Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development      

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.

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

“…Figure 4B, representing the local pattern of LD around the peak SNP, suggests that the LD level is relatively low in this genomic region. From a functional point of view, citrate and malate are two organic compounds found in most ripe fruits (Etienne et al, 2013) and have been demonstrated to be highly correlated with many important regulators of ripening in studies that have investigated early fruit development (Mounet et al, 2009;Centeno et al, 2011). This result suggests that, in this study, we were able to identify a peak SNP that is located near one or several putative candidate gene(s) playing a crucial role in the citrate and malate metabolic pathways.…”

Functional Promiscuity of Two Divergent Paralogs of Type III Plant Polyketide Synthases

“…The biological significance of metabolite-transcript correlations has usually been considered to reflect simple or complex associations between them (Mounet et al, 2009). We investigated the correlation between ReCHS gene expression profiles and the accumulation of metabolites (total flavonoids and total anthraquinones) to decipher the possible involvement of two divergent ReCHS paralogs toward either of the secondary metabolite groups.…”

Analyses of Tomato Fruit Brightness Mutants Uncover Both Cutin-Deficient and Cutin-Abundant Mutants and a New Hypomorphic Allele of GDSL Lipase

“…Samples were fixed and embedded in paraffin as previously described (Mounet et al, 2009). Eight-micrometer slides of exocarp were stained using saturated and filtered Sudan Red solution in ethanol.…”

“…The cDNA sizing was performed after a total RNA extraction from 100 mg fresh weight and a reverse transcription, as previously described (Mounet et al, 2009;Girard et al, 2012). The amplification was performed using GDSL2-cDNA4F and GDSL2-cDNA5R primers.…”