Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: Implications for flavor improvement

Guillaume Bauchet*, Stéphane Grenier, Nicolas Samson, Vincent Segura, Aniko Kende, Jules Beekwilder, Katarina Cankar, Jean Luc Gallois, Justine Gricourt, Julien Bonnet, Charles Baxter, Laurent Grivet, Mathilde Causse

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

20 Citations (Scopus)


Plant metabolites are important to world food security due to their roles in crop yield and nutritional quality. Here we report the metabolic profile of 300 tomato accessions (Solanum lycopersicum and related wild species) by quantifying 60 primary and secondary metabolites, including volatile organic compounds, over a period of 2 yr. Metabolite content and genetic inheritance of metabolites varied broadly, both within and between different genetic groups. Using genotype information gained from 10 000 single nucleotide polymorphism markers, we performed a metabolite genome-wide association mapping (GWAS) study. We identified 79 associations influencing 13 primary and 19 secondary metabolites with large effects at high resolution. Four genome regions were detected, highlighting clusters of associations controlling the variation of several metabolites. Local linkage disequilibrium analysis and allele mining identified possible candidate genes which may modulate the content of metabolites that are of significant importance for human diet and fruit consumption. We precisely characterized two associations involved in fruit acidity and phenylpropanoid volatile production. Taken together, this study reveals complex and distinct metabolite regulation in tomato subspecies and demonstrates that GWAS is a powerful tool for gene-metabolite annotation and identification, pathways elucidation, and further crop improvement.

Original languageEnglish
Pages (from-to)624-641
JournalNew Phytologist
Issue number2
Publication statusPublished - 2017


  • Flavor
  • Genome-wide association study (GWAS)
  • Genotype-by-environment (G × E)
  • Metabolites
  • Sugars: acids
  • Tomato breeding
  • Volatiles

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