Genetic control of tomato fruit quality: from QTL mapping to Genome Wide Association studies and breeding.

Consumers began to complain about the taste of tomato varieties in the late 1990's. Although tomato taste is influenced by environmental and post-harvest conditions, varieties show a large diversity for fruit quality traits. We herein review our past and present research work intended to improve tomato fruit quality. First, results from sensory analysis allowed identifying important traits for consumer preferences. Then, we dissected the genetic control of flavor related traits by mapping several QTL in the last 20 years, and identified the genes corresponding to a few major QTL. Since the availability of the tomato genome sequence, genome-wide association studies were performed on several panels of tomato accessions. We discovered a large number of associations for fruit composition and identified relevant allele combinations for breeding. We then performed a meta-analysis combining the results of several studies. We also checked the inheritance of quality traits at the hybrid level and assessed how genomic prediction could help selecting better tomato varieties.

Les consommateurs ont commencé à se plaindre du goût des variétés de tomates à la fin des années 1990. Bien que le goût de la tomate soit influencé par les conditions de culture et de post-récolte, les variétés présentent une grande diversité pour les caractéristiques de qualité des fruits. Nous passons ici en revue nos travaux de recherche passés et présents destinés à comprendre la diversité génétique et améliorer la qualité des fruits de tomate. Les résultats d'analyses sensorielles ont tout d'abord permis d'identifier les traits importants pour les préférences des consommateurs. Ensuite, nous avons disséqué le contrôle génétique des caractères liés à ces traits, cartographié de nombreux QTL depuis 20 ans et identifié les gènes correspondant à quelques QTL majeurs. Depuis la disponibilité de la séquence du génome de la tomate, des études d'association à l'échelle du génome ont été réalisées sur plusieurs panels d'accessions de tomate. Nous avons découvert un grand nombre d'associations pour la composition des fruits, et identifié les combinaisons d'allèles pertinentes pour la sélection. Nous avons ensuite réalisé une méta-analyse combinant les résultats de plusieurs études. Nous avons également vérifié l'hérédité des caractères de qualité au niveau hybride, et évalué comment la prédiction génomique pourrait aider à sélectionner de meilleures variétés de tomates.

Inheritance of Secondary Metabolites and Gene Expression Related to Tomato Fruit Quality.

Flavour and nutritional quality are important goals for tomato breeders. This study aimed to shed light upon transgressive behaviors for fruit metabolic content. We studied the metabolic contents of 44 volatile organic compounds (VOCs), 18 polyphenolics, together with transcriptome profiles in a factorial design comprising six parental lines and their 14 F1 hybrids (HF1) among which were five pairs of reciprocal HF1. After cluster analyses of the metabolome dataset and co-expression network construction of the transcriptome dataset, we characterized the mode of inheritance of each component. Both overall and per-cross mode of inheritance analyses revealed as many additive and non-additive modes of inheritance with few reciprocal effects. Up to 66% of metabolites displayed transgressions in a HF1 relative to parental values. Analysis of the modes of inheritance of metabolites revealed that: (i) transgressions were mostly of a single type whichever the cross and poorly correlated to the genetic distance between parental lines; (ii) modes of inheritance were scarcely consistent between the 14 crosses but metabolites belonging to the same cluster displayed similar modes of inheritance for a given cross. Integrating metabolome, transcriptome and modes of inheritance analyses suggested a few candidate genes that may drive important changes in fruit VOC contents.

Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids.

Tomato flavour is an important goal for breeders. Volatile organic compounds (VOCs) are major determinants of tomato flavour. Although most tomato varieties for fresh market are F1 hybrids, most studies on the genetic control of flavour-related traits are performed on lines. We quantified 46 VOCs in a panel of 121 small fruited lines and in a test cross panel of 165 hybrids (the previous panel plus 44 elite cherry tomato lines crossed with a common line). High and consistent heritabilities were assessed for most VOCs in the two panels, and 65% of VOC contents were strongly correlated between lines and hybrids. Additivity was observed for most VOCs. We performed genome wide association studies (GWAS) on the two panels separately, along with a third GWAS on the test cross subset carrying only F1 hybrids corresponding to the line panel. We identified 205, 183 and 138 associations, respectively. We identified numerous overlapping associations for VOCs belonging to the same metabolic pathway within each panel; we focused on seven chromosome regions with clusters of associations simultaneously involved in several key VOCs for tomato aroma. The study highlighted the benefit of testcross panels to create tasty F1 hybrid varieties.

Genetic diversity of tomato response to heat stress at the QTL and transcriptome levels.

Tomato is a widely cultivated crop, which can grow in many environments. However, temperature above 30°C impairs its reproduction, subsequently impacting fruit yield. We assessed the impact of high-temperature stress (HS) in two tomato experimental populations, a multi-parental advanced generation intercross (MAGIC) population and a core-collection (CC) of small-fruited tomato accessions. Both populations were evaluated for 11 traits related to yield components, phenology and fruit quality in optimal and HS conditions. HS significantly impacted all traits in both populations, but a few genotypes with stable yield under HS were identified. A plasticity index was computed for each individual to measure the extent of the heat impact for each trait. Quantitative trait loci (QTL) were detected in control and HS conditions as well as for plasticity index. Linkage and genome-wide association analyses in the MAGIC and CC populations identified a total of 98 and 166 QTLs, respectively. Taking the two populations together, 69 plasticity QTLs (pQTLs) were involved in tomato heat response for 11 traits. The transcriptome changes in the ovary of six genotypes with contrasted responses to HS were studied, and 837 genes differentially expressed according to the conditions were detected. Combined with previous transcriptome studies, these results were used to propose candidate genes for HS response QTLs.