In Focus

Next Generation Challenge Program on Chickpea Genomics (NGCPCG)



Legumes, by virtue of being rich source of proteins and nitrogen-fixers, are important components of agricultural activity. It is considered that chickpea (Cicer arietinum) was domesticated in North/Middle-East during Neolithic times to ultimately become the part of "Grain Ensemble". Its world-wide production crosses nine million tons. India accounts for 65% of world-wide land under chickpea cultivation and 60% production. Within India, chickpea contributes 45% of pulse basket and occupies 33% of the total land under pulse cultivation. Two common types of chickpea are represented by "Kabuli" and "Desi" and show low level of genetic variability. The size of chickpea genome is estimated to be 740 Mb. It is estimated that variability of over 20,000 accessions of chickpea at ICRISAT might be represented by a core and minicore germplasm collection of 1956 and 211 accessions, respectively.

           The productivity of grain legumes, in general, and chickpea, in particular, is low and it is further reduced tremendously mainly due to abiotic and biotic stresses. Thus, improvement in yield, nutritional quality and stress tolerance are main targets for research. Improvement of chickpea entails bridging the huge gap between genotype and phenotype. This requires development of resources to complement ongoing efforts on genetic enhancements which could include (i) generation of genome-wide sequence and assessment of natural variation at DNA level; (ii) analysis of biologically relevant genes/alleles correlating with specific traits on the basis of transcriptome, proteome and function; (iii) data analysis, management and dissemination; and (iv) genomics-assisted breeding.

            Next generation sequencing technologies have ushered in a new era in sequencing, genotyping and transcriptomics. Availability of the sequence of a reference genome of chickpea can be utilized to assess DNA level variability by way of high-throughput genotyping of selected germplasm and mapping populations. This could help generate an enriched DNA based genetic map of chickpea for mapping important traits. The gene content unraveled from sequence could aid in comparative genomics and support the understanding of the molecular basis of useful traits by transcriptomics, proteomics and regulatory networking. Some time back, Scientists of NIPGR initiated a programme on chickpea genome research. This has generated useful information on genome diversity, marker development, molecular mapping, ESTs, and gene function analysis.

            Keeping the above in view, to grow from existing strength and to diversify for innovation, Next Generation Challenge Programme on Chickpea Genomics has been initiated by nine NIPGR Scientists, with the following objectives :-

            1. Chickpea genome sequence analysis and its alignment to genetic map.

            2. Functional genomics of stress tolerance in chickpea

            3. Functional genomics of chickpea seed development and nutrition

       The research programme would develop enabling tools and genomic resources for chickpea community and seek national/ international collaboration.The outcome is expected to serve as key component for future research on chickpea molecular breeding, gene mapping, functional genomics and genetic enhancement for important agronomic traits.




Professor Akhilesh K. TyagiProject Coordinator
Co-Principal Investigator,
Dr. Niranjan ChakarbortyPrincipal
Dr. Subhra ChakarbortyPrincipal
Dr. Sabhyata BhatiaPrincipal
Dr. Debasis ChattopadhyayCo-Principal
Dr. Parveen Verma Co-Principal
Dr. Gitanjali YadavCo-Principal
Dr. Manoj MajeeCo-Principal
Dr. Mukesh Jain Co-Principal


Objective 1. Chickpea genome sequence analysis and its alignment to genetic map.

S. Bhatia

D. Chattopadhyay

M. Jain

G. Yadav

A. K. Tyagi

Objective 2. Functional genomics of stress tolerance in chickpea.

N. Chakraborty

D. Chattopadhyay

P. Verma

M. Majee

Objective 3. Functional genomics of chickpea seed development and nutrition.

S. Chakraborty

S. Bhatia

Sequencing Status


We have generated the draft sequence of a desi(ICC4958) type chickpea genome using next generation sequencing platforms, bacterial artificial chromosome end sequences and a genetic map. The 520 Mb assembly covers 70% of the predicted 740 Mb genome length and more than 80% of the gene space. Genome analysis predicts the presence of 27,571 genes and 210 Mb as repeat elements. The gene expression analysis performed using 274 million RNA-Seq reads identified several tissue-specific and stress-responsive genes. Although segmental duplicated blocks are observed, chickpea genome does not exhibit any indication of recent whole genome duplication. Nucleotide diversity analysis provides an assessment of a narrow genetic base within the chickpea cultivars. We have developed a resource for genetic markers by comparing the genome sequences of one wild and three cultivated chickpea genotypes. The draft genome sequence is expected to facilitate genetic enhancement and breeding to develop improved chickpea varieties.

For Genome Sequence:Click here

For downloading the paper from The Plant Journal site:Click here

Chickpea Advanced draft genome.

Further, we reported an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively.

For Advanced draft genome (Draft 2) sequence: Click Here

For downloading the paper from Scientific Reports: Click here


The whole transcriptome of chickpea (genotype ICC4958) has been sequenced using Roche 454 and Illumina next generation sequencing platforms, and assembled (de novo) into a total of 34,760 tentative consensus (TC) transcripts. The transcriptome sequence, annotation and gene expression data is publicly available via the Chickpea Transcriptome Database (CTDB).



Jain D and Chattopadhyay D (2013) Promoter of CaZF, a chickpea gene that positively regulates growth and stress tolerance, is activated by an AP2-family transcription factor CAP2. PLoS One 8: e56737.

Jain M, Misra G, Patel R, Priya P, Jhanwar S, Khan A, Shah N, Singh V, Garg R, Jeena G, Yadav M, Kant C, Sharma P, Yadav G, Bhatia S, Tyagi A and Chattopadhyay D (2013) A draft genome sequence of the pulse crop chickpea (Cicerarietinum L.). Plant Journal (In Press).DOI : 10.1111/tpj.12173.

Jaiswal P, Cheruku JR, Kumar K, Yadav S, Singh A, Kumari P, Dube SC, Upadhyaya KC and Verma PK (2012) Differential transcript accumulation in chickpea during early phases of compatible interaction with a necrotrophic fungus Ascochytarabiei. Mol. Biol. Rep. (In Press).

Kaur H, Verma P, Petla BP, Rao V, Saxena SC and Majee M (2013) Ectopic expression of the ABA-inducible dehydration-responsive chickpea L-myo-inositol 1-phosphate synthase 2 (CaMIPS2) in Arabidopsis enhances tolerance to salinity and dehydration stress. Planta (In Press).

Verma P, Kaur H, Petla BP, Rao V, Saxena SC and Majee M (2013) PROTEIN L- ISOASPARTYL METHYLTRANSFERASE2 gene is differentially expressed in chickpea and enhances seed vigor and longevity by reducing abnormal isoaspartyl accumulation predominantly in seed nuclear proteins. Plant Physiol. (In Press).


Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK, Garg R, Tyagi AK and Jain M (2012) Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS One 7: e52443.

Choudhary S, Guar R, Gupta S and Bhatia S (2012) EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. Theor. Appl. Genet. 124: 1449-1462.

Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D and Bhatia S (2012) High-Throughput SNP discovery and genotyping for constructing a saturated linkage map of Chickpea (Cicerarietinum L.). DNA Res. 19: 357-373.

Islam MN, Nizam S and Verma PK (2012) A highly efficient Agrobacterium mediated transformation system of chickpea wilt pathogen Fusariumoxysporum f. sp. ciceri using DsRed-Express to follow root colonization. Microbiol. Res. 167: 332-338.

Jaiswal P, Cheruku JR, Kumar K, Yadav S, Singh A, Kumari P, Dube SC, Upadhyaya KC and Verma PK (2012) Differential transcript accumulation in chickpea during early phases of compatible interaction with a necrotrophic fungus Ascochytarabiei. Mol. Biol. Rep. 39: 4635-4646

Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK and Jain M (2012) Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol. Journal 10: 690-702.

Wardhan V, Jahan K, Gupta S, Chennareddy S, Datta A, Chakraborty S and Chakraborty N (2012) Overexpression of CaTLP1, a putative transcription factor in chickpea (Cicerarietinum L.), promotes stress tolerance. Plant Mol. Biol. 79: 479-493

Yadav S, Kushwaha HR, Kumar K and Verma PK (2012) Comparative structural modelling of a monothiol GRX from chickpea: insight in iron-sulfur cluster assembly. Int. J. Biol. Macromol. 51: 266-273


Bhushan D, Jaiswal DK, Ray D, Basu D, Datta A, Chakraborty S and Chakraborty N (2011) Dehydration-responsive reversible and irreversible changes in the extracellular matrix: comparative proteomics of chickpea genotypes with contrasting tolerance. J. Proteome Res. 10: 2027-2046.

Garg R and Jain M (2011) Pyrosequencing data reveals tissue-specific expression of lineage-specific transcripts in chickpea. Plant Signal. Behav. 6: 1868-1870.

Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK and Jain M (2011) Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol. 156: 1661-1678.

Garg R, Patel RK, Tyagi AK and Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 18: 53-63.

Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V and Bhatia S (2011) Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genomics 12: 117.

Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Bhanu Prakash A, Farmer A, Bhide M, Shah T, Gaur PM, Upadhyaya HD, Bhatia S, Cook DR, May GD and Varshney RK (2011) Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theor. Appl. Genet.122: 1577-1589.

Gupta S, Wardhan V, Verma S, Gayali S, Rajamani U, Datta A, Chakraborty S and Chakraborty N (2011) Characterization of the secretome of chickpea suspension culture reveals pathway abundance and the expected and unexpected secreted proteins. J. Proteome Res. 10: 5006-5015.


Garg R, Sahoo A, Tyagi AK and Jain M (2010) Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.). Biochem. Biophys. Res. Comm. 396: 283-288.

Jain D and Chattopadhyay D (2010) Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum L.) varieties differing in drought tolerance. BMC Plant Biol. 10:24.

Nizam S, Singh K and Verma PK (2010) Expression of the fluorescent proteins DsRed and EGFP to visualize early events of colonization of the chickpea blight fungus Ascochyta rabiei. Current Genetics 56: 391-399.

Verma P, Singh A, Kaur H and Majee M (2010) Protein L :- isoaspartyl methyltransferase1 (CaPIMT1) from chickpea mitigates oxidative stress-induced growth inhibition of Escherichia coli. Planta 231:329-336.


Ashraf N, Ghai D, Barman P, Basu S, Gangisetty N, Mandal MK, Chakraborty N, Datta A and Chakraborty S (2009) Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity. BMC Genomics 10:415.

Choudhary S, Sethy NK, Shokeen B and Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor. Appl. Genet. 118: 591-608.

Jain D, Roy N and Chattopadhyay D (2009) CaZF, a plant transcription factor functions through and parallel to HOG and calcineurin pathways in Saccharomyces cerevisiae to provide osmotolerance. PLoS ONE 4: e5154.

Shukla RK, Tripathi V, Jain D, Yadav RK and Chattopadhyay D (2009) CAP2 enhances germination of transgenic tobacco seeds at high temperature and promotes heat stress tolerance in yeast. FEBS J. 276:5252-5262.

Tripathi V, Parasuraman B, Laxmi A and Chattopadhyay D (2009) CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plant. Plant Journal 58:778-790.

Tripathi V, Syed N, Laxmi A and Chattopadhyay D (2009) Role of CIPK6 in root growth and auxin transport. Plant Signal. Behav. 4:663-665.


Kaur H, Shukla RK, Yadav G, Chattopadhyay D and Majee M (2008) Two divergent genes encoding L-myoinositol-1-phosphate synthase I (CaMIPS1 and CaMIPS2) are differentially expressed in chickpea. Plant Cell Environ. 31:1701-1716.

Pandey A, Chakraborty S, Datta A and Chakraborty N (2008) Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol. Cell. Proteomics 7: 88-107.

Singh A, Singh IK and Verma PK (2008) Differential transcript accumulation in Cicer arietinum L. in response to a chewing insect Helicoverpa armigera and defense regulators correlate with reduced insect performance J. Exp. Bot. 59: 2379-2392.


Bhushan D, Pandey A, Choudhary MK, Datta A, Chakraborty S and Chakraborty N (2007) Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress. Mol. Cell. Proteomics 6: 1868 -1884.

Varshney RK, Hoisington DA, Upadhyaya HD, Gaur PM, Nigam SN, Saxena K, Vadez V, Sethy NK, Bhatia S, Aruna R, Gowda MVC and Singh NK (2007) Molecular genetics and breeding of grain legume crops for the semi-arid tropics. Varshney RK and Tuberosa R (eds.), Genomic Assisted Crop Improvement, Vol 2: Genomics Applications in Crops. Springer, Dordrecht, The Netherlands, pp 207-241.


Bhushan D, Pandey A, Chattopadhyay A, Choudhary MK, Chakraborty S, Datta A and Chakraborty N (2006) Extracellular matrix proteome of chickpea (Cicer arietinum L.) illustrates pathway abundance, novel protein functions and evolutionary perspect. J. Proteome Res. 5: 1711-1720.

Choudhary S, Sethy NK, Shokeen B and Bhatia S (2006) Development of sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Molecular Ecology Notes 6: 93-95.

Pandey A, Choudhary MK, Bhushan D, Chattopadhyay A, Chakraborty S, Datta A and Chakraborty N (2006) The nuclear proteome of chickpea (Cicer arietinum L.) reveals predicted and unexpected proteins. J. Proteome Res. 5: 3301-3311.

Sethy NK, Choudhary S, Shokeen B and Bhatia S (2006) Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis. Theor. Appl. Genet.112: 347-357.

Sethy NK, Shokeen B, Edwards KJ and Bhatia S (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 112: 1416-1428.

Shukla RK, Raha S, Tripathi V and Chattopadhyay D (2006) Expression of CAP2, an AP2-family transcription factor from chickpea enhances growth and tolerance to dehydration and salt tress in transgenic tobacco. Plant Physiology 142:113-123.


Boominathan P, Shukla R, Kumar A, Manna D, Negi D, Verma PK and Chatopadhyay D (2004) Long term transcript accumulation during the development of dehydration adaptation in Cicer arietinum L. Plant Physiology 135:1608-1620.

Tewrai-Singh N, Sen J, Kiesecker H, Reddy VS, Jacobsen HJ and Guha-Mukherjee (2004) Use of a herbicide or lysine and threonine for non-antibiotic selection of transgenic chickpea. Plant Cell Reports 22: 576-583.


Sethy NK, Shokeen B and Bhatia S (2003) Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer arietinum L.). Mol. Ecol. Notes 3: 428-430.




Sethy NK, Shokeen B and Bhatia S (2003) Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer arietinum L.). Mol. Ecol. Notes 3: 428-430.