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A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.

The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species.

The search for associations between molecular markers and variation of traits with agronomic importance is a main goal of Marker-Assisted Selection development, especially for perennials species. Knowledge of genetic diversity and structure is a prerequisite for such studies. In the same way, knowledge of structure and extant of Linkage Disequilibrium in populations is an important task. We strengthen and fine-tuned previously described genetic structure and diversity of Coffea canephora Pierre in order to assess the capabilities of association mapping based approaches for this species. We laid the basis for rapid characterization of genetic resources with the help of microsatellite markers and clarify the genetic origin of a previously nonstudied population. Future development of core-collections will benefit from these results. Structure and extent of Linkage Disequilibrium was determined at different scales and for different populations or genetic groups, with the help of 108 genome wide markers, giving the opportunities to identify suitable populations for the 2 assocation mapping categories, genome-wide scan and candidate region. A first try of association mapping confirms the important capabilities of such approaches for our species. Implications of genetic diversity and structure as well as Linkage Disequilibrium structure for future breeding purposes are discussed; La recherche d'associations entre marqueurs moléculaires et les variations de caractères d'intérêt agronomique est un enjeu majeur du développement de la sélection assistée par marqueurs, notamment pour des espèces pérennes. La connaissance de la diversité génétique et de la structure de celle-ci est un préalable indispensable à la mise en place de telles études. Au même titre, la connaissance de l'étendue et de l'intensité du déséquilibre de liaison au sein des populations considérées est également nécessaire. Nous avons donc entrepris de confirmer et de préciser la diversité et la structure génétique de Coffea canephora Pierre afin d'évaluer les potentialités d'études d'association sur cette espèce. Nous avons posé les bases d'une caractérisation rapide des collections de ressources génétiques de cette espèce à l'aide de marqueurs microsatellites et précisé l'origine génétique d'une population jusqu'à présent non étudiée. Cette base pourra également servir au développement de futures cores-collections. L'évaluation de la structure et de l'étendue du déséquilibre de liaison à différentes échelles et au niveau de différentes populations ou groupes de diversité à l'aide de 108 marqueurs répartis sur l'ensemble du génome nous a permis de proposer des populations utilisables pour les 2 types d'approches de génétique d'associations, scan génome entier ou région candidate. Un premier essai d'étude d'association a montré les potentialités importantes de ces approches pour notre espèce. Les implications de l'importance de la diversité génétique et de sa structure ainsi que de la structure du déséquilibre de liaison au sein de nos populations pour l'amélioration sont discutées.