MINING SINGLE NUCLEOTIDE POLYMORPHISM FROM PUBLICLY AVAILABLE ESTS OF BREAD WHEAT (TRITICUM AESTIVUM L.)
Keywords:
Wheat (Triticum aestivum), SNPs, SOLiD-SAGE, ESTs, Leaf rustAbstract
Objective: The present study was undertaken to discover Single Nucleotide Polymorphisms (SNPs) in bread wheat with reference to leaf rust disease.
Methods: Next Generation Sequencing platform sequencing by Oligonucleotide Ligation and Detection (SOLiD) was performed on four Serial Analysis of Gene Expression (SAGE) libraries of mock and leaf rust pathogen infected near-isogenic lines HD2329±Lr28. CLC Genomics Workbench was used for computational prediction of the SNPs. The predicted SNPs were filtered by Blast using wheat Expressed Sequence Tags (ESTs). The SNP-containing ESTs were annotated, and their expression was checked in response to inoculation of Puccinia triticina.
Results: We have identified 191 SNPs from data obtained through the These EST-SNPs participated in various physiological and biochemical processes that influence important traits, such as cell rescue, defense and disease resistance.
Conclusion: Very little knowledge exists on SNPs in hexaploid bread wheat (Triticum aestivum L.) because of the difficulty to discern the true polymorphic loci. This study has revealed fast and costs effective approach for SNP discovery which will be helpful in molecular breeding with important agronomic traits.
Â
Downloads
References
Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL. Arabidopsis map-based cloning in the post-genome era. Plant Physiol 2002;129:440–50.
Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J, et al. Single-feature polymorphism discovery in the barley transcriptome. Genome Biol 2005;6:R54.
Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, et al. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 2002;3:19.
Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, et al. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 2004;135:1198–205.
McNally KL, Bruskiewich R, Mackill D, Buell CR, Leach JE, Leung H. Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol 2006;141:26–31.
Zhu YL, Song QJ, Hyten DL, Van, Tassell CP, Matukumalli LK, Grimm DR, et al. Single-nucleotide polymorphisms in soybean. Genetics 2003;163:1123–34.
Ablett G, Hill H, Henry RJ. Sequence polymorphism discovery in wheat microsatellite flanking regions using pyrophosphate sequencing. Mol Breed 2006;17:281–9.
Ravel C, Praud S, Murigneux A, Canaguier A, Sapet F, Samson D, et al. Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genome 2006;49:1131–9.
Bundock PC, Cross MJ, Shapter FM, Henry RJ. Robust allele-specific polymerase chain reaction markers developed for single nucleotide polymorphisms in expressed barley sequences. Theor Appl Genet 2006;112:358–65.
Somers DJ, Kirkpatrick R, Moniwa M, Walsh A. Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 2003;46:431–7.
Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, et al. A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 2007;176:685–96.
Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, et al. Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics 2005;274:515–27.
Grivet L, Glaszmann JC, Arruda P. Sequence polymorphism from EST data in sugarcane: a fine analysis of 6-phosphogluconate dehydrogenase genes. Genet Mol Biol 2001;24:161–7.
Grivet L, Glaszmann JC, Vincentz M, da Silva F, Arruda P. ESTs as a source for sequence polymorphism discovery in sugarcane: an example of the Adh genes. Theor Appl Genet 2003;106:190–7.
Cordeiro GM, Eliott F, McIntyre CL, Casu RE, Henry RJ. Characterisation of single nucleotide polymorphisms in sugarcane ESTs. Theor Appl Genet 2006;113:331–43.
Longeri M, Zanotti M, Damiani G. Recombinant DRB sequences produced by mismatch repair of heteroduplexes during cloning in Escherichia coli. Eur J Immunogenet 2002;29:517-23.
Dubcovsky J, Dvorak J. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 2007;316:1862–6.
Haudry A, Cenci A, Ravel C, Bataillon T, Brunel D, Poncet C, et al. Grinding up wheat: a massive loss of nucleotide diversity since domestication. Mol Biol Evol 2007;24:1506–17.
Singh D, Bhaganagare G, Bandopadhyay R, Prabhu KV, Gupta PK, Mukhopadhyay K. Targeted spatio-temporal expression based characterization of state of infection and time-point of maximum defense in wheat NILs during leaf rust infection. Mol Biol Rep 2012;39:9373-82.
Altshuler D, Pollara VJ, Cowles CR, Etten WJV, Baldwin J, Linton L, et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 2000;407:513-6.
Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, et al. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008;18:763-70.
Conesa A, Götz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005;21:3674-6.
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Statistical Society: Series B 1995;57:289–300.
Kal AJ, van Zonneveld AJ, Benes V, den Berg MV, Koerkamp MG, Albermann K, et al. Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Mol Biol Cell 1999;10:1859-72.
Ganal MW, Altmann T, Roder MS. SNP identification in crop plants. Curr Opin Plant Biol 2009;12:211-7.
Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, Corneveaux JJ, et al. Identification of genetic variants using barcoded multiplexed sequencing. Nat Methods 2008;5:887-93.
Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, et al. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 2008;5:247-52.
Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 2013;496:91–5.
Fofana B, Banks TW, McCallum B, Strelkov SE, Cloutier S. Temporal gene expression profiling of the wheat leaf rust pathosystem using cDNA microarray reveals differences in compatible and incompatible defence pathways. Int. J. Plant Genomics 2007. doi: 10.1155/2007/17542. [Article in Press].