Bioinformatic Prediction of SNP Markers in WRKY Sequences of Palms
Keywords:
SNP, Arecaceae, Cocos nucifera, WRKY
Abstract
WRKY transcription factors are unique to plants and performs many imperative functions mainly disease resistance. In the present study we have analyzed the WRKY transcription factor gene sequences to assess the variation at single nucleotide level. We have retrieved 525 sequences of WRKY genes of palms of 334 Kb size. The sequences were purified by employing EST trimmer and were clustered into 31 contigs using CAP3. Single nucleotide Polymorphisms (SNP) and insertion/deletions (indels) were detected in contigs using the AUTOSNP software. Alternatively candidate SNP containing contigs were aligned by Clustal X to locate the SNPs. Results from these two methods were compared and false SNPs were eliminated. Finally, about 568 SNPs were found including 250 transitions, 120 transversions and 198 indels. The SNPs were seen at a frequency of 2.84/100bp in the WRKY sequences of palms. Primers were designed flanking to SNP/ indel sites with potential as markers in palms. We could obtain two novel WRKY-SNP markers (WRKY 7 and WRKY 12) which are not reported before in palms.
References
Batley, J., Barker, G., Helen, S., Keith, J. E, and Edwards, D. 2003. Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data. Plant Physiology 132 (1): 84–91.
Borrone, J. W., Kuhn, D. N. and Schnell, R, J. 2004. Isolation, characterization, and development of WRKY genes as useful genetic markers in Theobroma cacao. Theor Appl Genet 109 (3): 495–507.
Buetow, K. H., Edmonson, M. N., and Cassidy, A. B. 1999. Reliable identification of large numbers of candidate SNPs from public EST data. Nat Genet 21 (3): 323–325
Cheng, T. C., Xia, O. Y., Qian, J. F., Liu, C., Lin, Y., Zha, X. F. and Xiang, Z. H. (2004) Mining single nucleotide polymorphisms from EST data of silkworm, Bombyx mori, inbred strain Dazao. Insect Biochem. Mol. Biol. 34 (6). 523-530.
Douglas, E. S., Pamela, S. S. and Doyle, J. J. 1998. Book- Molecular systematics of plants 2- DNA sequencing, Kluwer Academic publishers. United States of America. Volume 2: 556
Eulgem, T., Rushton, P. J., Robatzek, S. and Somssich, I. E. 2000. The WRKY superfamily of plant transcription factors. Trends in plant Science 5 (5): 199-205.
Garg, K., Green, P. and Nickerson, D.A. 1999. Identification of candidate coding region single nucleotide polymorphisms in 165 human gene using assembled expressed sequence tags. 1999. Genome Res 9 (11): 1087-92.
Gu, Z., Hillier, L. and Kwok, P. Y. 1998. Single nucleotide polymorphism hunting in cyberspace. Hum Mutat 12 (4): 221–225.
Gupta, P. K., Roy, J. K. and Prasad, M. 2001. Single nucleotide polymorphisms: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science 80 (4): 524-535.
Huang, X., and Madan, A. 1999. CAP3: A DNA Sequence Assembly Program. Genome Research 9: 868-877.
Kim, H. J., Lee, H. R., Han, J. H., Yeom, S. I., Harn, C. H., and Kim, B. D. 2008. Marker production by PCR amplification with primer pairs from conserved sequences of WRKY genes in chili pepper. Molecules and Cells 25 (2): 196-204.
Lee, S. H., Park, E. W., Cho, Y. M., Ji-Woong, L., Kim, H. Y., Jun-Heon, L., Sung-Jong, O., Il-Cheong, C. and Du-Hak, Y. 2005. Confirming Single Nucleotide Polymorphisms from Expressed Sequence Tag Datasets Derived from Three Cattle cDNA Libraries. Biochem and Mol Bio 39 (2): 183-188.
Lopez, C. E., Quesadao, L.M., Bohorquez, A., Duque, M. C., Vargas, J., Joe, T. and Verdier, V. 2007. Mapping EST-derived SSRs and ESTs involved in resistance to bacterial blight in Manihot esculenta. Genome 50 (12): 1078–1088.
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 (4): 452–456.
Mauro, H. M., Meerow, A.W., Borrone, J. W., Kuhn, D. N. and Schnell, R. J. 2006. Ten informative markers developed from WRKY sequences in coconut (Cocos nucifera). Molecular Ecology Notes 6 (3): 904–906.
Mauro, H. M., Meerow, A.W., Borrone, J. W., Kuhn, D. N., Schnell, R. J. 2007. Usefulness of WRKY gene-derived markers for assessing genetic population structure: An example with florida coconut cultivars. Scientia Horticulturae 115 (1): 19-26.
Meerow, A. W., Noblick, L., Borrone, J. W., Couvreur, .L.P., Mauro-Herrera, M., Hahn, W. J., Kuhn, D. N., Nakamura, K., Oleas, N. H and Schnell, R. J. 2009. Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut. PLoS ONE 4 (10) e: 7353.
Nikiforov, T. T., Rendle, R. B., Goelat, P, Rogers, Y. H., Kotewicz, M. L., Anderson, S., Trainor, G. L. and Knapp, M. R. 1994. Genetic bit analysis: A solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Research 22 (20): 4167–4175.
Pandey, S. P. and Somssich, I. E. 2009. The Role of WRKY Transcription factors in Plant Immunity. Plant Physiology 150 (4): 1648-1655.
Picoult-Newberg, L., Ideker, T. E., Pohl, M. G., Taylor, S. L., Donaldson, M. A., Nickerson, D. A. and Boyce-Jacino, M. 1999. Mining SNPs From EST Databases. Genome Research 9: 167-174.
Riju, A., Chandrasekar, A., Sithara, K., Anoop, S., and Eapen, S. J. 2009. Identification of single nucleotide polymorphism in ginger using expressed sequence tags. Bioinformation 4(3): 119-122.
Riju, A., Rajesh, M. K., Fasila, S., Chandrasekar, A., Apshara, E., and Arunachalam, V. 2009. Mining of expressed sequence tag libraries of cocao for microsatellite markers using five computational tools. Journal of genetics 88 (2): 217-225.
Taillon-Miller, P., Gu, Z.J., Li, Q., Hillier, L. and Kwok, P. Y. 1998. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res 8 (7): 748–754.
Thiel, T., Michalek, W., Varsheney, R. K. and Graner, A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet 106 (3), 411–422.
Wu, K. L., Guo, Z. J., Wang, H. H. and Jing, Li. 2005. The WRKY family of transcription factors in Rice and Arabidopsis and their origins. DNA Research 12 (1): 9-26.
Xie, Z., Zhong-Lin, Z., Xiaolu, Z., Huang, J., Ruas, P., Daniel, T., and Qingxi, J. S. 2004. Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells. Plant Physiology 137 (1): 176-189.
Borrone, J. W., Kuhn, D. N. and Schnell, R, J. 2004. Isolation, characterization, and development of WRKY genes as useful genetic markers in Theobroma cacao. Theor Appl Genet 109 (3): 495–507.
Buetow, K. H., Edmonson, M. N., and Cassidy, A. B. 1999. Reliable identification of large numbers of candidate SNPs from public EST data. Nat Genet 21 (3): 323–325
Cheng, T. C., Xia, O. Y., Qian, J. F., Liu, C., Lin, Y., Zha, X. F. and Xiang, Z. H. (2004) Mining single nucleotide polymorphisms from EST data of silkworm, Bombyx mori, inbred strain Dazao. Insect Biochem. Mol. Biol. 34 (6). 523-530.
Douglas, E. S., Pamela, S. S. and Doyle, J. J. 1998. Book- Molecular systematics of plants 2- DNA sequencing, Kluwer Academic publishers. United States of America. Volume 2: 556
Eulgem, T., Rushton, P. J., Robatzek, S. and Somssich, I. E. 2000. The WRKY superfamily of plant transcription factors. Trends in plant Science 5 (5): 199-205.
Garg, K., Green, P. and Nickerson, D.A. 1999. Identification of candidate coding region single nucleotide polymorphisms in 165 human gene using assembled expressed sequence tags. 1999. Genome Res 9 (11): 1087-92.
Gu, Z., Hillier, L. and Kwok, P. Y. 1998. Single nucleotide polymorphism hunting in cyberspace. Hum Mutat 12 (4): 221–225.
Gupta, P. K., Roy, J. K. and Prasad, M. 2001. Single nucleotide polymorphisms: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science 80 (4): 524-535.
Huang, X., and Madan, A. 1999. CAP3: A DNA Sequence Assembly Program. Genome Research 9: 868-877.
Kim, H. J., Lee, H. R., Han, J. H., Yeom, S. I., Harn, C. H., and Kim, B. D. 2008. Marker production by PCR amplification with primer pairs from conserved sequences of WRKY genes in chili pepper. Molecules and Cells 25 (2): 196-204.
Lee, S. H., Park, E. W., Cho, Y. M., Ji-Woong, L., Kim, H. Y., Jun-Heon, L., Sung-Jong, O., Il-Cheong, C. and Du-Hak, Y. 2005. Confirming Single Nucleotide Polymorphisms from Expressed Sequence Tag Datasets Derived from Three Cattle cDNA Libraries. Biochem and Mol Bio 39 (2): 183-188.
Lopez, C. E., Quesadao, L.M., Bohorquez, A., Duque, M. C., Vargas, J., Joe, T. and Verdier, V. 2007. Mapping EST-derived SSRs and ESTs involved in resistance to bacterial blight in Manihot esculenta. Genome 50 (12): 1078–1088.
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 (4): 452–456.
Mauro, H. M., Meerow, A.W., Borrone, J. W., Kuhn, D. N. and Schnell, R. J. 2006. Ten informative markers developed from WRKY sequences in coconut (Cocos nucifera). Molecular Ecology Notes 6 (3): 904–906.
Mauro, H. M., Meerow, A.W., Borrone, J. W., Kuhn, D. N., Schnell, R. J. 2007. Usefulness of WRKY gene-derived markers for assessing genetic population structure: An example with florida coconut cultivars. Scientia Horticulturae 115 (1): 19-26.
Meerow, A. W., Noblick, L., Borrone, J. W., Couvreur, .L.P., Mauro-Herrera, M., Hahn, W. J., Kuhn, D. N., Nakamura, K., Oleas, N. H and Schnell, R. J. 2009. Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut. PLoS ONE 4 (10) e: 7353.
Nikiforov, T. T., Rendle, R. B., Goelat, P, Rogers, Y. H., Kotewicz, M. L., Anderson, S., Trainor, G. L. and Knapp, M. R. 1994. Genetic bit analysis: A solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Research 22 (20): 4167–4175.
Pandey, S. P. and Somssich, I. E. 2009. The Role of WRKY Transcription factors in Plant Immunity. Plant Physiology 150 (4): 1648-1655.
Picoult-Newberg, L., Ideker, T. E., Pohl, M. G., Taylor, S. L., Donaldson, M. A., Nickerson, D. A. and Boyce-Jacino, M. 1999. Mining SNPs From EST Databases. Genome Research 9: 167-174.
Riju, A., Chandrasekar, A., Sithara, K., Anoop, S., and Eapen, S. J. 2009. Identification of single nucleotide polymorphism in ginger using expressed sequence tags. Bioinformation 4(3): 119-122.
Riju, A., Rajesh, M. K., Fasila, S., Chandrasekar, A., Apshara, E., and Arunachalam, V. 2009. Mining of expressed sequence tag libraries of cocao for microsatellite markers using five computational tools. Journal of genetics 88 (2): 217-225.
Taillon-Miller, P., Gu, Z.J., Li, Q., Hillier, L. and Kwok, P. Y. 1998. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res 8 (7): 748–754.
Thiel, T., Michalek, W., Varsheney, R. K. and Graner, A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet 106 (3), 411–422.
Wu, K. L., Guo, Z. J., Wang, H. H. and Jing, Li. 2005. The WRKY family of transcription factors in Rice and Arabidopsis and their origins. DNA Research 12 (1): 9-26.
Xie, Z., Zhong-Lin, Z., Xiaolu, Z., Huang, J., Ruas, P., Daniel, T., and Qingxi, J. S. 2004. Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells. Plant Physiology 137 (1): 176-189.
Published
2011-10-01
How to Cite
Manju, K. P., & Arunachalam, V. (2011). Bioinformatic Prediction of SNP Markers in WRKY Sequences of Palms. CORD, 27(2), 17-25. https://doi.org/10.37833/cord.v27i2.113
Section
Articles
