D. 1989. RFLP-based genetic maps of wheat homoeologous group 7 chromosomes. Theor. Appl. Genet. 78: 495-504.
Endo, T.R., and Gill, B.S. 1996. The deletion stocks of common wheat. J. Hered. 87: 295-307.
Gao, X., LeProust, E., Zhang, H., Srivannavit, O., Gulari, E., Yu, P., Nishiguchi, C., Xiang, Q., and Zhou, X. 2001. A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids. Nucleic Acids Res. 29: 4744-4750.
Gerry, N.P., Witowski, N.E., Day, J., Hammer, R.P., Barany, G., and Barany, F. 1999. Universal DNA microarray method for multiplex detection of low abundance point mutations. J. Mol. Biol. 293: 251-262.
Halushka, M.K., Fan, J.B., Bentley, 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.
Hohmann, U., Endo, T.R., Herrmann, R.G., and Gill, B.S. 1995. Characterization of deletions in common wheat induced by an Aegilops cylindrica chromosome: detection of multiple chromosome rearrangements. Theor. Appl. Genet. 91: 611-617.
Huang, X., and Madan, A. 1999. CAP3: a DNA assembly program. Genome Res. 9: 868-877.
Kanazin, V., Talbert, H., See, D., DeCamp, P., Nevo, E., and Blake, T. 2002. Discovery and assay of single-nucleotide poly morphisms in barley (Hordeum vulgare). Plant Mol. Biol. 48: 529-537.
Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daley, M.J., Lincoln, S.E., and Newburg, L. 1987. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1: 174-181.
Marth, G.T., Korf, I., Yandell, M.D., Yeh, R.T., Gu, Z., Zakeri, H., Stitziel, N.O., Hillier, L., Kwok, P.Y., and Gish, W.R. 1999. A general approach to single nucleotide polymorphism discovery. Nat. Genet. 23: 452-456.
Pestsova, E., Ganal, M.W., and Roder, M.S. 2000. Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome, 43: 689-697.
Picoult-Newberg, L., Ideker, T.E., Pohl, M.G., Taylor, S.L., Donaldson, M.A., Nickerson, D.A., and Boyce, J.M. 1999. Mining SNPs for EST databases. Genome Res. 9: 167-174.
Prindahl, H., Wilkman, F.P., von der Masse, H., Zhou, X.G., Wolf, H., and Orntoft, T.F. 2002. Allelic imbalances in human bladder cancers: genome-wide detection with high density single nucleotide polymorphism arrays. J. Natl. Cancer Inst. 94: 216-223.
Rafalski, A. 2002. Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci. 162: 329-333.
Remington, D.L., Thornsberry, J.M., Matsuoka, Y., Wilson, L.M., Whitt, S.R., Doebley, J., Kresovich, S., Goodman, M.M., and Buckler, E.S. 2001. Structure of linkage disequilibrium and pheno typic associations in the maize genome. Proc. Natl. Acad. Sci. U.S.A. 98: 11 479 - 11 484.
Roder, M.S., Korzun, V., Wendehake, K., Plaschke, J., Tixier, M.-H., Leroy, P., and Ganal, M.W. 1998. A microsatellite map of wheat. Genetics, 149: 2007-2023.
Tenaillon, M.I., Swakins, M.C., Long, A.D., Gaut, R.L., Doebley, J.F., and Gaut, B.S. 2001. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. U.S.A. 98: 9161-9166.
Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., and Zabeau, M. 1995. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407-4414.
|
Language: | English.
|
Document Type: | Article: PDF Only.
|
Journal Subset: | Life Sciences.
|
ISSN: | 1480-3321
|
Annotation(s) | |
|
|