Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

Deokar, A A and Kondawar, V and Jain, P K and Karuppayil, S M and Raju, N L and Vadez, V and 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 Biology, 11 (70).

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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 downregulated 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.

Item Type: Article
Agro Tags: <b>Agrotags</b> - drought | genes | proteins | planting | chickpeas | transcription | drought stress | vegetative propagation | additives | irrigation <br><b>Fishtags</b> - drying <br><b>Geopoliticaltags</b> - india | usa | netherlands | act | mexico | delhi
Subjects: Mandate crops > Chickpea
Depositing User: Siva Shankar
Date Deposited: 18 May 2011 10:46
Last Modified: 10 Jun 2011 08:45
Official URL:
Funders: Indian Council of Agricultural Research
Acknowledgement: We gratefully acknowledge the "National Fund for Basic, Strategic and Frontier Application Research in Agriculture (NFBSFARA), Indian Council of Agricultural Research (ICAR), New Delhi, India, for financial support. Authors are thankful to Dr. Pooran Gaur of ICRISAT for sharing the parental genotypes and mapping population used in the study. Thanks are also due to P Lekha and Pavana Hiremath for their help in planning of some experiments and discussions. We are grateful to Dr Vani Shankar for editing the manuscript.
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