Séminaire IBIP – thématique « fruit and seed »
Les séminaires ont lieu sur le Campus Montpellier SupAgro/INRA de La Gaillarde (2, place P. Viala Montpellier)

Jeudi 10 mars 2016
à 14h00 – Amphi 206 (Cœur d’École)

Tomato fruit quality: genetic and genomic approaches

Mathilde Causse
Génétique et Amélioration des Fruits et Légumes, INRA Avignon

Tomato is the first vegetable grown all over the world. It is also a model organism for the fleshy–fruit plants. Today the genome is sequenced and many genomic resources are available.
Identifying the genes controlling the variation of quantitative traits, notably those related to fruit quality is still challenging. Genetic variations underlying quantitative traits (QTL) have been mapped by traditional linkage mapping for years and positional cloning identified a few QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of genetic background on QTL effect has been underlined. Thanks to the increase in molecular markers and the availability of the genome sequence, genome-wide association studies were then proposed to circumvent QTL limitations. In tomato, a self-pollinated crop, we have shown that association studies are possible, using the admixed nature of cherry tomato genomes that limits the impact of population structure in such an approach. Nevertheless, the results might be limited by linkage disequilibrium, which varies greatly along the genome. Multi-allelic Advanced Generation Inter-Cross (MAGIC) populations allow a wide range of variability to be analyzed and avoid dealing with population structure.
We have constructed a MAGIC population by crossing 8 tomato lines, representing a wide range of genetic diversity within the species. The large range of phenotypic variability represented by these lines was then characterized at different scales, metabolomic, proteomic and transcriptomic. The variation of a few genes/proteins, involved in primary metabolism and stress response, was related to metabolite content by network reconstruction. The whole genomes of the 8 founder lines were resequenced identifying more than 4 millions SNPs when mapped onto the reference genome. A set of 1536 SNPs markers was then selected to genotype the MAGIC population and used to construct a linkage map. A large increase in recombination frequencies compared to bi-parental populations was shown. QTLs for fruit composition traits were mapped and related to the variations detected at the genome sequence and expression levels in the parental lines. The advantages and limits of the different types of population, in the context of the available genome sequence and resequencing facilities, will be discussed.

Contact : Tou Cheu Xiong

Contacts IBIP :
Sabine Zimmermann
Alexandre Martiniere
Christine Granier
Chantal Baracco