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Shared and unique transcriptomic changes in chickpea in response to concurrent drought stress and Ralstonia solanacearum pathogen

ABSTRACT: Chickpea (Cicer arietinum) is the third largest legume grown worldwide and are prone to drought and various pathogen infections. These stresses often occur concurrently in the field conditions. Previous studies in other plant species indicated that plant senses concurrently occurring stresses as new state of stress however, the molecular events in response to that is largely unknown. In the present study, we studied the transcriptome changes in chickpea plants exposed to combination of drought stress and a potential wilt pathogen, Ralstonia solanacearum by microarray analysis. Chickpea plants were exposed to short duration individual drought (SD-drought, soil field capacity, FC-35%), long duration individual drought (LD-drought, FC-30%), short duration individual pathogen stress (SD-pathogen = 2 days pathogen infection), long duration individual pathogen stress (LD-pathogen = 4 days of infection) and short duration and long duration combined stress, SD-combined = 2 days of pathogen infection with progressive drought (FC-40% to FC- 35%), LD combined = 4 days of pathogen infection with progressive drought (FC-35% to 30%).Transcriptome analysis for the leaf samples from above treatment were done by microarray analysis using Agilent ChickpeaGXP_8X60K chip. Result indicated presence of specific molecular events and also some common but tailored events in response to combined stress. Global transcriptional analysis in chickpea leaves exposed to individual and combined drought stress and Ralstonia solanacearum infection.

ORGANISM(S): Cicer arietinum

PROVIDER: GSE89228 | GEO | 2017/06/13

SECONDARY ACCESSION(S): PRJNA350782

REPOSITORIES: GEO

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Project description:Background Drought is the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought tolerance is therefore of outmost importance for breeding. However, the complexity of the trait allowed only marginal progress. A solution to the current stagnation is expected from innovative molecular tools such as transcriptome analyses providing insight into stress-related gene activity and, combined with molecular markers and expression (e)QTL mapping, may accelerate knowledge-based breeding. SuperSAGE, an improved version of the serial analysis of gene expression (SAGE) technique, currently is the most advanced tool for transcriptome analysis. SuperSAGE generates genome-wide, high-quality transcription profiles from any eukaryote. The method produces 26bp long fragments (SuperTags26bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs. Further, SuperSAGE Tags may be immediately used to produce so called SuperTag microarrays and probes for real-time-PCR thereby overcoming the lack of genomic tools in non-model organisms. Results We applied SuperSAGE to the analysis of gene expression in chickpea roots in response to drought. To this end, we sequenced 80,238 26bp SuperTtags representing 17,493 unique transcripts (UniTags) from drought-stressed and non-stressed control roots. A total of 7,532 (43%) UniTags were more than 2.7-fold differentially expressed , and 880 (5.0%) were regulated more than 8-fold upon stress. Their large size enabled the unambiguous annotation of 2,798 (16.3%) UniTags to genes or proteins in public data bases and thus to stress-response processes. We designed a microSuperTag array carrying 3,000 of these SuperTags26bp tags. The chip data confirmed the SuperSAGE results in 79 % of cases whereas RT-PCR confirmed the SuperSAGE data in all cases. Conclusions This study represents the most comprehensive analysis of the drought-response transcriptome of chickpea available to date. It demonstrates that - inter alias - signal transduction, transcription regulation, osmolyte accumulation, chromosome organization, and ROS scavenging undergo strong transcriptional remodelling in chickpea roots already 6h after drought stress. Certain transcript isoforms characterizing these processes are potential targets for breeding for drought tolerance. We demonstrate that these can be easily accessed by micro-arrays and RT-PCR assays readily produced downstream of SuperSAGE. Our study proves that SuperSAGE has a good potential is best suited for molecular breeding also in non-model crops.

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Shared and unique transcriptomic changes in chickpea in response to concurrent drought stress and Ralstonia solanacearum pathogen

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