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Spatial-temporal order of regulation in tomato early fruit development

ABSTRACT: Early fruit development is crucial for crop production in tomato. After fertilization, the ovary undergoes a cell division and a cell expansion stages before maturation. Although the roles of regulatory signals such as hormone and carbohydrate during early fruit development have been studied, the spatial distribution and the sequential initiation of these regulatory signals is still poorly understood. Using the cultivated tomato “Moneymaker” as materials, we analyzed the transcriptome of the ovule and the ovary wall dissected from the different stages of the early developing fruits. These datasets provide us the whole picture about the spatial and temporal signal distribution of fruit formation which has not been studied in such a detailed manner. Our results suggest that the hormone signal was initiated in both ovule and ovary wall after fertilization. After that, the different signals were activated in ovule and ovary wall due to their distinct developmental processes. By analyzing the global expression profiling of hormone related genes, we found that the auxin might be synthesized in both ovule and ovary wall after fertilization. The expression pattern of sugar related genes revealed the different carbohydrate metabolism events occurred in ovule and ovary wall. At last, we identified a gene showed tissue and stage specific expression pattern and localized in previously reported fruit weight locus which might be selected during tomato breeding.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE72216 | GEO | 2015/11/28

SECONDARY ACCESSION(S): PRJNA293380

REPOSITORIES: GEO

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Spatial-temporal order of regulation in tomato early fruit development

Project description:Early fruit development is crucial for crop production in tomato. After fertilization, the ovary undergoes a cell division and a cell expansion stages before maturation. Although the roles of regulatory signals such as hormone and carbohydrate during early fruit development have been studied, the spatial distribution and the sequential initiation of these regulatory signals is still poorly understood. Using the cultivated tomato “Moneymaker” as materials, we analyzed the transcriptome of the ovule and the ovary wall dissected from the different stages of the early developing fruits. These datasets provide us the whole picture about the spatial and temporal signal distribution of fruit formation which has not been studied in such a detailed manner. Our results suggest that the hormone signal was initiated in both ovule and ovary wall after fertilization. After that, the different signals were activated in ovule and ovary wall due to their distinct developmental processes. By analyzing the global expression profiling of hormone related genes, we found that the auxin might be synthesized in both ovule and ovary wall after fertilization. The expression pattern of sugar related genes revealed the different carbohydrate metabolism events occurred in ovule and ovary wall. At last, we identified a gene showed tissue and stage specific expression pattern and localized in previously reported fruit weight locus which might be selected during tomato breeding.

2018-01-01 | GSE74827 | GEO

MicroRNAs Associated with AGL6 and IAA9 function in tomato fruit set

Project description:Fruit set is triggered after ovule fertilization, as a consequence of the downregulation of ovary growth repressors, such as the tomato transcription factors Auxin/indole-3-acetic acid 9 (IAA9) and Agamous-like 6 (AGL6). We produced small RNA libraries from IAA9- and AGL6-silenced ovaries to identify miRNAs differentially expressed in IAA9- and AGL6-silenced ovaries as compared with unpollinated control ovaries. The identified miRNAs represent a pool of regulatory sRNAs potentially involved in tomato fruit initiation.

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Gene regulation in parthenocarpic tomato fruit

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Microarray analysis of developing fruits from transgenic lines with increased or reduced SlARF9 mRNA levels in tomato.

2014-11-26 | GSE63637 | GEO

Transcription profiling of parthenocarpic tomato fruit

Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Experiment Overall Design: Wild-type fruit with seeds was compared with transgenic lines INO-IaaM, DefH9-IaaM, INO-RolB, and DefH9-RolB. To find genes with seed-specific expression, we also compared the control with wild-type fruit from which seeds had been manually removed. We had three biological replicates for each treatment and control except DefH9-RolB, for which only two replicates were available. Each CEL file from the microarray represents one plant from each line.

2009-09-15 | E-GEOD-14358 | biostudies-arrayexpress

Microarray analysis of developing fruits from transgenic lines with increased or reduced SlARF9 mRNA levels in tomato.

Project description:The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early tomato fruit development is Solanum lycopersicum ARF9 (SlARF9). To explore the physiological role of SlARF9 in tomato fruit set and development, we generated transgenic tomato lines in which the gene was overexpressed or silenced, and used microarray analysis to identify possible transcriptomic changes associated with the fruit developmental phenotypes observed in the transgenic lines. The transcript profiling analysis was done using pericarp tissue from fruits, 3-4mm in diameter, with each sample containing the pericarp of two fruits. For each seperate transgenic line, tissues were pooled from 2-3 plants (T2), resulting in a total of 6 samples for SlARF9-OE, 7 samples for SlARF9-RNAi, and 2 samples for wild type. The transcript profiling analysis was carried out using affymetrix EUTOM3 tomato exon array.

2014-11-26 | E-GEOD-63637 | biostudies-arrayexpress

Senescence time course of unfertilized Arabidopsis thaliana ovules

Project description:Flowers have a species-specific fertile period during which pollination and fertilization have to occur to initiate seed and fruit development. Within the flower, the functional life span of the ovule containing the female gametophyte is decisive for fertilization and the initiation of seed development. Here we performed an RNA-sequencing based transcriptome analysis of senescing unfertilized ovules during in a time series. We isolated ovules from Arabidopsis thaliana flowers emasculated at stage 12c at three different time points: 2 days after emasculation (DAE), 3 DAE, and 4 DAE. These time points correspond to intact mature ovules (2DAE), early ovule senescence (3 DAE), and late ovule senescence (4 DAE). We extracted total RNA from the ovules in 3 independent biological replicates, thus generating 9 RNA samples in total, for RNA-sequencing by Illumina HiSeq.

2023-05-30 | E-MTAB-12174 | biostudies-arrayexpress

Transcript profiling of tomato mutants producing anthocyanins in the fruit

Project description:Anthocyanins are high value plant antioxidants which are not present in the fruits of cultivated tomato. However, both the dominant gene Anthocyanin fruit (Aft) and the recessive gene atroviolacea (atv), introgressed into domesticated tomato from two different wild Solanum species, stimulate a limited anthocyanin pigmentation. Surprisingly, double mutant Aft/Aft atv/atv tomatoes are characterised by the presence of anthocyanins in the fruit peel, resulting in intensely purple pigmented fruit. We carried out a transcript profiling analysis using GeneChip® Tomato Genome Arrays, in order to identify differentially expressed genes when comparing wild type, Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits. The expression pattern of several genes involved in the anthocyanin pathway was analyzed in detail. Among the fruit peel-associated differentially expressed transcripts, genes involved in phenylpropanoid pathway, cell wall composition, biotic and abiotic stress responses, sugar and hormone metabolism were overrepresented in Aft/Aft atv/atv. Transcriptomic analysis thus revealed that the activation of anthocyanin synthesis in tomato fruit was accompanied by a complex remodulation of gene expression, likely affecting important agronomic and merceological traits.

2010-07-31 | GSE19792 | GEO

Genome-wide analysis of Botrytis cinerea genes targeting plant cell walls of different hosts [tomato]

Project description:The cell wall is among the first plant structures encountered by necrotrophic fungal pathogens, such as Botrytis cinerea. The composition of plant cell walls varies depending on the species, type of cell or tissue, and stage of development. Cell walls are important reservoirs of energy-rich sugars for pathogens, but also are barriers that impair colonization of host tissues. Growing fungal hyphae secrete enzymes that hydrolyze cell wall polysaccharides. Degradation of wall polysaccharides provides nutrients for the pathogen and improves the access of secreted Botrytis enzymes to all host cell wall targets and cytoplasmic constituents. Destruction of host cell walls results in tissue maceration, a hallmark of diseases caused by Botrytis. The Botrytis genome encodes 1,155 predicted carbohydrate-active enzyme (CAZy) genes; products of 275 are potentially secreted. Transcriptome sequencing identified Botrytis CAZy genes expressed during infections of lettuce leaves, ripe tomato fruit and grape berries. On all three hosts, Botrytis expresses a common group of 229 predicted CAZy genes including 28 pectin-modifying enzymes, 21 hemicellulose-modifying proteins, 18 enzymes targeting pectin and hemicellulose side-branches, and 16 enzymes that may degrade cellulose. Pectin polysaccharides are abundant in grape and tomato cell walls, but lettuce leaf walls are predominantly hemicelluloses and cellulose. These results suggest that Botrytis targets similar wall polysaccharide networks; e.g., pectins, on leaves and fruit, but also attacks unique host wall polysaccharide substrates The diversity of the Botrytis CAZy proteins may be partly responsible for its wide host range. 3 biological replicates consisting of groups of infected tomato fruits from different plants

2014-09-24 | E-GEOD-57586 | biostudies-arrayexpress

The tomato MYB21 acts in ovules to mediate jasmonate-regulated fertility (RNASeq)

Project description:The function of the plant hormone jasmonic acid (JA) in development of tomato flowers was analyzed with a mutant defective in JA perception (jasmonate-insensitive1-1, jai1-1). In contrast to Arabidopsis JA-insensitive plants that are male sterile, the tomato mutant jai1-1 exhibits major defects in female development resulting in female sterility. To identify putative JA-dependent regulatory components, transcriptomics was performed using isolated ovules of three different stages of flower development, from both wild type and jai1-1. Among the strongly down-regulated genes in jai1-1, one encoding a MYB transcription factor (SlMYB21) was found. Its orthologue in Arabidopsis has a crucial role in JA-regulated stamen development. SlMYB21 showed transcription factor activity in yeast, interaction with SlJAZ9 in yeast and in planta, and complemented the Arabidopsis mutant myb21-5. To analyze SlMYB21 function in tomato ovule development, CRISPR/Cas9 mutants were created and a TILLING mutant was identified, all showing female sterility and therefore corroborating a function of MYB21 in tomato ovule development. Transcriptomics from wild type, jai1-1 and myb21-2 carpels revealed processes that might be controlled by SlMYB21. The data suggest a positive regulation of JA biosynthesis by SlMYB21, but a negative regulation of the action of auxin and GA. The results demonstrate that SlMYB21 mediates at least partially the action of JA and might control the flower to fruit transition.

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