Molecular and phenotypic profiling from base to the crown in maritime pine wood-forming tissue

Research• Environmental, developmental and genetic factors affect variation in wood properties at the chemical, anatomical and physical levels. Here, the phenotypic variation observed along the tree stem was explored and the hypothesis tested that this variation could be the result of the differential expression of genes/proteins during wood formation. • Differentiating xylem samples of maritime pine (Pinus pinaster) were collected from the top (crown wood, CW) to the bottom (base wood, BW) of adult trees. These samples were characterized by Fourier transform infrared spectroscopy (FTIR) and analytical pyrolysis. Two main groups of samples, corresponding to CW and BW, could be distinguished from cell wall chemical composition. • A genomic approach, combining large-scale production of expressed sequence tags (ESTs), gene expression profiling and quantitative proteomics analysis, allowed identification of 262 unigenes (out of 3512) and 231 proteins (out of 1372 spots) that were differentially expressed along the stem. • A good relationship was found between functional categories from transcriptomic and proteomic data. A good fit between the molecular mechanisms involved in CW–BW formation and these two types of wood phenotypic differences was also observed. This work provides a list of candidate genes for wood properties that will be tested in forward genetic

L'adaptation à la sécheresse chez le pin maritime (Pinus pinaster Ait.) (patrons de diversité et différenciation nucléotidiques de gènes candidats et variabilité de caractères phénotypiques)

Les changements climatiques annoncés risquent de constituer des pressions de sélection importantes sur des caractères tels que la résistance à la secheress, notamment pour des espèces forestières comme le pin maritime. Dans ce contexte, une question essentielle est de savoir si ces espèces pourront s'adapter suffisamment rapidement aux nouvelles conditions climatiques. Les objectifs de cette thèse étaient d'évaluer le potentiel adaptatif de populations naturelles de pin maritime pour des caractères liés à la résistance au déficit hydrique, et d'identifier des gènes potentiellement impliqués dans la variation adaptative intra- et inter-populations. Pour y répondre, la variabilité phénotypique pour des caractères de croissance, de biomasse, et d'efficience d'utilisation en eau (EUE) a été évaluée dans un essai de populations naturelles provenant de milieux contrastés sur les plans climatiques et écologiques. Une grande variabilité phénotypique a été mise en évidence entre performances moyennes des populations, et pour les valeurs relatives d'héritabilité et de corrélations entre biomasse et EUE estimées dans chaque population. Ces résultats ont confirmé le rôle de la sélection dans l'adaptation locale du pin maritime, suggérant des stratégies de réponses à un déficit hydrique différentes selon les populations. Les patrons de diversité et différenciation nucléotidiques de gènes candidats à la résistance au stress hydrique ont également été étudiés. Certains gènes s'écartent significativement de patrons d'évolution neutre, avec des signatures cohérentes et complémentaires entre plusieurs méthodes, qui ont été interprétées en termes de scénarios de sélection. L'hétérogénéité de ces signatures entre gènes candidats et entre populations pour certains gènes, serait aussi cohérente avec un rôle de la sélection naturelle plutôt qu'avec celui d'évènements démographiques qui auraient affecté l'ensemble du génome de façon plus homogène. Enfin, quelques associations remarquables ont été mises en évidence entre la variaton de l'EUE entre populations et au sein des populations, et celles de marqueurs SNPs de gènes de déhydrines, de lignification ou de formation de la paroi cellulaire. Ce travail ouvre ainsi des perspectives encourageantes pour la compréhension de l'architecture génétique moléculaire de l'adaptation à la sécheresse chez cette espèce.BORDEAUX1-BU Sciences-Talence (335222101) / SudocSudocFranceF

Data from: Outlier loci highlight the direction of introgression in oaks

Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Q. petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and non-outlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with non-outlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species’ contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized

Nothofagus_assemblies

Nothofagus_assemblie

Complete genotypes (826 samples and 262SNPs - Genalex format)

Complete genotypes (826 samples and 262SNPs - Genalex format

Data from: Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae)

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (Single Nucleotide Polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, five of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models and Bayesian analyses of SNP-climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically-defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establishing mitigation measures for long-lived keystone forest trees in the face of impending climate change

Genetic association for growth and biomass in maritime pine

International audienc