title: Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression.
abstract: CONCLUSIONS
  In tomato, genotype by watering interaction resulted from genotype re-ranking more than scale changes. Interactive QTLs according to watering regime were detected. Differentially expressed genes were identified in some intervals.
  As a result of climate change, drought will increasingly limit crop production in the future. Studying genotype by watering regime interactions is necessary to improve plant adaptation to low water availability. In cultivated tomato (Solanum lycopersicum L.), extensively grown in dry areas, well-mastered water deficits can stimulate metabolite production, increasing plant defenses and concentration of compounds involved in fruit quality, at the same time. However, few tomato Quantitative Trait Loci (QTLs) and genes involved in response to drought are identified or only in wild species. In this study, we phenotyped a population of 119 recombinant inbred lines derived from a cross between a cherry tomato and a large fruit tomato, grown in greenhouse under two watering regimes, in two locations. A large genetic variability was measured for 19 plant and fruit traits, under the two watering treatments. Highly significant genotype by watering regime interactions were detected and resulted from re-ranking more than scale changes. The population was genotyped for 679 SNP markers to develop a genetic map. In total, 56 QTLs were identified among which 11 were interactive between watering regimes. These later mainly exhibited antagonist effects according to watering treatment. Variation in gene expression in leaves of parental accessions revealed 2259 differentially expressed genes, among which candidate genes presenting sequence polymorphisms were identified under two main interactive QTLs. Our results provide knowledge about the genetic control of genotype by watering regime interactions in cultivated tomato and the possible use of deficit irrigation to improve tomato quality.
authors.affiliation: INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France.
authors.forename: Elise
authors.initials: E
authors.lastname: Albert
authors.affiliation: INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France.
authors.forename: Justine
authors.initials: J
authors.lastname: Gricourt
authors.affiliation: INRA, UR 1115, Plante et Système de cultures Horticoles, 228 Route de l'aérodrome, Centre de Recherche PACA, Domaine Saint Paul, CS40509, 84914, Avignon Cedex 9, France.
authors.forename: Nadia
authors.initials: N
authors.lastname: Bertin
authors.affiliation: GAUTIER Semences, route d'Avignon, 13630, Eyragues, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Bonnefoi
authors.affiliation: INRA, Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Rue de Noetzlin, Plateau du Moulon, 91405, Orsay, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Pateyron
authors.affiliation: INRA, Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Rue de Noetzlin, Plateau du Moulon, 91405, Orsay, France.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Tamby
authors.affiliation: INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Bitton
authors.affiliation: INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France. mathilde.causse@avignon.inra.fr.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Causse
mesh_terms: D057914:Agricultural Irrigation; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D018744:DNA, Plant / Q000235:genetics; D055864:Droughts; D005638:Fruit; D015870:Gene Expression; D017343:Genes, Plant; D005838:Genotype; D040582:Inheritance Patterns; D018551:Solanum lycopersicum / Q000235:genetics* / Q000502:physiology; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
chemical_list: D018744:DNA, Plant