Plant Molecular Biology

, Volume 89, Issue 3, pp 263–278 | Cite as

A transcriptomic approach to identify regulatory genes involved in fruit set of wild-type and parthenocarpic tomato genotypes

  • Fabrizio Ruiu
  • Maurizio Enea Picarella
  • Shunsuke Imanishi
  • Andrea Mazzucato


The tomato parthenocarpic fruit (pat) mutation associates a strong competence for parthenocarpy with homeotic transformation of anthers and aberrancy of ovules. To dissect this complex floral phenotype, genes involved in the pollination-independent fruit set of the pat mutant were investigated by microarray analysis using wild-type and mutant ovaries. Normalized expression data were subjected to one-way ANOVA and 2499 differentially expressed genes (DEGs) displaying a >1.5 log-fold change in at least one of the pairwise comparisons analyzed were detected. DEGs were categorized into 20 clusters and clusters classified into five groups representing transcripts with similar expression dynamics. The “regulatory function” group (685 DEGs) contained putative negative or positive fruit set regulators, “pollination-dependent” (411 DEGs) included genes activated by pollination, “fruit growth-related” (815 DEGs) genes activated at early fruit growth. The last groups listed genes with different or similar expression pattern at all stages in the two genotypes. qRT-PCR validation of 20 DEGs plus other four selected genes assessed the high reliability of microarray expression data; the average correlation coefficient for the 20 DEGs was 0.90. In all the groups were evidenced relevant transcription factors encoding proteins regulating meristem differentiation and floral organ development, genes involved in metabolism, transport and response of hormones, genes involved in cell division and in primary and secondary metabolism. Among pathways related to secondary metabolites emerged genes related to the synthesis of flavonoids, supporting the recent evidence that these compounds are important at the fruit set phase. Selected genes showing a de-regulated expression pattern in pat were studied in other four parthenocarpic genotypes either genetically anonymous or carrying lesions in known gene sequences. This comparative approach offered novel insights for improving the present molecular understanding of fruit set and parthenocarpy in tomato.


Fruit set Ovary development Parthenocarpic mutants Solanumlycopersicum L. Transcription factors Transcriptome profiling 



The authors thank Joaquín Cañizares, Filomena Carriero, Celestina Mariani and Ivo Rieu for sharing material of the parthenocarpic systems studied. J. Cañizares is also acknowledged for critical reading of the manuscript; Luigi Selleri, Marco Cirilli and Pietro Mosconi for expert technical assistance and two anonymous reviewers for substantial help in improving the paper.

Author contributions statement

F.R. and A.M. conceived and designed the research. F.R. and M.E.P. performed phenotypic and gene validation analysis, S.I. performed the microarray hybridization, F.R., M.E.P. and S.I. analysed the data, F.R. and A.M. wrote the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary material 1 (PDF 6322 kb)
11103_2015_367_MOESM2_ESM.xlsx (565 kb)
Supplementary material 2 (XLSX 565 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Fabrizio Ruiu
    • 1
    • 3
  • Maurizio Enea Picarella
    • 1
  • Shunsuke Imanishi
    • 2
  • Andrea Mazzucato
    • 1
  1. 1.Department of Science and Technologies for Agriculture, Forestry, Nature and Energy (DAFNE)University of TusciaViterboItaly
  2. 2.NARO Institute of Vegetable and Tea ScienceNational Agriculture and Food Research Organization (NARO)TsuJapan
  3. 3.Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly

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