Genomic Resources

Now the chickpea genome has been sequenced!

Coordinators:

o	R Varma Penmetsa, UC-Davis, USA
o	Sabhyata Bhatia, NIPGR, India


About:
Molecular markers and genomic tools are the pre-requisites for undertaking molecular breeding activities. Although in the past development of genomic resources in chickpea has been slow, a few hundred SSR markers were developed at University of Frankfurt. However, recent years have witnessed development of large number of SSR markers and several hundreds are already available in public domain. Similar has been the case for the ESTs, however, at present about 30,000 Sanger ESTs are available in public domain. It seems that next generation sequencing technologies will generate a huge amount of genomic resources in chickpea.


Key publications :

i) SSRs Winter P, Pfaff T, Udupa SM, Hüttel B, Sharma PC, Sahi S, Arrequin-Espinoza R, Weigand F, Muehlbauer FJ, Kahl G (1999) Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (C. arietinum L.). Mol Genet Genomics 262:90–101 Hüttel B, Winter P, Weising K, Choumane W, Weigand F (1999) Seguence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome 42:210–217 Sethy NK, Choudhary S, Shokeen B, Bhatia S (2006a) Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis. Theor Appl Genet 112:347– 357 Sethy NK, Shokeen B, Edwards KJ, Bhatia S (2006b) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet 112:1416-1428 Rajesh PN, Coyne C, Meksem K, Dev Sharma K, Gupta V, Muehlbauer FJ (2004) Construction of a HindIII bacterial artificial chromosome library and its use in identification of clones associated with disease resistance in chickpea. Theor Appl Genet 108:663–669 Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB (2005) Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor Appl Genet 110:492–510 Choudhary S, Sethy NK, Shokeen B, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118:591-608 ii) ESTs Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH (2005) Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biol 5:16 Coram TE, Pang CKE (2005) Isolation and analysis of candidate ascochyta blight defence genes in chickpea. Part I. Generation and analysis of an expressed sequence tag (EST) library. Physiological and Molecular plant pathology 66:192-200 Gao WR, Wanga XS, Liu OY, Peng H, Chen C, Li JG (2008) Comparative analysis of ESTs in response to drought stress in chickpea (C. arietinum L.). Biochem Biophys Res Commun 376:578–583 iii) SNPs Varshney RK, Nayak S, Jayashree B, Eshwar K, Upadhyaya HD, Hoisington DA (2007) Development of cost-effective SNP assays for chickpea genome analysis and breeding. SAT eJournal 3:1 Rajesh PN, Muehlbauer FJ (2008) Discovery and detection of single nucleotide polymorphism (SNP) in coding and genomic sequences in chickpea (Cicer arietinum L.). Euphytica 162:291-300


Publications in 2009:

Choudhary S, Sethy NK, Shokeen B, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118: 591–608 Datta S, Kaashyap M, Kumar S (2009) Amplification of chickpea-specific SSR primers in Cajanus species and their validity in diversity analysis. Plant Breed doi:10.1111/j.1439-0523.2009.01678.x