title: Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: National Research Center on Plant Biotechnology, IARI Campus, New Delhi 110012, India.
authors.forename: Amit A
authors.initials: AA
authors.lastname: Deokar
authors.forename: Vishwajith
authors.initials: V
authors.lastname: Kondawar
authors.forename: Pradeep K
authors.initials: PK
authors.lastname: Jain
authors.forename: S Mohan
authors.initials: SM
authors.lastname: Karuppayil
authors.forename: N L
authors.initials: NL
authors.lastname: Raju
authors.forename: Vincent
authors.initials: V
authors.lastname: Vadez
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.forename: R
authors.initials: R
authors.lastname: Srinivasan
mesh_terms: D000222:Adaptation, Physiological; D018533:Biomass; D029863:Cicer / Q000235:genetics* / Q000502:physiology; D003890:Desiccation; D055864:Droughts; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D005838:Genotype; D006824:Hybridization, Genetic; D005810:Multigene Family; D010641:Phenotype; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D018520:Plant Shoots / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D013312:Stress, Physiological; D014867:Water / Q000378:metabolism
chemical_list: D014867:Water