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

Research output: Contribution to journalArticleAcademicpeer-review

10 Citations (Scopus)

Abstract

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.

LanguageEnglish
Pages624-641
JournalNew Phytologist
Volume215
Issue number2
DOIs
Publication statusPublished - 2017

Fingerprint

Lycopersicon esculentum
Fruit
flavor
tomatoes
metabolites
genomics
loci
Acids
fruits
acids
Genome
Molecular Sequence Annotation
Volatile Organic Compounds
Metabolome
Food Supply
Genome-Wide Association Study
Nutritive Value
Linkage Disequilibrium
Single Nucleotide Polymorphism
Alleles

Keywords

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

Cite this

Bauchet, Guillaume ; Grenier, Stéphane ; Samson, Nicolas ; Segura, Vincent ; Kende, Aniko ; Beekwilder, Jules ; Cankar, Katarina ; Gallois, Jean Luc ; Gricourt, Justine ; Bonnet, Julien ; Baxter, Charles ; Grivet, Laurent ; Causse, Mathilde. / Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit : Implications for flavor improvement. In: New Phytologist. 2017 ; Vol. 215, No. 2. pp. 624-641.
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Bauchet, G, Grenier, S, Samson, N, Segura, V, Kende, A, Beekwilder, J, Cankar, K, Gallois, JL, Gricourt, J, Bonnet, J, Baxter, C, Grivet, L & Causse, M 2017, 'Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: Implications for flavor improvement', New Phytologist, vol. 215, no. 2, pp. 624-641. https://doi.org/10.1111/nph.14615

Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit : Implications for flavor improvement. / Bauchet, Guillaume; Grenier, Stéphane; Samson, Nicolas; Segura, Vincent; Kende, Aniko; Beekwilder, Jules; Cankar, Katarina; Gallois, Jean Luc; Gricourt, Justine; Bonnet, Julien; Baxter, Charles; Grivet, Laurent; Causse, Mathilde.

In: New Phytologist, Vol. 215, No. 2, 2017, p. 624-641.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit

T2 - New Phytologist

AU - Bauchet, Guillaume

AU - Grenier, Stéphane

AU - Samson, Nicolas

AU - Segura, Vincent

AU - Kende, Aniko

AU - Beekwilder, Jules

AU - Cankar, Katarina

AU - Gallois, Jean Luc

AU - Gricourt, Justine

AU - Bonnet, Julien

AU - Baxter, Charles

AU - Grivet, Laurent

AU - Causse, Mathilde

PY - 2017

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N2 - 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.

AB - 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.

KW - Flavor

KW - Genome-wide association study (GWAS)

KW - Genotype-by-environment (G × E)

KW - Metabolites

KW - Sugars: acids

KW - Tomato breeding

KW - Volatiles

U2 - 10.1111/nph.14615

DO - 10.1111/nph.14615

M3 - Article

VL - 215

SP - 624

EP - 641

JO - New Phytologist

JF - New Phytologist

SN - 0028-646X

IS - 2

ER -