title: Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits.
abstract: Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.
authors.affiliation: INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France.
authors.forename: Elise
authors.initials: E
authors.lastname: Albert
authors.affiliation: INRA, UR0588, Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, Centre de Recherche Val de Loire, CS 40001, Orléans, 45075, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Segura
authors.affiliation: INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France.
authors.forename: Justine
authors.initials: J
authors.lastname: Gricourt
authors.affiliation: GAUTIER Semences, route d'Avignon, Eyragues, 13630, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Bonnefoi
authors.affiliation: GAUTIER Semences, route d'Avignon, Eyragues, 13630, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Derivot
authors.affiliation: INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France Mathilde.Causse@paca.inra.fr.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Causse
mesh_terms: D003681:Dehydration; D005638:Fruit / Q000235:genetics / Q000502:physiology / Q000592:standards*; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D017343:Genes, Plant / Q000235:genetics* / Q000502:physiology; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium / Q000235:genetics; D018551:Solanum lycopersicum / Q000235:genetics* / Q000502:physiology; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics / Q000502:physiology; D040641:Quantitative Trait Loci / Q000235:genetics* / Q000502:physiology
keywords: 
  Solanum lycopersicum
  ; Acid and vitamin C content; GWA; QTL; candidate genes; drought; fleshy fruit quality; genotype by environment interaction; sugar.