Sugarcane Transcript Profiling Assessed by cDNA-AFLP Analysis during the Interaction with Sugarcane Mosaic Virus
Author(s)
Cibele N. F. Medeiros,
Marcos C. Gonçalves*,
Ricardo Harakava,
Silvana Creste,
Paula M. Nóbile,
Luciana R. Pinto,
Dilermando Perecin,
Marcos G. A. Landell
Affiliation(s)
Sugarcane Research Center, Instituto Agron?mico de Campinas (IAC), Ribeir?o Preto, Brazil . Plant Virology Laboratory, CPDSV, Instituto Biológico, S?o Paulo, Brazil . Plant Pathology Biochemistry Laboratory, CPDSV, Instituto Biológico, S?o Paulo, Brazil . Faculdade de Ciências Agrárias e Veterinárias, Universida de Estadual Paulista, Jaboticabal, Brazil.
Sugarcane Research Center, Instituto Agron?mico de Campinas (IAC), Ribeir?o Preto, Brazil . Plant Virology Laboratory, CPDSV, Instituto Biológico, S?o Paulo, Brazil . Plant Pathology Biochemistry Laboratory, CPDSV, Instituto Biológico, S?o Paulo, Brazil . Faculdade de Ciências Agrárias e Veterinárias, Universida de Estadual Paulista, Jaboticabal, Brazil.
ABSTRACT
Sugarcane mosaic caused by Sugarcane Mosaic Virus (SCMV) is one of the most important virus diseases of sugarcane. In the present study, changes in the transcription profile obtained by cDNA-AFLP analysis were investigated in two sugarcane varieties contrasting to SCMV resistance, when challenged with a severe virus strain. Healthy plants derived from meristem tip tissue culture were mechanically inoculated under greenhouse controlled conditions and sampled at 24, 48 and 72 hours after inoculation. A total of 392 transcript-derived fragments (TDFs) were verified in the resistant variety against 380 in the susceptible one. The two sugarcane genotypes showed differential behavior in the number of induced and repressed TDFs along the time-course samplings. Ten out of 23 sequenced TDFs (unique from the resistance variety), showed identity with known plant sequences, mostly related to plant defense mechanisms against pathogens. The cDNA-AFLP technique was effective in revealing changes in the transcription profile within and between contrasting varieties when challenged by SCMV.
Cite this paper
Medeiros, C. , Gonçalves, M. , Harakava, R. , Creste, S. , Nóbile, P. , Pinto, L. , Perecin, D. and Landell, M. (2014) Sugarcane Transcript Profiling Assessed by cDNA-AFLP Analysis during the Interaction with Sugarcane Mosaic Virus. Advances in Microbiology, 4, 511-520. doi: 10.4236/aim.2014.49057.
Medeiros, C. , Gonçalves, M. , Harakava, R. , Creste, S. , Nóbile, P. , Pinto, L. , Perecin, D. and Landell, M. (2014) Sugarcane Transcript Profiling Assessed by cDNA-AFLP Analysis during the Interaction with Sugarcane Mosaic Virus. Advances in Microbiology, 4, 511-520. doi: 10.4236/aim.2014.49057.
References
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http://dx.doi.org/10.1007/s12033-008-9139-3 [22] Cheng, S.F., Huang, Y.P., Wu, Z.R., Hu, C.C., Hsu, Y.H. and Tsai, C.H. (2010) Identification of Differentially Expressed Genes Induced by Bamboo Mosaic Virus Infection in Nicotiana benthamiana by cDNA-Amplified Fragment Length Polymorphism. BMC Plant Biology, 10, 286.
http://dx.doi.org/10.1186/1471-2229-10-286 [23] Soosaar, J.L.M., Burch-Smith, T.M. and Dinesh-Kumar, S.P. (2005) Mechanisms of Plant Resistance to Viruses. Nature Reviews Microbiology, 3, 789-798. http://dx.doi.org/10.1038/nrmicro1239 [24] Mcclintock, B. (1984) The Significance of Responses of the Genome to Challenge. Science, 226, 792-801. http://dx.doi.org/10.1126/science.15739260 [25] Slotkin, R.K. and Martienssen, R. (2007) Transposable Elements and the Epigenetic Regulation of the Genome. Nature Reviews Genetics, 8, 272-285. http://dx.doi.org/10.1038/nrg2072 [26] Domingues, D.S., Cruz, G.M.Q., Metcalfe, C.J., Nogueira, F.T.S., Vicentini, R., Alves, C.S. and Sluys, M.-A.V. (2012) Analysis of Plant LTR-Retrotransposons at the Fine Scale Family Level Reveals Individual Molecular Patterns. BMC Genomics, 13, 137. http://dx.doi.org/10.1186/1471-2164-13-137 [27] Zvereva, A.S. and Pooggin, M.M. (2012) Silencing and Innate Immunity in Plant Defense against Viral and Non-Viral Pathogens. Viruses, 4, 2578-2597. http://dx.doi.org/10.3390/v4112578 [28] Barros, F.C., Sagata, E., Ferreira, L.C.C. and Juliatti, F.C. (2010) Indu??o de Resistência em Plantas contra Fitopatógenos. Biosciense Journal, 26, 231-239. [29] Evered, D., Harnett, S., Antoniw, J.F. and White, R.F. (2007) The Role of Pathogenesis-Related Proteins. http://onlinelibrary.wiley.com/doi/10.1002/9780470513569.ch5/pdf [30] Xie, Y.D., Li, W., Guo, D., Dong, J., Zhang, Q., Fu, Y., Ren, D., Peng, M. and Xia, Y. (2010) The Arabidopsis Gene SIGMA FACTOR-BINDING PROTEIN 1 Plays a Role in the Salicylate- and Jasmonate-Mediated Defense Responses. Plant, Cell and Environment, 33, 828-839.
[1] Xu, D.L., Zhou, G.H., Xie, Y.J., Mock, R. and Li, R. (2010) Complete Nucleotide Sequence and Taxonomy of Sugarcane Streak Mosaic Virus, Member of a Novel Genus in the Family Potyviridae. Virus Genes, 40, 432-439. http://dx.doi.org/10.1007/s11262-010-0457-8 [2] Joy, D.A., Feng, X.R., Mu, J.B., Furuya, T., Chotivanich, K., Krettli, A.U., Ho, M., Wang, A., White, N.J., Suh, E., Beerli, P. and Su, X.Z. (2003) Early Origin and Recent Expansion of Plasmodium falciparum. Science, 300, 318-321. http://dx.doi.org/10.1126/science.1081449 [3] Goncalves, M.C., Pinto, L.R., Souza, S. and Landell, M.G. (2012) Virus Diseases of Sugarcane. A Constant Challenge to Sugarcane Breeding in Brazil. Functional Plant Science & Biotechnology, 6, 125-130. [4] Goncalves, M.C., Santos, A.S., Maia, I.G., Chagas, C.M. and Harakava, R. (2007) Characterization of an Isolate of Sugarcane Mosaic Virus Breaking Down Resistance of Commercial Sugarcane Varieties. Fitopatologia Brasileira, 32, 32-39. [5] Bachem, C.W.B., Oomen, R.J.F.J. and Visser, R.G.F. (1998) Transcript Imaging with cDNA-AFLP: A Step-by-Step Protocol. Plant Molecular Biology Reporter, 16, 157-173.
http://dx.doi.org/10.1023/A:1007468801806 [6] Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van De Lee, T., Hornes, M., Frijters, A., Peleman, J., Kulper, M. and Zabeau, M. (1995) AFLP: A New Technique for DNA Finger Printing. Nucleic Acids Research, 23, 4407-4414. http://dx.doi.org/10.1093/nar/23.21.4407 [7] Milioni, D., Sado, P.E., Stacey, N.J., Roberts, K. and Mccann, M.C. (2002) Early Gene Expression Associated with the Commitment and Differentiation of a Plant Tracheary Elements Revealed by cDNA-Amplified Fragment Length Polymorphism Analysis. Plant Cell, 14, 2813-2824.
http://dx.doi.org/10.1105/tpc.005231 [8] Bachem, C.W.B., Van der Hoeven, R.S., De Bruijn, S.M., Vreugdenhil, D., Zabeau, M. and Visser, R.G.F. (1996) Visualization of Differential Gene Expression Using a Novel Method of RNA Fingerprinting Based on AFLP: Analysis of Gene Expression during Potato Tuber Development. The Plant Journal, 9, 745-753. http://dx.doi.org/10.1046/j.1365-313X.1996.9050745.x [9] Lao, M., Arencibia, A.D., Carmona, E.R., Acevedo, R., Rodriguez, E., Leon, O. and Santana, I. (2008) Differential Expression Analysis by cDNA-AFLP of Saccharum spp. after Inoculation with the Host Pathogen Sporisorium scitamineum. Plant Cell Reports, 27, 1103-1111.
http://dx.doi.org/10.1007/s00299-008-0524-y [10] Salmon, A., Bellis, H., Chable, V. and Manzanares-Dauleux, M.J. (2009) Identification of Differentially Expressed Genes Related to Aberrant Phenotypes in Brassica oleracea var. Botrytis. Plant Breeding, 128, 631-639. http://dx.doi.org/10.1111/j.1439-0523.2008.01602.x [11] Butterfield, M.K., Rutherford, R.S., Carson, D.L. and Huckett, B.I. (2004) Application of Gene Discovery to Varietal Improvement in Sugarcane. South African Journal of Botany, 70, 167-172. [12] Guimaraes, E.R. (2007) Cigarrinha-das-raizes em cana-de-acucar: Resistencia genotipica e interacao planta-praga. Master Dissertation, Faculdade de Ciencias Agrarias e Veterinarias, Universidade Estadual Paulista, Jaboticabal. [13] Carmona, E., Vargas, D., Borroto, C.J., Lopez, J., Fernández, A.I., Arencibia, A. and Borrás-Hidalgo, O. (2004) cDNA-AFLP Analysis of Differential Gene Expression during the Interaction between Sugarcane and Puccinia melanocephala. Plant Breeding, 123, 499-501.
http://dx.doi.org/10.1111/j.1439-0523.2004.00935.x [14] Thokoane, L.N. and Rutherford, R.S. (2001) cDNA-AFLP Differential Display of Sugarcane (Saccharum spp., Hybrids) Genes Induced by Challenge with the Fungal Pathogen Ustilago scitaminea (Sugarcane Smut). Proceedings of the South African Sugar Technologists Association, 75, 104-107. [15] Yang, Z.N. and Mirkov, T.E. (1997) Sequence and Relationships of Sugarcane Mosaic and Sorghum Mosaic Virus Strains and Development of RT-PCR-Based RFLPs for Strain Discrimination. Phytopathology, 87, 932-939. http://dx.doi.org/10.1094/PHYTO.1997.87.9.932 [16] Creste, S., Tulmann-Neto, A. and Figueira, A. (2001) Detection of Single Sequence Repeat Polymorphisms in Denaturing Polyacrylamide Sequencing Gels by Silver Staining. Plant Molecular Biology Reporter, 19, 299-306. http://dx.doi.org/10.1007/BF02772828 [17] Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acids Research, 25, 3389-3402. http://dx.doi.org/10.1093/nar/25.17.3389 [18] Gal-On, A. and Shiboleth, Y.M. (2006) Cross Protection. In: Loebenstein G. and Carr, J.P., Eds., Natural Resistance Mechanisms of Plants to Viruses, Springer, Dordrecht, 261-288.
http://dx.doi.org/10.1007/1-4020-3780-5_12 [19] Borrás-Hidalgo, O., Thomma, B.P.H.J., Carmona, E., Borroto, C.J., Pujol, M., Arencibia, A. and Lopez, J. (2005) Identification of Sugarcane Genes Induced in Disease-Resistant Somaclones upon Inoculation with Ustilago scitaminea or Bipolaris sacchari. Plant Physiology and Biochemistry, 43, 1115-1121. http://dx.doi.org/10.1016/j.plaphy.2005.07.011 [20] Wang, J., Wang, P. and Bughrara, S.S. (2005) Detection of an Efficient Restriction Enzyme Combination for cDNA-AFLP Analysis in Festuca mairei and Evaluation of the Identity of Transcript-Derived Fragments. Molecular Biotechnology, 29, 211-220. http://dx.doi.org/10.1385/MB:29:3:211 [21] Xiao, X., Li, H. and Tang, C. (2009) A Silver-Staining cDNA-AFLP Protocol Suitable for Transcript Profiling in the Latex of Hevea. Molecular Biotechnology, 42, 91-99.
http://dx.doi.org/10.1007/s12033-008-9139-3 [22] Cheng, S.F., Huang, Y.P., Wu, Z.R., Hu, C.C., Hsu, Y.H. and Tsai, C.H. (2010) Identification of Differentially Expressed Genes Induced by Bamboo Mosaic Virus Infection in Nicotiana benthamiana by cDNA-Amplified Fragment Length Polymorphism. BMC Plant Biology, 10, 286.
http://dx.doi.org/10.1186/1471-2229-10-286 [23] Soosaar, J.L.M., Burch-Smith, T.M. and Dinesh-Kumar, S.P. (2005) Mechanisms of Plant Resistance to Viruses. Nature Reviews Microbiology, 3, 789-798. http://dx.doi.org/10.1038/nrmicro1239 [24] Mcclintock, B. (1984) The Significance of Responses of the Genome to Challenge. Science, 226, 792-801. http://dx.doi.org/10.1126/science.15739260 [25] Slotkin, R.K. and Martienssen, R. (2007) Transposable Elements and the Epigenetic Regulation of the Genome. Nature Reviews Genetics, 8, 272-285. http://dx.doi.org/10.1038/nrg2072 [26] Domingues, D.S., Cruz, G.M.Q., Metcalfe, C.J., Nogueira, F.T.S., Vicentini, R., Alves, C.S. and Sluys, M.-A.V. (2012) Analysis of Plant LTR-Retrotransposons at the Fine Scale Family Level Reveals Individual Molecular Patterns. BMC Genomics, 13, 137. http://dx.doi.org/10.1186/1471-2164-13-137 [27] Zvereva, A.S. and Pooggin, M.M. (2012) Silencing and Innate Immunity in Plant Defense against Viral and Non-Viral Pathogens. Viruses, 4, 2578-2597. http://dx.doi.org/10.3390/v4112578 [28] Barros, F.C., Sagata, E., Ferreira, L.C.C. and Juliatti, F.C. (2010) Indu??o de Resistência em Plantas contra Fitopatógenos. Biosciense Journal, 26, 231-239. [29] Evered, D., Harnett, S., Antoniw, J.F. and White, R.F. (2007) The Role of Pathogenesis-Related Proteins. http://onlinelibrary.wiley.com/doi/10.1002/9780470513569.ch5/pdf [30] Xie, Y.D., Li, W., Guo, D., Dong, J., Zhang, Q., Fu, Y., Ren, D., Peng, M. and Xia, Y. (2010) The Arabidopsis Gene SIGMA FACTOR-BINDING PROTEIN 1 Plays a Role in the Salicylate- and Jasmonate-Mediated Defense Responses. Plant, Cell and Environment, 33, 828-839.