BMC Genomics 2009, 10:415 http://www.biomedcentral.com/1471-2164/10/415 gated. Plant pathogenesis related genes like cationic per- oxidase, disease resistance related protein DRRG 49C, pathogen and wound-inducible antifungal protein CBP20 and pathogenesis related protein were also represented more in the resistant genotype. Cationic peroxidase has been shown to be associated with incompatible plant- pathogen interaction [96]. It is known that ECM/cell wall modifying enzymes play important role against invading pathogens. Genes encoding many such enzymes, for example, callose synthase was present in the resistant gen- otype. Furthermore, brassinosteroid regulated protein, BRU1 was present more in the resistant genotype. Domain search of BRU1 showed that it has xyloglucan endotransglycosylase activity and is involved in cell wall remodeling. Selenium binding proteins were found to be more abundant in the incompatible genotype suggesting their possible role in imparting plant disease resistance. Studies have shown that overexpression of a homologue of mammalian selenium binding protein in rice results in enhanced resistance to blast fungus and bacterial blight [97]. Nonaspanin, an endomembrane protein, involved in intracellular vesicular trafficking was present specifi- cally in the resistant genotype. Further, presence of ESTs encoding proteins like narbonin, cupin domain protein and AKIN gamma specifically in the resistant genotype is indicative of their possible role in pathogen stress. While narbonin is known to be a seed storage protein [98], cupin domain proteins have diverse functional roles in seed germination, seedling development and modifica- tion of cell wall carbohydrates [99], however, their role in pathogen stress is yet to be elucidated. It was intriguing that most of the genes reported, earlier, to be involved in auxin signaling pathway were specific to susceptible genotype, thereby suggesting a possible role of auxin signalling in compatible plant-pathogen interac- tion. Such genes included auxin-induced putative aldo/ keto reductase family protein, aux/IAA protein and puta- tive auxin-induced protein. However, auxin responsive SAUR protein was present in both the genotypes but with a much higher frequency in susceptible one. Auxin-regu- lated dual specificity cytosolic kinase was the only auxin- responsive gene found in the resistant genotype. A con- temporary study has suggested the involvement of auxin signaling pathway in the susceptibility of a plant to path- ogen attack [100]. Many other ESTs were also found to be more redundant in susceptible genotype. These include ESTs encoding chlorophyll a/b binding protein, cystatin and branched chain amino acid (BCAA) aminotrans- ferase. Cystatin belongs to cysteine proteinase inhibitor superfamily and has been reported to have antifungal activity [89]. BCAA aminotransferase serves in detoxifica- tion mechanism that maintains the pool of free branched chain amino acids at low and non toxic levels under dehy- dration [101]. Fusarium grows in the vascular system of the plant and the mycelial growth of the fungus may cause blockage of vascular tissue, which mimics the symptoms of dehydration and therefore, may lead to the accumula- tion of BCAA aminotransferase. Interestingly, we found many genes that have never been implicated in plant stress response, for example, deoxyhypusine synthase (DHS), which was found to be present in the susceptible genotype. Recent studies have shown that the silencing of DHS delays ripening in tomato [102]. Ripening often leads to weakening of cell wall and by doing so it may pre- dispose a plant to pathogen attack. Of very highly abun- dant contigs with total number of ESTs exceeding 20, thereby inferring their strong role in stress response, we found that genes encoding putative extensin, putative senescence-associated protein and RNA-binding region RNP-1 were more abundant in resistant genotype. On the other hand, genes encoding pfkB-type carbohydrate kinase known to be involved in preservation of intracellu- lar adenylate pools and alcohol dehydrogenase 1 were more abundant in the susceptible genotype. Next, it was of interest to find out the relationship between the genotype specific EST abundance with their expression pattern during incompatible interaction. Com- parison of microarray expression data with the origin of the respective genes revealed the following three types of correlations. Firstly, genes specific to or more abundant in the resistant genotype like those encoding chalcone reductase, DRRG 49C, cytochrome P450, cytochrome P450 monooxygenase CYP83G1, peroxidase, putative kinetochore protein, GOS11 and serine/threonine kinase showed induction during incompatible plant pathogen interaction. Secondly, genes which were represented only in the susceptible genotype did not show any significant expression in the incompatible interaction. These included drought responsive element binding protein, Calcium-binding EF-hand, Targeting for Xklp2 and Pro- tein kinase TonB box. Thirdly, many genes which were either absent or represented to a lesser extent in the resist- ant genotype but abundant in the susceptible one were found to be downregulated and included putative ripen- ing related protein, putative ADP, ATP carrier-like protein, probable pyridoxal biosynthesis protein PDX1 and triose- phosphate isomerase. Identification of putative new regulators of plant immune response Although biological processes including immune response are controlled by intricate regulatory networks of gene expression that is thought to be regulated by many regulatory genes, only few such genes have been reported till date. While exploring the gene expression patterns dur- ing chickpea-Fusarium interactions, we identified several novel regulatory genes specifically showing differential expression of transcripts, which strongly suggests putative Page 14 of 21 (page number not for citation purposes)