BMC Genomics 2009, 10:415 http://www.biomedcentral.com/1471-2164/10/415 functions for them in plant immune response. These include ESTs encoding putative protein kinase APK1A, SAR DNA-binding protein-1, BEL1-like homeodomain transcription factor, NAC domain containing protein, RabGAP/TBC and GTP-binding protein. Protein kinase cascades are critical for regulating plant defense systems against various kinds of pathogens and operate as efficient signal transmission networks linking extracellular stimuli with intracellular targets. The upregulation of APK1 strongly suggests its possible role in defense signaling. This protein was identified in Arabidopsis, however, its role has not yet been identified [103]. The expression of BEL1 and SAR DNA-binding protein-1 was found to be downregulated. BEL transcription factor plays role in pat- tern formation in ovules [104], SAR DNA binding protein is known to have multifunctional roles in chromatin organisation and ribosome biogenesis [105] while NAC domain protein is implicated in developmental processes. Thus, it will be of great interest to elucidate their role in plant immunity. The expression of RabGAP/TBC and GTP-binding protein was induced at 24 h after Fusarium infection suggesting their possible involvement in plant defense. A gene of RabGAP class has been shown to be involved in spermatogenesis in rats [106], however, there is no report regarding their role in immune response. These results support the existence of different regulatory systems that operates in vascular wilt inducible root spe- cific immune gene expression during plant defense. This divergence may be attributed to the specific interaction of a host to one of the specific pathogen of many that it encounters. Conclusion Genetic make up of any organism results from a subset of genes that it inherits. The regulated expression of genes is tightly controlled and shaped by the transcription machinery of the cell. Therefore, development of geno- type dependent organ specific kinetically controlled func- tional ESTs, identification of gene families and their associated transcriptomic and proteomic studies would reveal more and more yet unidentified sense and anti- sense transcripts; and transcript associated SNPs. This approach would essentially unravel the molecular basis of specificity at individual level that ultimately dictates the cellular physiology leading to the phenome variation. Our study is directed towards creating a gene resource (CaEST database) of chickpea for the systematic analysis of genotype-dependent organ-specific stimuli-responsive gene signatures that would provide an initial platform for gene discovery and functional genomics of this third most important but understudied food legume. This approach may be used in future to dissect diverse and overlapping biochemical pathways encompassed by the identified transcripts at individual level. This will also be important in long-term efforts to develop faithful, quantitative mod- els for plant processes. The efficiency of subtracted geno- type specific immune responsive EST sequencing is especially reflected in the number of new genes identified in this study, which is still moderate in size. A total of 2013 unigenes are reported that characterize the immune responsive transcripts of this important legume, of which approximately twelve percent represent new chickpea genes hitherto undiscovered. Our discovery of a large number of SNPs in expressed sequences should allow the genetic mapping of many genes underlying agricultural characteristics in chickpea. Although WR315 and JG62 may be presumably quite similar to one another at the nucleotide sequence level, we find they are equally differ- ent to each other in their transcript profile. In addition, the use of this approach in our present study led to the identification of 807 genes of unknown function now assigned to the immune response pathway with an organ specific localization, opens up a new area of investigation wherein the combining of our CaUnigene dataset with other databases can be used to draw relationships at sys- tem level. The results identified a set of 649 non-cannon- ical stress responsive genes which has never been associated with immune response. Further, homology search of the derived amino acid sequence data from the present study provides a firm indication of a number of components of the root to which function is still to be ascribed. The ESTs identified in this study represent the major attempt so far to define chickpea transcriptome. The microarray analysis of immune-responsive transcrip- tome uncovers new regulators of host-pathogen interac- tion. Assigning a functional role to each of these new immune regulators will be challenging and quite valuable in order to know the physiological significance of plant immunity. Nevertheless, the sequence information of chickpea is unavailable and the number of functionally annotated ESTs is low at this time, as this number increases, the transcriptome data will be proven even more useful. The recent identification of immune respon- sive genes from other organisms would eventually lead to develop a comparative species-specific immune respon- sive transcriptome in which this report becomes one of the first attempts. This is an initial attempt in the direction that will be expanded upon during future transcriptomic studies of plant processes. Our future efforts will focus onto enriching CaUnigene database and increasing the number of analyzed genes thereof, with an aim to draw a complete functional map of organ specific stimuli respon- sive transcriptome at individual level. Further, we will focus onto identifying the dynamics associated with the organ specific transcriptome towards cells metabolic and regulatory pathways at different physiological conditions shaping the phenome diversity. Page 15 of 21 (page number not for citation purposes)