Single nucleotide polymorphism discovery in barley using autoSNPdb

Plant Biotechnology Journal

Volumn 7, Issue 4, 2009, Pages 326-333

  Duran, Chris ^a   Appleby, Nikki ^a   Vardy, Megan ^a   Imelfort, Michael ^a   Edwards, David ^a   Batley, Jacqueline ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

AutoSNPdb; Barley; Expressed sequence tag (EST); Genetic variation; In silico; Single nucleotide polymorphism (SNP)

Indexed keywords

PLANT DNA;

ARTICLE; BARLEY; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC DATABASE; GENETIC MARKER; GENETICS; INTERNET; METHODOLOGY; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

DATABASES, GENETIC; DNA, PLANT; GENETIC MARKERS; HORDEUM; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

HORDEUM;

EID: 64749116576     PISSN: 14677644     EISSN: 14677652     Source Type: Journal    
DOI: 10.1111/j.1467-7652.2009.00407.x     Document Type: Article

References (23)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403 410.
2. Barker, G., Batley, J., O'Sullivan, H., Edwards, K.J. Edwards, D. (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics, 19, 421 422.
3. Batley, J., Barker, G., O'Sullivan, H., Edwards, K.J. Edwards, D. (2003a) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol. 132, 84 91.
4. Batley, J., Mogg, R., Edwards, D., O'Sullivan, H. Edwards, K.J. (2003b) A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. Mol Breed. 11, 111 120.
5. Bundock, P.C. Henry, R.J. (2004) Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley. Theor. Appl. Genet. 109, 543 551.
6. Bundock, P.C., Christopher, J.T., Eggler, P., Ablett, G., Henry, R.J. Holton, T.A. (2003) Single nucleotide polymorphisms in cytochrome P450 genes from barley. Theor. Appl. Genet. 106, 676 682.
7. Coulondre, C., Miller, J.H., Farabaugh, P.J. Gilbert, W. (1978) Molecular basis of base substitution hot spots in Escherichia coli. Nature, 274, 775 780.
8. Davierwala, A.P., Ramakrishna, W., Ranejekar, P.K. Gupta, V.S. (2000) Sequence variations at a complex microsatellite locus in rice and its conservation in cereals. Theor. Appl. Genet. 215, 1291 1298.
9. Deutsch, S., Iseli, C., Bucher, P., Antonarakis, S.E. Scott, H.S. (2001) A cSNP map and database for human chromosome 21. Genome Res. 11, 300 307.
10. Duran, C., Appleby, N., Clark, T., Wood, D., Imelfort, M., Batley, J. Edwards, D. (2009) AutoSNPdb, an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res. 37, 951 953.
11. Ewing, B. Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186 194.
12. Ewing, B., Hillier, L., Wendl, M.C. Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175 185.
13. Garg, K., Green, P. Nickerson, D.A. (1999) Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags. Genome Res. 9, 1087 1092.
14. Gupta, P.K., Roy, J.K. Prasad, M. (2001) Single nucleotide polymorphisms, A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr. Sci. 80, 524 535.
15. Huang, X.Q. Madan, A. (1999) cap3, a DNA sequence assembly program. Genome Res. 9, 868 877.
16. Kota, R., Varshney, R.K., Prasad, M., Zhang, H., Stein, N. Graner, A. (2008) EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome. Funct. Integr. Genomics, 8, 223 233.
17. Marth, G.T., Korf, I., Yandell, M.D., Yeh, R.T., Gu, Z.J., Zakeri, H., Stitziel, N.O., Hillier, L., Kwok, P.Y. Gish, W.R. (1999) A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23, 452 456.
18. Mogg, R., Batley, J., Hanley, S., Edwards, D., O'Sullivan, H. Edwards, K.J. (2002) Characterisation of the flanking regions of Zea mays microsatellites reveals a large number of useful sequence polymorphisms. Theor. Appl. Genet. 105, 532 543.
19. Picoult-Newberg, L., Ideker, T.E., Pohl, M.G., Taylor, S.L., Donaldson, M.A., Nickerson, D.A. Boyce-Jacino, M. (1999) Milling SNPs from EST databases. Genome Res. 9, 167 174.
20. Robinson, A.J., Love, C.G., Batley, J., Barker, G. Edwards, D. (2004) Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics, 20, 1475 1476.
21. Rostoks, N., Mudie, S., Cardle, L., Russell, J., Ramsay, L., Booth, A., Svensson, J.T., Wanamaker, S.I., Walia, H., Rodriguez, E.M., Hedley, P.E., Liu, H., Morris, J., Close, T.J., Marshall, D.F. Waugh, R. (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol. Genet. Genomics, 274, 515 527.
22. Syvanen, A.C. (2001) Accessing genetic variation. Genotyping single nucleotide polymorphisms. Nat. Rev. Genet. 2, 930 942.
23. Thorisson, G.A., Smith, A.V., Krishnan, L. Stein, L.D. (2005) The International Hapmap Project web site. Genome Res. 15, 1592 1593.