ArticlePlant physiology2009
Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development.
Article in Plant physiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
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98 citing papers in PubMed, 215 citations in OpenAlex.
- Integrated transcriptome-metabolome analyses reveal regulatory networks underlying soluble solids accumulation in Capsicum chinense fruits.The Plant journal : for cell and molecular biology · 2026Article
- Untargeted Metabolomics Unravel the Effect of SlPBB2 on Tomato Fruit Quality and Associated Plant Metabolism.Metabolites · 2026Article
- Transcriptomic Analysis of Early Fruit Development in Micro-Tom Tomato Reveals Conserved and Cultivar-Specific Mechanisms.Plants (Basel, Switzerland) · 2026Article
- Identification of theFrontiers in genetics · 2026Article
- Depth Imaging-Based Framework for Efficient Phenotypic Recognition in Tomato Fruit.Plants (Basel, Switzerland) · 2025Article
- Unlocking gene regulatory networks for crop resilience and sustainable agriculture.Nature biotechnology · 2025Review
- Comprehensive Genome-Wide Investigation and Transcriptional Regulation of the bZIP Gene Family in Litchi Fruit Development.Plants (Basel, Switzerland) · 2025Article
- CHH hypermethylation contributes to the early ripening of grapes revealed by DNA methylome landscape of 'Kyoho' and its bud mutant.Horticulture research · 2025Article
- Review
- Co-regulatory network analysis of the main secondary metabolite (SM) biosynthesis in Crocus sativus L.Scientific reports · 2024Article
- Characterization of Transcriptome Dynamics during Early Fruit Development in Olive (International journal of molecular sciences · 2023Article
- Exogenous application of ALA enhanced sugar, acid and aroma qualities in tomato fruit.Frontiers in plant science · 2023Article
- The cutin polymer matrix undergoes a fine architectural tuning from early tomato fruit development to ripening.Plant physiology · 2022Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- Formation of Unique Placental Seed Capsules in the Maturation Process of the Tomato Fruit.International journal of molecular sciences · 2022Article
- Regulation mechanisms of flavonoids biosynthesis of Hancheng Dahongpao peels (Zanthoxylum bungeanum Maxim) at different development stages by integrated metabolomics and transcriptomics analysis.BMC plant biology · 2022Article
- All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter.Journal of experimental botany · 2022Article
- Firming up your tomato: a natural promoter variation in a MADS-box gene is causing all-flesh tomatoes.Journal of experimental botany · 2022Article
- Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes.Nature communications · 2021Article
- Transcriptome and metabolome analysis to reveal major genes of saikosaponin biosynthesis in Bupleurum chinense.BMC genomics · 2021Article
38 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Variations in early fruit development and composition may have major impacts on the taste and the overall quality of ripe tomato (Solanum lycopersicum) fruit. To get insights into the networks involved in these coordinated processes and to identify key regulatory genes, we explored the transcriptional and metabolic changes in expanding tomato fruit tissues using multivariate analysis and gene-metabolite correlation networks. To this end, we demonstrated and took advantage of the existence of clear structural and compositional differences between expanding mesocarp and locular tissue during fruit development (12-35 d postanthesis). Transcriptome and metabolome analyses were carried out with tomato microarrays and analytical methods including proton nuclear magnetic resonance and liquid chromatography-mass spectrometry, respectively. Pairwise comparisons of metabolite contents and gene expression profiles detected up to 37 direct gene-metabolite correlations involving regulatory genes (e.g. the correlations between glutamine, bZIP, and MYB transcription factors). Correlation network analyses revealed the existence of major hub genes correlated with 10 or more regulatory transcripts and embedded in a large regulatory network. This approach proved to be a valuable strategy for identifying specific subsets of genes implicated in key processes of fruit development and metabolism, which are therefore potential targets for genetic improvement of tomato fruit quality.
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