Background: Cultivated chickpea (Cicer arietinum) has a narrow genetic base making it difficult for breeders to produce new elite cultivars with durable resistance to major biotic and abiotic stresses. As an alternative to genome mapping, microarrays have recently been applied in crop species to identify and assess the function of putative genes thought to be involved in plant abiotic stress and defence responses. In the present study, a cDNA microarray approach was taken in order to determine if the transcription of genes, from a set of previously identified putative stress-responsive genes from chickpea and its close relativeLathyrus sativus, were altered in chickpea by the three abiotic stresses; drought, cold and high-salinity. For this, chickpea genotypes known to be tolerant and susceptible to each abiotic stress were challenged and gene expression in the leaf, root and/or flower tissues was studied. The transcripts that were differentially expressed among stressed and unstressed plants in response to the particular stress were analysed in the context of tolerant/susceptible genotypes.Results: The transcriptional change of more than two fold was observed for 109, 210 and 386 genes after drought, cold and high-salinity treatments, respectively. Among these, two, 15 and 30 genes were consensually differentially expressed (DE) between tolerant and susceptible genotypes studied for drought, cold and high-salinity, respectively. The genes that were DE in tolerant and susceptible genotypes under abiotic stresses code for various functional and regulatory proteins. Significant differences in stress responses were observed within and between tolerant and susceptible genotypes highlighting the multiple gene control and complexity of abiotic stress response mechanism in chickpea.Conclusion: The annotation of these genes suggests that they may have a role in abiotic stress response and are potential candidates for tolerance/susceptibility.

SUMMARY: Stripe rust [caused by Puccinia striiformis Westend. f. sp. tritici Eriks. ( Pst )] is a destructive disease of wheat ( Triticum aestivum L.) worldwide. Genetic resistance is the preferred method for control and the Yr5 gene, originally identified in Triticum spelta var. album , represents a major resistance ( R ) gene that confers all‐stage resistance to all currently known races of Pst in the United States. To identify transcripts associated with the Yr5 ‐mediated incompatible interaction and the yr5 ‐compatible interaction, the Wheat GeneChip was used to profile the changes occurring in wheat isolines that differed for the presence of the Yr5 gene after inoculation with Pst . This time‐course study (6, 12, 24 and 48 h post‐inoculation) identified 115 transcripts that were induced during the R ‐gene‐mediated incompatible interaction, and 73 induced during the compatible interaction. Fifty‐four transcripts were induced in both interactions and were considered as basal defence transcripts, whilst 61 transcripts were specific to the incompatible interaction [hypersensitive response (HR)‐specific transcripts] and 19 were specific to the compatible interaction (biotrophic interaction‐specific transcripts). The temporal pattern of transcript accumulation showed a peak at 24 h after infection that may reflect haustorial penetration by Pst at ~16 h. An additional 12 constitutive transcript differences were attributed to the presence of Yr5 after eliminating those considered as incomplete isogenicity. Annotation of the induced transcripts revealed that the presence of Yr5 resulted in a rapid and amplified resistance response involving signalling pathways and defence‐related transcripts known to occur during R ‐gene‐mediated responses, including protein kinase signalling and the production of reactive oxygen species leading to a hypersensitive response. Basal defence also involved substantial induction of many defence‐related transcripts but the lack of R ‐gene signalling resulted in weaker response.

SUMMARY: Stripe rust [caused by Puccinia striiformis Westend. f. sp. tritici Eriks. ( Pst )] is a destructive disease of wheat ( Triticum aestivum L.) worldwide. High‐temperature adult‐plant (HTAP) resistance to stripe rust is race non‐specific, inherited quantitatively and durable. Previously, we identified and mapped the single Yr39 HTAP stripe rust resistance gene in the spring wheat cultivar Alpowa, which was identified on chromosome 7BL and accounted for 64.2% of the variation in resistance. To identify transcripts associated with Yr39 ‐mediated resistance, we selected two F ₇ recombinant inbred lines (RILs) from an ‘Avocet S/Alpowa’ cross that differed at the Yr39 locus to represent an incompatible ( Yr39 ) and compatible ( yr39 ) interaction with Pst . Using the Affymetrix Wheat GeneChip, we profiled the transcript changes occurring in flag leaves of these two RILs over a time‐course after treatment with Pst urediniospores and mock‐inoculation. This time‐course study identified 99 induced transcripts that were classified as HTAP resistance‐specific. The temporal pattern of transcript accumulation showed a peak at 48 h after infection, which was supported by microscopic observation of fungal development and quantitative PCR assays that showed a rapid increase in fungal biomass after this time in the compatible interaction. More than half (50.5%) of the annotated transcripts specifically induced during HTAP resistance were involved in defence and/or signal transduction, including R gene homologues and transcripts associated with pathogenesis‐related protein production, phenylpropanoid biosynthesis and protein kinase signalling. This study represents the first transcript profiling of HTAP resistance to stripe rust in wheat, and we compare our results with other transcript studies of race‐specific and race non‐specific resistance.

Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, continues to cause severe damage worldwide. Durable resistance is necessary for sustainable control of the disease. High-temperature adult-plant (HTAP) resistance, which expresses when the weather becomes warm and plants grow older, has been demonstrated to be durable. We conducted numerous studies to understand the molecular mechanisms of different types of stripe rust resistance using a transcriptomics approach. Through comparing gene expression patterns with race-specific, all-stage resistance controlled by various genes, we found that a greater diversity of genes is involved in HTAP resistance than in all-stage resistance. The genes involved in HTAP resistance are induced more slowly and their expression induction is less dramatic than genes involved in all-stage resistance. The high diversity of genes and less dramatic induction may explain durability and the incomplete expression level of HTAP resistance. Identification of transcripts may be helpful in identifying resistance controlled by different genes and in selecting better combinations of genes to combine for achieving adequate and durable resistance.

Summary: Using microarray technology and a set of chickpea (Cicer arietinum L.) unigenes, grasspea (Lathyrus sativus L.) expressed sequence tags (ESTs) and lentil (Lens culinaris Med.) resistance gene analogues, the ascochyta blight (Ascochyta rabiei (Pass.) L.) resistance response was studied in four chickpea genotypes, including resistant, moderately resistant, susceptible and wild relative (Cicer echinospermum L.) genotypes. The experimental system minimized environmental effects and was conducted in reference design, in which samples from mock‐inoculated controls acted as reference against post‐inoculation samples. Robust data quality was achieved through the use of three biological replicates (including a dye swap), the inclusion of negative controls and strict selection criteria for differentially expressed genes, including a fold change cut‐off determined by self–self hybridizations, Student's t‐test and multiple testing correction (P < 0.05). Microarray observations were also validated by quantitative reverse transcriptase‐polymerase chain reaction (RT‐PCR). The time course expression patterns of 756 microarray features resulted in the differential expression of 97 genes in at least one genotype at one time point. k‐means clustering grouped the genes into clusters of similar observations for each genotype, and comparisons between A. rabiei‐resistant and A. rabiei‐susceptible genotypes revealed potential gene ‘signatures’ predictive of effective A. rabiei resistance. These genes included several pathogenesis‐related proteins, SNAKIN2 antimicrobial peptide, proline‐rich protein, disease resistance response protein DRRG49‐C, environmental stress‐inducible protein, leucine‐zipper protein, polymorphic antigen membrane protein, Ca‐binding protein and several unknown proteins. The potential involvement of these genes and their pathways of induction are discussed. This study represents the first large‐scale gene expression profiling in chickpea, and future work will focus on the functional validation of the genes of interest.