Integrated Analysis of Transcriptomes and Pectinase Gene Families Reveals a Novel Pathway Mediating Tomato Fruit Malformation

Tomato fruit malformation causes substantial yield and economic losses, but its molecular mechanisms are not well understood. This study compared floral traits of WT ‘QT57’ and malformed-fruit mutant ‘QT2’, integrated transcriptomic data, and qRT-PCR analysis to screen key candidate genes, and analyzed the pectinase gene family. The results found the ‘QT2’ mutant differed from WT ‘QT57’ in flower and fruit development. Expression analysis of CLAVATA-WUSCHEL pathway genes preliminarily validated the compensatory mechanism of SlCRCa and SlCRCb in ‘QT2’ malformed fruit. Six pectinase genes were identified as key candidates via RNA-seq and qRT-PCR analysis. Transcriptomic and qRT-PCR analyses of the pectinase gene family revealed their potential role in regulating tomato fruit malformation. Family analysis showed 34 pectinase genes distributed unevenly across 12 chromosomes. Subcellular localization confirmed SlPL7 in the nucleus and SlPME9 in the cell membrane/endoplasmic reticulum. The PL and PME genes were evolutionarily close, suggesting a potential functional overlap. Gibberellin-responsive elements were found in most pectinase genes. Pectinase genes may regulate tomato fruit malformation through the gibberellin-WUS pathway, carbohydrate metabolism, or cell wall metabolic disorder. This pathway provides new targets gene for the precise regulation of fruit malformation and offers significant reference value for practical production.

• Publication year

  2025

• Venue

  International Journal of Molecular Sciences

• Publication date

  2025-11-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.3390/ijms262110739PMID 41226771PMCID 12608487
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Combined Physiology and Transcriptome Analyses Provide Insights into Malformed Fruit of Cocos nucifera L.

  2025cited by this paper
• Firmness Loss in Blueberry (Vaccinium corymbosum) Is Associated With Increased PG Activity, Upregulation of Softening-Related Genes, and Pectin Metabolism.

  2025cited by this paper
• STP2-mediated sugar transport in tomato shoot apieces is critical for CLV3 arabinosylation and fruit locule development under low temperatures.

  2025cited by this paper
• IAA treatment accelerates post-harvest softening in ‘Docteur Jules Guyot’ pear via activation of pectinase-encoding genes

  2025cited by this paper
• Varying fruit loads modified leaf nutritional status, photosynthetic performance, and bean biochemical composition of coffee trees

  2024cited by this paper
• Silencing of a Pectin Acetylesterase (PAE) Gene Highly Expressed in Tobacco Pistils Negatively Affects Pollen Tube Growth

  2023cited by this paper
• Cold stress induces malformed tomato fruits by breaking the feedback loops of stem cell regulation in floral meristem.

  2022cited by this paper
• Tomato CRABS CLAW paralogues interact with chromatin remodelling factors to mediate carpel development and floral determinacy

  2021cited by this paper
• Flower development and fruit malformation in strawberries after short-term exposure to high or low temperature

  2021cited by this paper
• CisPG21 and CisCEL16 are involved in the regulation of the degradation of cell walls during secretory cavity cell programmed cell death in the fruits of Citrus sinensis (L.) Osbeck.

  2020cited by this paper
• Characterization of the pectin methyl-esterase gene family and its function in controlling pollen tube growth in pear (Pyrus bretschneideri).

  2020cited by this paper
• fastp: an ultra-fast all-in-one FASTQ preprocessor

  2018cited by this paper
• Genome-Wide Identification and Analysis of Polygalacturonase Genes in Solanum lycopersicum

  2018cited by this paper
• A chromatin loop represses WUSCHEL expression in Arabidopsis

  2018cited by this paper
• Integrative analysis of pectin methylesterase (PME) and PME inhibitors in tomato (Solanum lycopersicum): Identification, tissue-specific expression, and biochemical characterization.

  2018cited by this paper
• Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers

  2017cited by this paper
• Silencing of SlPL , which encodes a pectate lyase in tomato, confers enhanced fruit firmness, prolonged shelf‐life and reduced susceptibility to grey mould

  2017cited by this paper
• Regulation of floral stem cell termination in Arabidopsis

  2015cited by this paper
• PECTATE LYASE-LIKE 9 from Brassica campestris is associated with intine formation.

  2014cited by this paper
• AGAMOUS Terminates Floral Stem Cell Maintenance in Arabidopsis by Directly Repressing WUSCHEL through Recruitment of Polycomb Group Proteins[W]

  2011cited by this paper
• The polygalacturonase gene BcMF2 from Brassica campestris is associated with intine development

  2008cited by this paper
• Organ-specific, developmental, hormonal and stress regulation of expression of putative pectate lyase genes in Arabidopsis.

  2007cited by this paper
• Comprehensive expression profiling of the pectin methylesterase gene family during silique development in Arabidopsis thaliana

  2006cited by this paper
• VIGS vectors for gene silencing: many targets, many tools.

  2004cited by this paper
• Pectin methylesterases: sequence-structural features and phylogenetic relationships.

  2004cited by this paper
• The OsFOR1 gene encodes a polygalacturonase-inhibiting protein (PGIP) that regulates floral organ number in rice

  2003cited by this paper
• Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

  2001cited by this paper
• Pectin degradation in ripening and wounded fruits

  2001cited by this paper
• Tomato flower abnormalities induced by low temperatures are associated with changes of expression of MADS-Box genes

  1998cited by this paper
• A maize pectin methylesterase-like gene, ZmC5, specifically expressed in pollen

  1998cited by this paper
• The regulation of nutrient and flavor metabolism in tomato fruit

  year unknowncited by this paper

• No citing papers are available for this paper.