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Next generation sequencing of miR6024 overexpressing tomato transgenics in control state and under Alternaria solani stress

ABSTRACT: miR6024 overexpression may lead to changes in the transcriptome profile of tomato plants. Further changes may be noticed on infecting these plants with the necrotrophic pathogen Alternaria solani. These changes can only be gauged by carrying out a comparative transcriptome analysis with the wild type plants under similar conditions. We have used tomato (Pusa Ruby) for generation of miR6024 overexpressing transgenics. Disease study on these plants were carried out with the necrotrophic fungus A. solani. We carried an RNA-seq analysis using Illumina hiseq sequencing of 5 RNA libraries created from leaf tissues of wild type, OVX6024 transgenics and A. solani infected wild type and OVX6024 plants. The analysis revealed that 334 and 781 genes were significantly regulated in the transgenic plants and the infected transgenic plants respectively, with respect to their suitable wild type controls. GO enrichment analysis and pathway analysis have been carried out as well. This work is supported by grants from DBT and SERB, GoI.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE166013 | GEO | 2021/07/02

REPOSITORIES: GEO

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Project description:A comparative study ware made to know the Early Blight resistance mechanism between resistant and susceptible plants at vegetative stage. Transcriptional changes during compatible and resistant reaction between A. solani and tomato genotypes have been identified using Affymetrix tomato gene chips. Results were confirmed by reverse transcription-polymerase chain reaction with the samples collected after 24hrs of inoculation from inoculated and control susceptible and resistant genotypes. The number of up and down regulated genes in three different combinations of treatments i.e. Early Blight Resistant Treated and Control (EBTT and EBTC) and Early Blight Suceptible Treated and Control (EBST and EBSC) has observed and compared. In EBST vs. EBSC condition, 3478 genes are up regulated and 2663 are down regulated. Similarly when analysis is done between EBST and EBRT, 2475 genes are up regulated and 3662 are down regulated. Total 3442 genes are up regulated and 2695 genes are found to be down regulated in resistant line of tomato for early blight when the analysis is done for EBRT Vs. EBRC. These genes, that are induced in the resistant genotype EC-520061(Solanum habrochaites , wild) of tomato, after Alternaria solani infection, have been classified in to following categories, response to stress, cellular component, Metabolic activity, regulation of transcription, regulation of translation, and few were unknown. Data from this study are a resource for understanding the mechanism, which works for resistance against pathogen of early blight in tomato, which is critical and will be useful in improving this trait through transgenic approach or gene silencing. Tomato plants were exposed to A. solani spores and after 24 hrs (at the stage of penetration of tissues with fungal hyphae) samples were collected from both susceptible and resistant genotypes for RNA extraction and hybridization on Affymetrix chips. To study the molecular mechanism of biotic stress resistance, transcripts of both the genotypes were compared in response to A. solani.

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Next generation sequencing of miR6024 overexpressing tomato transgenics in control state and under Alternaria solani stress

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