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Génomique écologique de l'adaptation locale chez le pin maritime (Pinus pinaster)

Abstract : In the current context of global change, natural ecosystems are threatened worldwide. Predictions show that climate change will cause a value loss for the European forest of 21 to 50% by 2071-2100. In France, the Nouvelle-Aquitaine region depends on forests, which occupy 34% of the territory. Maritime pine (Pinus pinaster) is of fundamental importance for this region: it represents 40% of the wood resources. This emblematic conifer of the Mediterranean basin and the southwestern Atlantic area has a discontinuous range distribution, which makes studying its genetic adaptation especially interesting.This PhD thesis aims to study maritime pine genetic adaptation to environmental conditions at various temporal scales and at different tree life-stages.The first chapter explores the susceptibility of different maritime pine populations to two pathogens: Armillaria ostoyae, a root pathogen and Diplodia sapinea, a systemic one. For this study, we used populations from CLONAPIN, a clonal collection representing all the gene-pools of maritime pine. We estimated H2 (broad-sense heritability) and Qst (quantitative genetic differentiation) for pest susceptibility, as well as H2 and Qst of other adaptive traits: height and phenology. The CLONAPIN collection having been genotyped, we were able to do a genotype-phenotype association study with all the mentioned traits. Finally, correlations were established between the genetic component of the traits and climatic variables. We observed moderate H2 for most traits, whereas Qst was generally high, showing a strong population differentiation. Susceptibility to D. sapinea was strongly correlated to high temperatures. SNPs (Single Nucleotide Polymorphisms) associated with the traits had a small genotype effect, pointing to a polygenic nature of the traits.The second chapter is set within the European project GenTree, aiming at studying genetic adaptation and evolutionary potential of natural tree populations. For our study, we were interested in maritime pine populations from Spain, Italy and France and in Scots pine (Pinus sylvestris) populations from Spain, Germany, Lithuania and Finland. As part of this project, 25 trees from each population were phenotyped for height, diameter, wood density, specific leaf area (SLA) and carbon isotopic discrimination. Seeds were sampled on the phenotyped trees, while conserving the family structure. Common gardens were established with these seeds in Spain and France for maritime pine, and in Spain, Germany, Lithuania and Finland for Scots pine. In each garden, all of the species’ sampled populations were sowed, trying to imitate natural regeneration. Germination, survival and growth stages were monitored during one (P. pinaster) and two years (P. sylvestris). Thanks to these data, we estimated different components of fitness, which demonstrate a strong population effect, and detect significant selection gradients in these populations. They show the importance of mother needle traits in P. pinaster, and mother size in P. sylvestris.The third chapter is based on Corsican populations. This island has the particularity of representing a single gene-pool of P. pinaster, which was able to adapt locally to the different environments of the territory. We took advantage of the common garden PINCORSE, composed of families issued from 33 Corsican populations. These different populations were phenotyped over several years for height, and a subset for phenology and carbon isotopic discrimination too. With these data, we computed h2 (narrow-sense heritability) and Qst, and conducted an association study based on over 50k newly generated SNPs.These studies present an innovative work bringing new insights on the adaptive capacities of maritime pine. Genetic data on performance of tree populations are essential to the genetic improvement program of maritime pine, tree-breeding and forest genetic resource conservation strategies in environments facing major changes.
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Agathe Hurel. Génomique écologique de l'adaptation locale chez le pin maritime (Pinus pinaster). Sciences agricoles. Université de Bordeaux, 2019. Français. ⟨NNT : 2019BORD0405⟩. ⟨tel-02935290⟩

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