Identification of Possible Mechanisms of Chickpea (Cicer arietinum L.) Drought Tolerance Using cDNA-AFLP

Authors
M. Pouresmael 1
J. Mozafari 2
R. A. Khavari-Nejad 1
F. Najafi 1
F. Moradi 3
1 Department of Plant Physiology, Faculty of Biological Sciences, Kharazmi University, 15719-14911, Tehran, Islamic Republic of Iran.
2 National Plant Gene Bank, Seed and Plant Improvement Institute, Mahdasht Avenue, Karaj, Islamic Republic of Iran.
3 Department of Molecular Physiology, Agriculture Biotechnology Research Institute, Karaj, Islamic Republic of Iran.
Abstract
Drought sensitivity is considered as a major concern for chickpea (C. arietinum) seed production. Determination of drought adaptation mechanisms is an essential constituent of this crop breeding programs. With this purpose, the present research was conducted to distinguish the molecular basis of chickpea drought tolerance using cDNA-AFLP approach. The expression profile was compared between drought tolerant (ICCV2 and FLIP9855C) and susceptible lines (ILC3279) of chickpea under three drought treatments including well-watered, intermediate, and severe stress; where soil water content was kept at 85–90%, 55–60%, and 25–30% of Field capacity, respectively. Totally, 295 transcript-derived fragments (TDFs) were visualized. Among the differentially expressed TDFs, 72 TDFs were sequenced. Sequenced cDNAs were categorized in different functional groups involved in macromolecules metabolism, cellular transport, signal transduction, transcriptional regulation, cell division and energy production. Based on the results, ribosomal protein S8, mitochondrial chaperone, proteases, hydrolases, UDP -glucuronic acid decarboylase, 2-hydroxyisoflavanone dehydratase, NADPH dehydrogenase, chloride channels, calmodulin, ABC transporter, histone deacetylase and factors involved in chloroplast division were among genes that were affected by drought stress. Similarity search in data base showed that cell wall elasticity, isoflavonoids, maintenance of structure and function of proteins through increase in expression of mitochondrial chaperones, programed cell death, and remobilization of storage material from leaves to seeds were among mechanisms that distinguished differences between drought tolerant and drought susceptible lines.

Keywords

1. Bachem, Ch.W.B., Hoeven, R. S., 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. Plant J., 9: 745-753.
2. Bachem, C. W. B., Oomen, R. J. F. J. and Visser, R. G. E. 1998. Transcript Imaging with cDNA-AFLP: A Step-by-step Protocol. Plant Mol. Biol. Rep., 16: 157–174.
3. Breyne, P., Dreesen, R., Cannoot, B., Rombaut, D., Vandepoele, K., Rombauts, S., Vanderhaeghen, R., Inze, D. and Zabeau, M. 2003. Quantitative cDNA-AFLP Analysis for Genome-wide Expression Studies. Mol. Gen. Genomics, 269: 173–179.
4. Claverie J M. and Notredame C. 2007. Bioinformatics for Dummies. 2nd Edition, Wiley Publishing Inc., New York, 436 PP.
5. Clifford, S. C., Arndt, S. K., Corlett, J. E., Joshi, S., Sankhla, N., Popp, M. and Jones, H. G.1998. The Role of Solute Accumulation, Osmotic Adjustment and Changes in Cell Wall Elasticity in Drought Tolerance in Ziziphus mauritiana (Lamk.). J. Exp. Bot., 49: 967–977.
6. Davies, Ch., Ramakrishnan, V. and White, S. W. 1996. Structural Evidence for Specific S8–RNA and S8- Protein Interactions within the 30S Ribosomal Subunit: Ribosomalprotein S8 from Bacillus stearothermophilus. Structure, 4: 1093–1104.
7. Deokar, A. A., Kondawar, V., Jain, P. K., Karuppayil, S. M., Raju, N. L., Vadez, V., Varshney, R. K. and Srinivasan, R. 2011. Comparative Analysis of Expressed Sequence Tags (ESTs) between Drought-tolerant and -Susceptible Genotypes of Chickpea under Terminal Drought Stress. BMC Plant Biol., 11: 70.
8. Fu, W., Wu, K. and Duan, J. 2007. Sequence and Expression Analysis of Histone Deacetylases in Rice. Biochem. Biophys. Res. Communications, 356: 843–850.
9. Grabelnych, O. I., Sumina, O. N., Funderat, S. P., Pobezhimova, T. P., Voinikov, V. K. and Kolesnichenko, A. V. 2004. The Distribution of Electron Transport between the Main Cytochrome and Alternative Pathways in Plant Mitochondria during Short-term Cold Stress and Cold Hardening. J. Therm. Biol., 29:165–175.
10. Hoson, T. 1998. Apoplast as the Site of Response to Environmental Signals. J. Plant Res., 111: 167-177.
11. Jayaraman, A., Puranik, S., Kumar Rai, N., Vidapu , S., Pankaj Sahu P., Lata, Ch. and Prasad, M. 2008. cDNA-AFLP Analysis Reveals Differential Gene Expression in Response to Salt Stress in Foxtail Millet (Setaria italica L.). Mol. Biotechnol., 40: 241–251.
12. Jones, H. G. and Corlett, J. E. 1992. Current Topics in Drought Physiology. J. Agric. Sci., 119:291–296.
13. Keinanen, S. I., Hassinen, V. H., Ka¨renlampi, S. O. and Tervahauta, A. I. 2007. Isolation of Genes Up-regulated by Copper in a Copper-tolerant Birch (Betula pendula) Clone. Tree Physiol., 27: 1243–1252.
14. Kim, Y. J., Kyung Cho, E., In Lee, S., Oh Lim, Ch. and Choi, Y. J. 2010. Differential Expression of Rice Calmodulin Promoters in Response to Stimuli and Developmental Tissue in Transgenic Tobacco Plants. BMB Report., 43: 9-16.
15. Klein, M., Geisler, M., Suh, S. J., Kolukisaoglu, H. Ü., Azevedo, L., Plaza, S., Curtis, M. D., Richter, A., Weder, B., Schulz, B. and Martinoia, E. 2004. Disruption of AtMRP4, a Guard Cell Plasma Membrane ABCC-type ABC Transporter, Leads to Deregulation of Stomatal Opening and Increased Drought Susceptibility. Plant J., 39: 21-236.
16. Lee, S. and Park, M. 2012. Regulation of Reactive Oxygen Species Generation under Drought Conditions in Arabidopsis. Plant Signal. Behav., 7: 599 – 601.
17. Leucci, M. R., Lenucci, M. S., Piro, G. and Dalessandro, G. 2008. Water Stress and Cell Wall Polysaccharides in the Apical Root Zone of Wheat Cultivars Varying in Drought Tolerance. J. Plant Physiol., 165: 1168-1180.
18. Lim, P. O., Kim, H. J. and Nam, H. G. 2007. Leaf Senescence. Annu. Rev. Plant Biol., 58: 115–36.
19. Liu, H. T., Li, B., Shang, Z. L., Li, X. Z., Mu, R. L., Sun, D. Y. and Zhou, R. G. 2003. Calmodulin Is Involved in Heat Shock Signal Transduction in Wheat. Plant Physiol., 132: 1186–1195.
20. Liu, S. H., Fu, H. –X., Xu, B. Y., Zhu, L. H., Zhai, H. Q. and Li, Z. K. 2007. Cell Death in Response to Osmotic and Salt Stresses in Two Rice (Oryza sativa L.) Ecotypes. Plant Sci., 172: 897–902.
21. Liu, Y., Zhan, G. T. and Wang, J. 2008. Photosynthesis and Metabolite Levels in Dehydrating Leaves of Reaumuria soongorica. Acta. Biol. Cracov. Bot., 50: 19–26.
22. Martínez, J. P., Silva, H., Ledent, J. F. and Pinto, M. 2007. Effect of Drought Stress on the Osmotic Adjustment, Cell Wall Elasticity and Cell Volume of Six Cultivars of Common Beans (Phaseolus vulgaris L.). Eur. J. Agron., 26: 30–38.
23. Merianos, H. J., Wang, J. and Moore, P. B. 2004. The structure of a ribosomal protein S8/spc Operon mRNA Complex. RNA, 10: 954-964.
24. Molina, C., Zaman-Allah, M., Khan, F., Fatnassi, N., Horres, R., Rotter, B., Steinhauer, D., Amenc, L., Drevon, J. J., Winter, P. and Kahl, G. 2011. The Salt-responsive Transcriptome of Chickpea Roots and Nodules via DeepSuperSAGE. BMC Plant Biol., 11: 31.
25. Molina, C., Rotter, B., Horres, R., Udupa, S. M., Besser, B., Bellarmino, L., Baum, M., Matsumura, H., Terauchi, R., Kahl, G. and Winter, P. 2008. SuperSAGE: the Drought Stress-responsive Transcriptome of Chickpea Roots. BMC Genomic., 9: 553.
26. Nimbalkar, S. B., Harsulkar, A. M., Giri, A. P., Sainani, M. N., Franceschi, V. and Gupta, V. S. 2006. Differentially Expressed Gene Transcripts in Roots of Resistant and Susceptible Chickpea Plant (Cicer arietinum L.) upon Fusarium oxysporum Infection. Physiol. Mol. Plant, 68: 176–188.
27. Pastore, D., Trono, D., Laus, M. N., Fonzo, N. D. and Flagella, Z. 2007. Possible Plant Mitochondria Iinvolvement in Cell Adaptation to Drought Stress. A Case Study: Durum Wheat Mitochondria. J. Exp. Bot., 58: 195–210.
28. Pouresmael, M., Khavari-Nejad, R. A., Mozafari, J., Najafi, F. and Moradi, F. 2013. Efficiency of Screening Criteria for Drought Tolerance in Chickpea. Archiv. Agron. Soil Sci., 59: 1675-1693.
29. Rizhsky, L., Liang, H.J., Shuman, J., Shulaev, V., Davletova, S. and Mittler, R. 2004. When Defense Pathways Collide. The Response of Arabidopsis to a Combination of Drought and Heat Stress. Plant Physiol., 134: 1683–1696.
30. Rodrıguez, M., Canales, E., Borroto, C. J., Carmona, E., Lopez, J., Pujol, M. and Borras-Hidalgo, O. 2006. Identification of Genes Induced upon Water-Deficit Stress in a Drought-tolerant Rice Cultivar. J. Plant Physiol., 163: 577-584.
31. Schaller, A. 2004. A Cut above the Rest: the Regulatory Function of Plant Proteases. Planta, 220: 183–197.
32. Segovia, M. and Berges, J. A. 2005. Effects of Inhibitors of Protein Synthesis and DNA Replication on the Induction of Proteolytic Activities, Caspase-like Activities and Cell Death in the Unicellular Chlorophyte Dunaliella tertiolecta. Eur. J. Phycol., 40: 21-30.
33. Selvam, J. N., Kumaravadivel, N., Gopikrishnan, A., Kumar, B.K., Ravikesavan, R. and Boopathi, M. N. 2009. Identification of a Novel Drought Tolerance Gene in Gossypium hirsutum L. cv KC3. Communication. Biometry Crop Sci., 4: 9-13.
34. Shabala, S. 2009. Salinity and Programmed Cell Death: Unraveling Mechanisms for Ion Specific Signaling. J. Exp. Bot., 60: 709-712.
35. Shi, H., Quintero, F. J., Pardo, J. M. and Zhu, J. K. 2002. The Putative Plasma Membrane Na1/H1 Antiporter SOS1 Controls Long-distance Na1 Transport in Plants. Plant Cell, 14: 465–477.
36. Shimamura, M., Akashi, T., Sakurai, N., Suzuki, H., Saito, K., Shibata, D., Ayabe, Sh., and Aoki, T. 2007. 2-Hydroxyisoflavanone Dehydratase Is a Critical Determinant of Isoflavone Productivity in Hairy Root Cultures of Lotus japonicas. Plant Cell Physiol., 48: 1652–1657.
37. Suzuki, K., Suzuki, Y. and Kitamura, Sh. 2003. Cloning and Expression of a UDP-glucuronic Acid Decarboxylase Gene in Rice. J. Exp. Bot., 54: 1997-1999.
38. Tian, R. H., Zhang, G. Y., Yan, C. H. and Dai, Y. R. 2000. Involvement of Poly (ADP- ribose) Polymerase and Activation of Caspase-3-like Protease in Heat Shock-ionduced Apoptosis in Tobacco Suspension Cell. FEBS Lett., 474: 11-15.
39. Varshney, R. K., Hiremath, P. J., Lekha, P., Kashiwagi, J., Balaji, J., Deokar, A. A., Vadez, V., Xiao, Y., Srinivasan, R., Gaur, P. M., Siddique, K. H., Town, C. D. and Hoisington, D. A. 2009. A Comprehensive Resource of Drought- and Salinity- Responsive ESTs for Gene Discovery and Marker Development in Chickpea (Cicer arietinum L.). BMC Genomic.,10: 523.
40. Vuylsteke, M., Peleman, J. D. and Eijk, M. 2007. AFLP Technology for DNA Fingerprinting. Nat. Protoc., 2: 1387–1398.
41. Wang, W., Vinocu1, B., Shoseyov, O. and Altman, A. 2004. Role of Plant Heat-Shock Proteins and molecular chaperones in the abiotic stress response. Trend. Plant Sci., 9: 244–252.
42. Wang, X., Tang, Ch., Zhang, G., Li, Y., Wang, Ch., Liu, B., Qu, Z., Zhao, J., Han, Q., Huang, L., Chen, X. and Kang, Z. 2009. cDNA-AFLP Analysis Reveals Differential Gene Expression in Compatible Interaction of Wheat Challenged with Puccinia striiformis f. sp. Tritici. BMC Genomic., 10:289- 301.
43. Wang, J., Li, X., Liu, Y. and Zhao, X. 2010a. Salt Stress Induces Programmed Cell Death in Thellungiella halophila Suspension-Cultured Cells. J. Plant Physiol., 167:1145–1151.
44. Wang, T., Zhang, E., Chen, X., Li, L. and Liang, X. 2010 b. Identification of Seed Proteins Associated with Resistance to Pre-harvested Aflatoxin Contamination in Peanut (Arachis hypogaea L.). BMC Plant Biol., 10: 267-278.
45. Ye, M. R,, Liu, A. R., Chen, L. M. and Wu, C. Y. 2008. Effects of Soybean Isoflavones on Rape Seedlings under Drought Stress. Acta Bot. Yunnanica, 3: 351-354.
46. Zhang, Q., Shirley, N., Lahnstein, J. and Fincher, G. B. 2005. Characterization and Expression Patterns of UDP-D-glucuronate Decarboxylase Genes in Barley. Plant Physiol., 138: 131–141.
47. Zwiazek, J. J. 1991. Cell Wall Changes in White Spruce (Picea glauca) Needles Subjected to Repeated Drought Stress. Physiol. Plant., 32: 513–518.
Journal of Agricultural Science and Technology
Volume 17, Issue 5
September and October 2015
Pages 1303-1317