Caractérisation de la diversité génétique chez la tomate

Characterisation of tomato genetic diversity. In the period of agricultural intensification, modern plant breeding techniques have often resulted in drastic reduction of plant genetic diversity. Conservation of biodiversity is recognised as an important issue as many plant breeding programs routinely rely on germplasms as sources to develop agronomic traits of interest. Constant evaluation of plant genetic resources happens via the development of functional tools which accurately reflect existing diversity. Molecular markers are widely used to assay genetic diversity due to relative ease of utility, high polymorphism levels and furthermore, may be combined with other data, e.g. physiological approaches to facilitate direct targeting of interesting traits. In the framework of the French Solanaceae Biological Resources Center (CRB) to maintain diverse genetic resources, the Research Unit for Genetic Improvement of Fruit and Vegetables at INRA-Montfavet (UGAFL) holds a large collection of tomato (Solanum lycopersicum) and related wild species (Solanum subsection Lycopersicon). High phenotypic variation is displayed by the tomato fruit, especially in fruit size owing to domestication. UGAFL has accrued many accessions differing for fruit type, size and composition, well representing the natural variation observed for this genus. This collection thus provides the material basis for a number of breeding programs involved in improving pathogen resistance, nutritional and organoleptic qualities of tomato. Our project, in collaboration between UGAFL and the Laboratory of Cell Biology at INRA-Versailles, intended to characterise the genetic diversity of the collection comprising of 85 accessions, including 53 tomato lines/cultivars and 32 accessions of related wild species using different tools. We developed novel markers based on SSAP (Sequence-Specific Amplification Polymorphisms) analysis of insertion polymorphisms from three distinct families of copia-type retrotransposons (Tnt1, ToRTL1 and T135). Results show that combined SSAP insertion profiles of Tnt1, ToRTL1 and T135 are congruent and useful for inferring host-species phylogeny. Groups of species accessions were recovered,while the tree topology is in agreement with other previous phylogenetic analyses, distinguishing groups of red and green fruited species, self compatible and self incompatible species. This also demonstrates a strong association between hostspecies phylogeny and the distribution of retrotransposon insertions. Diversity within the tomato collection is much lower compared to wild species. Nonetheless, SSAP insertion profiles reflect the genetic background of the lines and several clear groupings according to fruit types were recovered, such as clusters of round or fleshy types with large fruits, as well as clusters of industrial-long self-pruning types. Most cherry and small-fruited types occupy less derived positions than larger-fruited tomatoes, agreeing with the hypothesis of small fruit size being an ancestral character. Altogether, our results show that retrotransposon insertion polymorphisms proved highly useful for diversity analyses by successfully genotyping all accessions and reflecting underlying genetic divergences of host genomes. Subsequent integration of SSAP markers with other physiological markers, such as proteomic markers, or with neutral markers, will be performed.

La conservation et l'évaluation de la diversité génétique passe par la recherche d'outils capables de la traduire fidèlement. Pour cela, des approches génétiques, comme les marqueurs moléculaires, et physiologiques, comme les analyses protéomiques, peuvent être combinées. Dans le cadre du CRB Solanacées, l'INRA conserve et caractérise de larges collections de tomates (Solanum lycopersicum) et de plusieurs espèces sauvages apparentées, sur lesquelles s'appuient les programmes de recherche sur les résistances aux bioagresseurs et sur la qualité organoleptique et nutritionnelle des fruits. Nous avons développé des analyses de la diversité génétique de ces collections, en particulier pour la taille du fruit. Nous avons utilisé de nouveaux types de marqueurs moléculaires basés sur les polymorphismes d'insertion de rétrotransposons, séquences mobiles capables de s'amplifier dans le génome et de créer de la diversité génétique. Ces polymorphismes d'insertion se sont révélés informatifs pour l'étude de la diversité génétique au sein de collections de tomate et reflètent les types de fruits et les généalogies. En outre, les relations interspécifiques révélées au sein du genre sont en accord avec les analyses phylogénétiques antérieures. Ces informations sont en cours de confrontation avec celles apportées par des marqueurs neutres et par des approches protéomiques.