A transcriptomic approach to identify regulatory genes involved in fruit set of wild-type and parthenocarpic tomato genotypes
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.
KeywordsFruit 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.
- Avivi Y, Lev-Yadun S, Morozova N, Libs L, Williams L, Zhao J, Varghese G, Grafi G (2000) Clausa, a tomato mutant with a wide range of phenotypic perturbations, displays a cell type-dependent expression of the homeobox gene LeT6/TKn2. Plant Physiol 124:541–552PubMedCentralCrossRefPubMedGoogle Scholar
- Koltunow AM, Vivian-Smith A, Tucker MR, Peach N (2002) The central role of the ovule in apomixis and parthenocarpy. In: O’Neill SD, Roberts JA (eds) Plant reproduction. Academic Press, Sheffield, pp 221–256Google Scholar
- Mapelli S, Frova C, Torti G, Soressi GP (1978) Relationship between set, development and activities of growth regulators in tomato fruits. Plant Cell Physiol 19:1281–1288Google Scholar
- Mazzucato A, Olimpieri I, Siligato F, Picarella ME, Soressi GP (2008) Characterization of genes controlling stamen identity and development in a parthenocarpic tomato mutant indicates a role for the DEFICIENS ortholog in the control of fruit set. Physiol Plant 132:526–537CrossRefPubMedGoogle Scholar
- Muños S, Ranc N, Botton E, Bérard AL, Rolland S, Duffé P, Carretero Y, Le Paslier M-C, Delalande C, Bouzayen M, Brunel D, Causse M (2011) Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. Plant Physiol 156:2244–2254PubMedCentralCrossRefPubMedGoogle Scholar
- Nesi N, Debeaujon I, Jond C, Stewart AJ, Jenkins GI, Caboche M, Lepiniec LC (2002) The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat. Plant Cell 14:2463–2479PubMedCentralCrossRefPubMedGoogle Scholar
- Nwafor C, Gribaudo I, Schneider A, Wehrens R, Grando M, Costantini L (2014) Transcriptome analysis during berry development provides insights into co-regulated and altered gene expression between a seeded wine grape variety and its seedless somatic variant. BMC Genomics 15:1030PubMedCentralCrossRefPubMedGoogle Scholar
- Philouze J, Maisonneuve B (1978) Heredity of the natural ability to set parthenocarpic fruits in the soviet variety Severianin. Tomato Genet Coop 28:12–13Google Scholar
- Popescu SC, Popescu GV, Bachan S, Zhang Z, Seay M, Gerstein M, Snyder M, Dinesh-Kumar SP (2007) Differential binding of calmodulin related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci USA 104:4730–4735PubMedCentralCrossRefPubMedGoogle Scholar
- Schijlen EGWM, De Vos CHR, Martens S, Jonker HH, Rosin FM, Molthoff JW, Tikunov YM, Angenent GC, Van Tunen AJ, Bovy AG (2007) RNA interference silencing of chalcone synthase, the first step in the flavonoid biosynthesis pathway, leads to parthenocarpic tomato fruits. Plant Physiol 144:1520–1530PubMedCentralCrossRefPubMedGoogle Scholar
- Schwabe WW, Mills JJ (1981) Hormones and parthenocarpic fruit set: a literature survey. Hort Abstr 51:661–698Google Scholar
- Shinozaki Y, Hao S, Kojima M, Sakakibara H, Ozeki-Iida Y, Zheng Y, Fei Z, Zhong S, Giovannoni JJ, Rose JKC, Okabe Y, Heta Y, Ezura H, Ariizumi T (2015) Ethylene suppresses tomato (Solanum lycopersicum) fruit set through modification of gibberellin metabolism. Plant J 83:237–251CrossRefPubMedGoogle Scholar
- Tabata R, Ikezaki M, Fujibe T, Aida M, Tian C, Ueno Y, Yamamoto KT, Machida Y, Nakamura K, Ishiguro S (2010) Arabidopsis AUXIN RESPONSE FACTOR6 and 8 regulate jasmonic acid biosynthesis and floral organ development via repression of class 1 KNOX genes. Plant Cell Physiol 51:164–175CrossRefPubMedGoogle Scholar
- Tsai W-C, Lee P-F, Chen H-I, Hsiao Y-Y, Wei W-J, Pan Z-J, Chuang M-H, Kuoh C-S, Chen W-H, Chen H-H (2005) PeMADS6, a GLOBOSA/PISTILLATA-like gene in Phalaenopsis equestris involved in petaloid formation, and correlated with flower longevity and ovary development. Plant Cell Physiol 46:1125–1139CrossRefPubMedGoogle Scholar
- Wang H, Schauer N, Usadel B, Frasse P, Zouine M, Hernould M, Latché A, Pech J-C, Fernie AR, Bouzayen M (2009) Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling. Plant Cell 21:1428–1452PubMedCentralCrossRefPubMedGoogle Scholar