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

A transcriptomic approach to identify regulatory genes involved in fruit set of wild-type and... 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Plant Molecular Biology Springer Journals

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

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Publisher
Springer Journals
Copyright
Copyright © 2015 by Springer Science+Business Media Dordrecht
Subject
Life Sciences; Plant Sciences; Biochemistry, general; Plant Pathology
ISSN
0167-4412
eISSN
1573-5028
D.O.I.
10.1007/s11103-015-0367-1
Publisher site
See Article on Publisher Site

Abstract

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.

Journal

Plant Molecular BiologySpringer Journals

Published: Aug 30, 2015

References

  • Clausa, a tomato mutant with a wide range of phenotypic perturbations, displays a cell type-dependent expression of the homeobox gene LeT6/TKn2
    Avivi, Y; Lev-Yadun, S; Morozova, N; Libs, L; Williams, L; Zhao, J; Varghese, G; Grafi, G
  • A potato tuber-expressed mRNA with homology to steroid dehydrogenases affects gibberellin levels and plant development
    Bachem, CWB; Horvath, B; Trindade, L; Claassens, M; Davelaar, E; Jordi, W; Visser, RGF
  • A fertilization-independent developmental program triggers partial fruit development and senescence processes in pistils of Arabidopsis
    Carbonell-Bejerano, P; Urbez, C; Carbonell, J; Granell, A; Perez-Amador, MA
  • The Solanum lycopersicum auxin response factor 7 (SlARF7) regulates auxin signaling during tomato fruit set and development
    Jong, M; Wolters-Arts, M; Feron, R; Mariani, C; Vriezen, WH
  • Fertilization-dependent auxin response in ovules triggers fruit development through the modulation of gibberellin metabolism in Arabidopsis
    Dorcey, E; Urbez, C; Blázquez, M
  • AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth
    Elliott, RC; Betzner, AS; Huttner, E; Oakes, MP; Tucker, WQ; Gerentes, D; Perez, P; Smyth, DR
  • Hidden variability of floral homeotic B genes in Solanaceae provides a molecular basis for the evolution of novel functions
    Geuten, K; Irish, V
  • Fruits: a developmental perspective
    Gillaspy, G; Ben-David, H; Gruissem, W
  • Expression of aberrant forms of AUXIN RESPONSE FACTOR8 stimulates parthenocarpy in Arabidopsis and tomato
    Goetz, M; Hooper, LC; Johnson, SD; Rodrigues, JCM; Vivian-Smith, A; Koltunow, AM
  • Stamenless, a tomato mutant with homeotic conversions in petals and stamens
    Gómez, P; Jamilena, M; Capel, J; Zurita, S
  • Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships
    Henriksson, E; Olsson, ASB; Johannesson, H; Johansson, H; Hanson, J; Engström, P; Söderman, E
  • Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato
    Huang, Z; Houten, J; Gonzalez, G; Xiao, H; Esther van der Knaap, E
  • Plant MetGenMAP: an integrative analysis system for plant systems biology
    Joung, J-G; Corbett, AM; Fellman, SM; Tieman, DM; Klee, HJ; Giovannoni, JJ; Fei, Z

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