SRNA profiling between the 7B-1 male-sterile tomato and its wild type in response to abiotic stress
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ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE65964 | GEO | 2015/10/01
SECONDARY ACCESSION(S): PRJNA275584
REPOSITORIES: GEO
Similar Datasets
Project description:The 7B-1 tomato (Solanum lycopersicum L. cv Rutgers) is a male-sterile mutant with enhanced tolerance to abiotic stress, which makes it a potential candidate for hybrid seed breeding and stress engineering. Transcriptomic profiles of the 7B-1 male-sterile and wild type (WT) anthers were studied using mRNA sequencing (RNA-Seq). In total, 768 differentially expressed genes (DEGs) were identified, including 132 up-regulated and 636 down-regulated transcripts. Gene ontology (GO) enrichment analysis of DEGs suggested a general impact of the 7B-1 mutation on metabolic processes, such as proteolysis and carbohydrate catabolic process. Sixteen candidates with key roles in regulation of anther development were subjected to further analysis using qRT-PCR and in situ hybridization. Cytological studies showed several defects associated with anther development in the 7B-1 mutant, including unsynchronized anther maturation, dysfunctional meiosis, arrested microspores, defect in callose degradation and abnormal tapetum development. TUNEL assay showed a defect in programmed cell death (PCD) of tapetal cells in 7B-1 anthers. The present study provides insights into the transcriptome of the 7B-1 mutant. We identified several genes with altered expression level in 7B-1 (including beta-1,3 glucanase, GA2oxs, cystatin, cysteine protease, pectinesterase, TA29, and actin) that could potentially regulate anther developmental processes, such as meiosis, tapetum development, and cell-wall formation/degradation.
2017-02-09 | GSE85859 | GEO
Project description:The RNA-seq was used to identify differentially regulated miRNAs between a male sterile and wild type tomato during anther development.
2015-10-01 | GSE65788 | GEO
Project description:The 7B-1 tomato (Solanum lycopersicum L. cv Rutgers) is a male-sterile mutant with enhanced tolerance to abiotic stress, which makes it a potential candidate for hybrid seed breeding and stress engineering. To underline the molecular mechanism regulating the male-sterility in 7B-1, transcriptomic profiles of the 7B-1 male-sterile and wild type (WT) anthers were studied using mRNA sequencing (RNA-Seq). In total, 768 differentially expressed genes (DEGs) were identified, including 132 up-regulated and 636 down-regulated transcripts. Gene ontology (GO) enrichment analysis of DEGs suggested a general impact of the 7B-1 mutation on metabolic processes, such as proteolysis and carbohydrate catabolic process. Sixteen candidates with key roles in regulation of anther development were subjected to further analysis using qRT-PCR and in situ hybridization. Cytological studies showed several defects associated with anther development in the 7B-1 mutant, including unsynchronized anther maturation, dysfunctional meiosis, arrested microspores, defect in callose degradation and abnormal tapetum development. TUNEL assay showed a defect in programmed cell death (PCD) of tapetal cells in 7B-1 anthers. The present study provides insights into the transcriptome of the 7B-1 mutant. We identified several genes with altered expression level in 7B-1 (including beta-1,3 glucanase, GA2oxs, cystatin, cysteine protease, pectinesterase, TA29, and actin) that could potentially regulate anther developmental processes, such as meiosis, tapetum development, and cell-wall formation/degradation.
| S-EPMC5298235 | biostudies-literature
Project description:A comparative study ware made to know the abiotic stress tolerance machanism between tolerant and susceptible plants at flowering stage. The tolerance in response to abiotic stresses are sum of expression of thousands of genes at a particular stage. Tomato plants were exposed to drought and heat stress for RNA extraction and hybridization on Affymetrix microarrays. To study the molecular mechanism of abiotic stress tolerance to increase the tolerance in tomato plants, transcripts of tolerant and susceptible plants at flowering stage were compared in response to heat and water stress.
2010-06-23 | E-GEOD-22304 | biostudies-arrayexpress
Project description:To compare the global gene expression between male sterile line (ms1035) and fertile line (T-1082), RNA-seq was performed using different tstages of floral buds. A strand-specific RNA-seq library was constructed and sequence using Illumina Hiseq 2500. Differentailly expressed genes were identified using CLC Genomics Workbench 6.0 and DESeq tool of R.
2017-08-10 | GSE102374 | GEO
Project description:To elucidate the molecular and metabolic changes in tomato plants that occur by the interaction of tomato roots and MBI600 elicitors, fifteen-day-old tomato seedlings were transferred to liquid MS (2 seedlings/2mL of medium in wells of 24-well-plates) and after 3 hours the medium was supplied with MBI600 CFCF to 1/5 v/v volume or with flg22 peptide (Eurogentec) to a final concentration of 1μΜ. Seedlings were collected in different time points after treatment (6 and 24h). Three independent experiments were performed. Each experiment included 2 biological replicates per treatment and each replicate was a pool of two seedlings. Sixteen genes were selected and their transcript levels were tested by Real-Time qPCR. A pathway analysis was performed and the complex signaling network that is implicated in MBI600-host interactions was mapped. The coordinated expression of genes that participate in biosynthetic pathways or are responsive to auxin, JA/ET, SA and redox signalling of biotic and abiotic stress responses, suggests that PGPR elicitors and metabolites activate (non-specifically) plant defense.
2018-12-11 | GSE123589 | GEO
Project description:The 7B-1 tomato line (Solanum lycopersicum cv. Rutgers) is a photoperiod-sensitive male-sterile mutant, with potential application in hybrid seed production. Small RNAs (sRNAs) in tomato have been mainly characterized in fruit development and ripening, but none have been studied with respect to flower development and regulation of male-sterility. Using sRNA sequencing, we identified miRNAs that are potentially involved in anther development and regulation of male-sterility in 7B-1 mutant.Two sRNA libraries from 7B-1 and wild type (WT) anthers were sequenced and thirty two families of known miRNAs and 23 new miRNAs were identified in both libraries. MiR390, miR166, miR159 were up-regulated and miR530, miR167, miR164, miR396, miR168, miR393, miR8006 and two new miRNAs, miR#W and miR#M were down-regulated in 7B-1 anthers. Ta-siRNAs were not differentially expressed and likely not associated with 7B-1 male-sterility. miRNA targets with potential roles in anther development were validated using 5'-RACE. QPCR analysis showed differential expression of miRNA/target pairs of interest in anthers and stem of 7B-1, suggesting that they may regulate different biological processes in these tissues. Expression level of most miRNA/target pairs showed negative correlation, except for few. In situ hybridization showed predominant expression of miR159, GAMYBL1, PMEI and cystatin in tapetum, tetrads and microspores.Overall, we identified miRNAs with potential roles in anther development and regulation of male-sterility in 7B-1. A number of new miRNAs were also identified from tomato for the first time. Our data could be used as a benchmark for future studies of the molecular mechanisms of male-sterility in other crops.
| S-EPMC4625851 | biostudies-literature
Project description:We reported earlier that 7B-1 mutant in tomato (Solanum lycopersicum L., cv. Rutgers), an ABA overproducer, is defective in blue light (B) signaling leading to B-specific resistance to abiotic and biotic stresses. Using a methylation-sensitive amplified polymorphism (MSAP) assay, a number of genes were identified, which were differentially methylated between 7B-1 and its wild type (WT) seedlings in white (W), blue (B), red (R) lights and dark (D) or in response to exogenous ABA and mannitol-induced stresses. The genomic methylation level was almost similar in different lights between 7B-1 and WT seedlings, while significant differences were observed in response to stresses in D, but not B. Using a cDNA-AFLP assay, several transcripts were identified, which were differentially regulated between 7B-1 and WT by B or D or in response to stresses. Blue light receptors cryptochrome 1 and 2 (CRY1 and CRY2) and phototropin 1 and 2 (PHOT1 and PHOT2) were not affected by the 7B-1 mutation at the transcriptional level, instead the mutation had likely affected downstream components of the light signaling pathway. 5-azacytidine (5-azaC) induced DNA hypomethylation, inhibited stem elongation and differentially regulated the expression of a number of genes in 7B-1. In addition, it was shown that mir167 and mir390 were tightly linked to auxin signaling pathway in 5-azaC-treated 7B-1 seedlings via the regulation of auxin-response factor (ARF) transcripts. Our data showed that DNA methylation remodeling is an active epigenetic response to different lights and stresses in 7B-1 and WT, and highlighted the differences in epigenetic and transcriptional regulation of light and stress responses between 7B-1 and WT. Furthermore, it shed lights on the crosstalk between DNA hypomethylation and miRNA regulation of ARFs expression. This information could also be used as a benchmark for future studies of male-sterility in other crops.
| S-EPMC4388563 | biostudies-literature
Project description:Characterization of the transcriptomic responses of grafted tomato seedlings leaves after the root inoculations with the two beneficial microorganisms Paraburkholderia graminis and Azospirillum brasiliensis. Paraburkholderia graminis treatment led to a higher number of differentially expressed genes than Azospirillum brasiliensis, with a higher amount of up-regulated than down-regulated genes for both treatments. These DEGs were manly involved in response to oxidative stress, response to biotic and abiotic stress, water transport, regulation of transcription and hormones. Only few DEGs were shared among the two treatments, including genes involved in flowering time and in tolerance against abiotic stresses.
2022-10-16 | E-MTAB-11398 | biostudies-arrayexpress
Project description:By using DNA methylation of introgression lines as a marker of past paramutation, we characterise in details the paramutation of the \textit{H06} locus in crosses between Solanum lycopersicum and a range of tomato relatives and cultivars. Paramutation of H06 depends on the timing of sRNA production and conforms to the RNA-directed model of paramutation. By scanning the methylomes of tomato introgression lines for shared regions of differential methylation, thousands of candidate regions for paramutation are identified. Analysing the segregation of the methylation patterns for a subset of these regions shows variations in the penetrance of paramutation-like interactions.
2017-08-18 | GSE97206 | GEO