Journal article
Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress
BMC Plant Biology, Vol.11(1), Art. 70
2011
Abstract
Background
Chickpea (Cicer arietinum L.) is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs) by suppression subtraction hybridization (SSH) to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea.
Results
EST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant) and ICC 1882 (drought resistant) exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs) (10 each) for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons), 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71%) unigenes showed significant BLASTX similarity (<1E-06) in the NCBI non-redundant (nr) database. Gene ontology functional classification terms (BLASTX results and GO term), were retrieved for 2006 (92.0%) sequences, and 656 sequences were further annotated with 812 Enzyme Commission (EC) codes and were mapped to 108 different KEGG pathways. In addition, expression status of 830 unigenes in response to terminal drought stress was evaluated using macro-array (dot blots). The expression of few selected genes was validated by northern blotting and quantitative real-time PCR assay.
Conclusion
Our study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide a better insight into the selection of candidate genes (both up- and downregulated) associated with drought tolerance. These results can be used to identify suitable targets for manipulating the drought-tolerance trait in chickpea.
Details
- Title
- Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress
- Authors/Creators
- A.A. Deokar (Author/Creator) - National Research Centre on Plant BiotechnologyV. Kondawar (Author/Creator) - National Research Centre on Plant BiotechnologyP.K. Jain (Author/Creator) - National Research Centre on Plant BiotechnologyS.M. Karuppayil (Author/Creator) - School of Life Sciences, S.R.T.M. University, Dnyanteerth, Vishnupuri, IndiaN.L. Raju (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsV. Vadez (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsR.K. Varshney (Author/Creator) - Centro Internacional de Mejoramiento de Maíz Y TrigoR. Srinivasan (Author/Creator) - National Research Centre on Plant Biotechnology
- Publication Details
- BMC Plant Biology, Vol.11(1), Art. 70
- Publisher
- BioMed Central Ltd as part of Springer Nature
- Identifiers
- 991005545053607891
- Copyright
- © 2011 Deokar et al
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.49 Plant Stress Responses
- Web Of Science research areas
- Plant Sciences
- ESI research areas
- Plant & Animal Science