Transcriptomics

Now the chickpea genome has been sequenced!

Coordinators :

o	Peter Winter, GenXPro, Frankfurt, Germany
o	Eddie Pang, RMIT University, Australia


About :
Identification of genes underlying a trait of interest is of prime importance to crop improvement. Generation of ESTs are probably the first step towards understanding the transcriptome and isolate genes of interest. In case of chickpea, however, comprehensive EST resource has been developed very recently at ICRISAT and NIPGR. Recently, a set of 443,969 sequence tags were generated through FLX-454 sequencing from a pool of normalized cDNA assembled from developmental stages and abiotic stresses challenged tissues of a reference chickpea genotype (ICC 4958). Analysis of Sanger as well as FLX-454 sequence data provided 103,215 tentative unique sequences (TUSs). In parallel, transcriptomes of drought and Helicoverpa challenged tissues were sequenced using Solexa sequencing approach. Over 37 million drought responsive tags were obtained from ICC 4958 and ICC 81.2 million tags were generated from Helicoverpa challenged tissues of ICCC 37 and ICC 506 genotypes. To understand differential gene expression in response to stresses, transcript profiling has also been undertaken in chickpea using SuperSAGE technology and microarray analysis. It is anticipated that next generation sequencing technologies would facilitate transcript profiling at large scale in coming years.


Key publications :

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 (2006) Expression profiling of chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnol J 4:647–666 Shukla RK, Raha S, Tripathi V, Chattopadhyay D (2006) Expression of CAP2, an AP2-family transcription factor from chickpea enhances growth and tolerance to dehydration and salt stress in transgenic tobacco. Plant Physiol 142:113-123 Coram TE, Mantri NL, Ford R, Pang CKE (2007) Functional genomics in chickpea: an emerging frontier for molecular-assisted breeding. Functional Plant Biol 34:861–873 Mantri NL, Ford R, Coram TE, Pang CKE (2007) Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought. BMC Genomics 8:303 Ashraf N, Ghai D, Barman P, Basu S, Nagaraju G, Mandal MK, Chakraborty N, Datta A, Chakraborty S (2009) Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrates predicted and unexpected genes and novel regulators of plant immunity. BMC Genomics 10:415 Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, Winter P (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9:553


Publications in 2009:

Kavousi HR, Marashi H, Mozafari J and Bagheri AR (2009) Expression of phenylpropanoid pathway genes in chickpea defense against Race 3 of Ascochyta rabei. Plant Path J 8: 127-132. Varshney RK, Hiremath PJ, Pazhamala L, Junichi K, Jayashree B, Deokar AA, Vadez V, Xiao Y, Srinivasan R, Gaur PM, Siddique KHM, Town CD and Hoisington DA (2009) A comprehensive resource of drought- and salinity responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10:523