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A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)

Rajeev K Varshney12*, Pavana J Hiremath1, Pazhamala Lekha1, Junichi Kashiwagi13, Jayashree Balaji1, Amit A Deokar4, Vincent Vadez1, Yongli Xiao5, Ramamurthy Srinivasan4, Pooran M Gaur1, Kadambot HM Siddique6, Christopher D Town5 and David A Hoisington1

Author Affiliations

1 International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, AP, India

2 Genomics Towards Gene Discovery Sub Programme, Generation Challenge Programme (GCP), c/o CIMMYT, Int. Apartado Postal 6-641, 06600, Mexico, D. F., Mexico

3 Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, 060-8589, Japan

4 National Research Centre on Plant Biotechnology (NRCPB), IARI Campus, New Delhi-110012, India

5 J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850, USA

6 Institute of Agriculture, The University of Western Australia (UWA) (M082), 35 Stirling Highway, Crawley WA 6009, Australia

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BMC Genomics 2009, 10:523  doi:10.1186/1471-2164-10-523

Published: 15 November 2009



Chickpea (Cicer arietinum L.), an important grain legume crop of the world is seriously challenged by terminal drought and salinity stresses. However, very limited number of molecular markers and candidate genes are available for undertaking molecular breeding in chickpea to tackle these stresses. This study reports generation and analysis of comprehensive resource of drought- and salinity-responsive expressed sequence tags (ESTs) and gene-based markers.


A total of 20,162 (18,435 high quality) drought- and salinity- responsive ESTs were generated from ten different root tissue cDNA libraries of chickpea. Sequence editing, clustering and assembly analysis resulted in 6,404 unigenes (1,590 contigs and 4,814 singletons). Functional annotation of unigenes based on BLASTX analysis showed that 46.3% (2,965) had significant similarity (≤1E-05) to sequences in the non-redundant UniProt database. BLASTN analysis of unique sequences with ESTs of four legume species (Medicago, Lotus, soybean and groundnut) and three model plant species (rice, Arabidopsis and poplar) provided insights on conserved genes across legumes as well as novel transcripts for chickpea. Of 2,965 (46.3%) significant unigenes, only 2,071 (32.3%) unigenes could be functionally categorised according to Gene Ontology (GO) descriptions. A total of 2,029 sequences containing 3,728 simple sequence repeats (SSRs) were identified and 177 new EST-SSR markers were developed. Experimental validation of a set of 77 SSR markers on 24 genotypes revealed 230 alleles with an average of 4.6 alleles per marker and average polymorphism information content (PIC) value of 0.43. Besides SSR markers, 21,405 high confidence single nucleotide polymorphisms (SNPs) in 742 contigs (with ≥ 5 ESTs) were also identified. Recognition sites for restriction enzymes were identified for 7,884 SNPs in 240 contigs. Hierarchical clustering of 105 selected contigs provided clues about stress- responsive candidate genes and their expression profile showed predominance in specific stress-challenged libraries.


Generated set of chickpea ESTs serves as a resource of high quality transcripts for gene discovery and development of functional markers associated with abiotic stress tolerance that will be helpful to facilitate chickpea breeding. Mapping of gene-based markers in chickpea will also add more anchoring points to align genomes of chickpea and other legume species.