Search

Through repeated cycles of selection and recombination, tree breeding programs deliver genetically improved varieties for a range of target characteristics such as biomass production, stem form, resistance to biotic stresses, wood properties, etc. However, in the context of increased drought and heat waves, it is not yet known whether growth performance will impede drought resistance. To address this question, we compared the hydraulic properties, such as hydraulic efficiency and hydraulic safety, in four varieties over successive varieties of genetically improved maritime pines (i.e., Pinus pinaster Aït.) for growth and stem form. We measured 22 functional traits related to hydraulic efficiency, hydraulic safety, xylem anatomy and wood density. We found that improved varieties presented higher hydraulic conductivity with larger tracheid lumen size and tracheid lumen fraction, and smaller wall thickness reinforcement and tracheid density, but not at the cost of reduced embolism resistance. The reported absence of trade-off between hydraulic conductivity and embolism resistance is a strong asset to improve biomass productivity, through increased hydraulic efficiency, without impacting drought resistance, and should enable new maritime pine varieties to cope with a drier climate. Our study is one of the first to reveal the hydraulic mechanisms over successive varieties of genetic improvement for tree growth. It provides guidelines for sustainable forest management through breeding for other forest tree species.

SummarySpecialized or secondary metabolites (SMs) play a key role in plant resistance against abiotic stresses and defences against bioaggressors. For example, in sessile oaksQuercus petraea, phenolics contribute to reduce herbivore damage and improve drought resistance. Here, we explored the natural variation of SMs in nine European provenances of sessile oaks and aimed to detect its underlying genetic bases.We sampled mature leaves from high and low branches on 225 sessile oak trees located in a common garden and used untargeted metabolomics to characterise the variation of 219 specialized metabolites. In addition, we used whole genome low-depth sequencing to genotype individuals for 1.4M genetic markers. We then performed genome-wide association analyses to identify the genetic bases underlying the variation of leaf SMs.We found that leaf SMs displayed extensive within-provenance variation, but very little differentiation between provenances. For ∼10% of the metabolites we detected, most of this variation could be explained by a single genetic marker.Our results suggest that genetic variation for most leaf SMs is unlikely to be locally adaptive, and that selective pressures may act locally to maintain diversity at loci associated with leaf SM variation within oak populations.

Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.

19 Pág., Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions., Agence Nationale de la Recherche, Grant/ Award Number: FLAG project (ANR-12- ADAP-0007-01); European Commission, Grant/Award Number: TOPWOOD project (MSCA-RISE-2014-645654- TOPWOOD) and grant agreement No. 676876 (GenTree); Ministère de l'Écologie, du Développement Durable et de l'Énergie, Grant/Award Number: GRAAL project (10-MCGOT-GICC-8-CVS-139)

International audience; The presence of heterospecific neighbours can affect the amount of damage caused by insect pests to focal plants. However, how plant neighbours influence herbivore performance is poorly understood, in particular when they are closely related. We tested the independent and interactive effects of tree species identity and tree neighbour type (conspecific vs. heterospecific) on the performance of a major oak pest, the oak processionary moth larvae (OPM, Thaumetopoea processionea L.) fed on Quercus robur L. and Q. petraea Liebl. We performed a factorial greenhouse experiment in which we grew two oak saplings per pot, either from the same species or from both species. We quantified growth and mortality of OPM larvae, leaf phenolic compounds, C:N ratio and bud phenology. OPM larvae performed significantly better on Q. petraea than on Q. robur, regardless of plant neighbour type. Phenolic compounds and C:N, but not phenology, differed between oak species and neighbour species identity. Only bud phenology had a significant effect on OPM performance, which was better when young larvae had access to recently unfolded leaves, regardless of oak species and neighbour identity. Although oak neighbour identity altered the expression of leaf traits, this effect had no measurable consequences on OPM performance. Our results showed that OPM performed better when feeding on Q. petraea than on Q. robur. We also found that oak neighbours altered the expression of leaf traits associated with defence, but that this effect did not cascade onto OPM performance. These findings should be replicated in the field in order to improve forest management strategies against OPM attacks.

[Motivation] Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes., [Main types of variable contained] We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope 13C and 15N in leaves., [Spatial location and grain] We surveyed between 18 and 22 populations per species, 141 in total, across Europe., [Time period] Leaf sampling took place between 2016 and 2017., [Major taxa and level of measurement] We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea., [Software format] The data files are in ASCII text, tab delimited, not compressed., All authors acknowledge support from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 676876 (Project GenTree). Laboratory work was also supported by other projects: COMEDIAS (CGL2017- 83170-R, Spanish Ministry of Science, Innovation and Universities), REMEDINAL IV (TE-CM S2018/EMT-4338, Project of the Autonomous Community of Madrid, Spain), SPONFOREST (BIODIVERSA-3, PCIN-2016-055), and International Laboratory of Global Change (LINCGlobal 4540-143AP). The Swiss contribution was supported by the Swiss Secretariat for Education, Research and Innovation (SERI) under contract no. 6.0032. BC was funded by a Scholarship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazil).

Drought and waterlogging impede tree growth and may even lead to tree death. Oaks, an emblematic group of tree species, have evolved a range of adaptations to cope with these constraints. The two most widely distributed European species, pedunculate (PO; Quercus robur L.) and sessile oak (SO; Quercus petraea Matt. Lieb), have overlapping ranges, but their respective distribution are highly constrained by local soil conditions. These contrasting ecological preferences between two closely related and frequently hybridizing species constitute a powerful model to explore the functional bases of the adaptive responses in oak. We exposed oak seedlings to waterlogging and drought, conditions typically encountered by the two species in their respective habitats, and studied changes in gene expression in roots using RNA-seq. We identified genes that change in expression between treatments differentially depending on species. These “species × environment”-responsive genes revealed adaptive molecular strategies involving adventitious and lateral root formation, aerenchyma formation in PO, and osmoregulation and ABA regulation in SO. With this experimental design, we also identified genes with different expression between species independently of water conditions imposed. Surprisingly, this category included genes with functions consistent with a role in intrinsic reproductive barriers. Finally, we compared our findings with those for a genome scan of species divergence and found that the expressional candidate genes included numerous highly differentiated genetic markers between the two species. By combining transcriptomic analysis, gene annotation, pathway analyses, as well as genome scan for genetic differentiation among species, we were able to highlight loci likely involved in adaptation of the two species to their respective ecological niches.

National audience; Production de bois, espace de loisirs, puits de carbone…Les forêts offrent de multiples services essentiels aux humains et à la Terre. Face à des aléas météorologiques qui s’intensifient avec le réchauffement climatique et des changements globaux menaçants (commerce international, déforestation), certains massifs dépérissent à un rythme inquiétant et nous invite à revoir la façon de gérer les forêts.

1- Pure forests are often seen as being more prone to damage by specialist pest insects than mixed forests, and particularly mixed forests associating host and nonhost species. We addressed the effect of tree diversity on oak colonization and defoliation by a major specialist pest, the oak processionary moth (OPM).2- We quantified the number of male OPM moths captured and larval defoliation in pure stands of two oak host species (Quercus robur and Quercus petraea) and in mixed stands associating the two oak species or each oak species with another nonhost broadleaved species. We conducted two complementary studies to test the effect of host species and stand composition: (i) we used pheromone trapping to compare the number of males OPM captured throughout the distribution of oak hosts in France and (ii) we noted the presence of OPM nests and estimated defoliation in mature forests of north-eastern France.3- Oak species and stand composition significantly influenced the number of male OPM captured and defoliation by OPM larvae. Quercus petraea was consistently more attractive to and more defoliated by OPM than Q. robur. Both oak trees were attacked more in pure stands than in mixed stands, in particular mixed stands associating oaks with another (nonhost) broadleaved species. 4- The results of the present study support the view that mixed forests are more resistant to specialist pest insects than pure stands, and also indicate that this trend depends on forest composition. Our study provides new insights into OPM ecology and has potential implications for forest management, including the management of urban forests where OPM causes serious human health issues.

International audience; The advent of next-generation genome sequencing technologies has allowed approaching the sequencing and analysis of large and complex conifer genomes. Maritime pine (Pinus pinaster Ait.) is an economically and ecologically important conifer species widely distributed in South-West Europe, which shows a significant genetic and adaptive variability. This chapter takes on the task of reviewing the insights into the maritime pine genome sequencing breakthrough and its impact on downstream analysis. Maritime pine genome sequencing and assembly approaches are described along with the impact of related tools. A section of the state-of-the-art research on comparative, functional, structural, and translational genomics aimed at dissecting the genetic basis and the specific regulation of biological processes underlying the expression of traits of interest in maritime pine and other conifers is also described. Perspectives about the impact of these tools as well as additional research approaches are discussed.

Water use efficiency (WUE) is an important adaptive trait for soil water deficit. The molecular and physiological bases of WUE regulation in crops have been studied in detail in the context of plant breeding. Knowledge for most forest tree species lags behind, despite the need to identify populations or genotypes able to cope with the longer, more intense drought periods likely to result from climate warming. We aimed to bridge this gap in knowledge for sessile oak (Quercus petraea (Matt.) Liebl.), one of the most ecologically and economically important tree species in Europe, using a factorial design including trees with contrasted phenotypic values (low and high WUE) and two watering regimes (control and drought). By monitoring the ecophysiological response, we first qualified genotypes for their WUE (by using instantaneous and long-term measures). We then performed RNA-seq to quantify gene expression for the three most extreme genotypes exposed to the two watering regimes. By analyzing the interaction term, we were able to capture the molecular strategy of each group of plants for coping with drought. We identified putative candidate genes potentially involved in the regulation of transpiration rate in high-WUE phenotypes. Regardless of water availability, trees from the high-WUE phenotypic class overexpressed genes associated with drought responses, and in the control of stomatal density and distribution, and displayed a downregulation of genes associated with early stomatal closure and high transpiration rate. Fine physiological screening of sessile oaks with contrasting WUE, and their molecular characterization (i) highlighted subtle differences in transcription between low- and high-WUE genotypes, identifying key molecular players in the genetic control of this trait and (ii) revealed the genes underlying the molecular strategy that evolved in each group to potentially cope with water deficit, providing new insight into the within-species diversity in drought adaptation strategies.

Research conductedWith the ongoing global warming, there are serious concerns about the persistence of locally adapted populations. Indeed, with the raising of temperature, the phenological cycle of tree species may be strongly affected since higher winter temperatures may have a negative impact on endodormancy release if chilling requirements are not fulfilled during winter and late frost in spring may expose trees if buds flush too early. Thus, Environmental gradients (showing continuous variations of environmental conditions) constitute a design of choice to analyze the effect of winter dormancy in locally adapted population.MethodsIn the present study, we used an elevation gradient in the Pyrenees to explore the gene expression network involved in dormancy regulation in natural populations of sessile oak locally adapted to temperature. Terminal buds were harvested during dormancy induction and release at different elevations. Then, gene expression was quantified using RNAseq and we used a likelihood ratio test to identify genes displaying significant dormancy, elevation or dormancy-by-elevation interaction effects.Key resultsOur results highlight molecular processes in locally adapted populations along this elevation cline, and made it possible to identify key dormancy-by-elevation responsive genes revealing that locally adapted populations have evolved distinct molecular strategies to adapt their bud phenology in response to environmental variation (i.e. temperature).

International audience; Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('F-ST-islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that F-ST-islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.

The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of convergent linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last three hundred years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. Our results therefore provide evidence of selection operating on long-lived species during recent climatic changes.

Oaks are dominant forest tree species widely distributed across the northern hemisphere, where they constitute natural resources of economic, ecological, social and historical value. Hybridization and adaptive introgression have long been thought to be major evolutionary drivers of the ecological success of oaks. However, the maintenance of species barriers remains a key question, given the extent of interspecific gene flow. We used a demographically-explicit genome scan approach combining approximate Bayesian computation and backward simulations to scan the genomes of four European white oak species for reproductive barriers. We first confirmed earlier findings of interspecific contact since the last glacial maximum. We then made use of the tremendous genetic variation among these four species (31 million SNPs) to identify genomic regions enriched in SNPs deviating from demographic expectations under a hypothesis of recent secondary contact. The outlier-enriched regions detected were of restricted size and widely distributed, over all the chromosomes. We identified 215 regions, containing 227 oak genes. A Literature-based functional annotation of these genes highlighted important functions driving the reproductive isolation of the four species. These functions included tolerance to biotic and abiotic constraints, and intrinsic mating barriers. The functions of the annotated genes were highly consistent with the ecological preferences of the four species. These genes may, therefore, be considered candidate genes in studies of species responses to past and ongoing environmental changes.

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in

The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome- wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.

International audience; Forests have received much media attention of late, for the employment they provide, the economic development they underpin, the biodiversity and heritage they support, their role in mitigating the effects of climate change and protecting the landscape, and the sense of well‐being or improvement in living conditions they provide (Häggström, 2019). Given their ecological dominance, forest trees are also considered to be model organisms for studies aimed at improving our understanding of the ecological and evolutionary processes underlying plant diversification and adaptation on Earth. This knowledge can be used in the design of conservation strategies for genetic resources and adaptive practices to increase the ability of managed forest stands (Lefevre et al . , 2014) and allow natural populations to evolve (Hamilton & Miller, 2016). New Phytologist has always been a major channel for the publication of important outcomes in this area of active research, as illustrated in a recent Tansley review by Cavender‐Bares (2019) dedicated to American oaks, and a special issue dedicated to Eucalyptus genomics (Strauss & Myburg, 2015). With this Feature Issue dedicated to oaks, highlighting new findings and opinions in the area of ecological and evolutionary genomics, New Phytologist affirms its commitment to studies of the intricacy of ecology and evolution in the age of genomics.

SummaryThe tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity.We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world’s oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity.The support we find for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios., Measurement(s)growth ring • wood densityTechnology Type(s)measuring table • calculationFactor Type(s)tree speciesSample Characteristic - OrganismBetula pendula • Fagus sylvatica • Picea abies • Populus nigra • Pinus pinaster • Pinus sylvestris • Quercus petraeaSample Characteristic - LocationEurope Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11294993

17 Pág., A decade of genetic association studies in multiple organisms suggests that most complex traits are polygenic; that is, they have a genetic architecture determined by numerous loci, each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and time is crucial to understand the genetic basis of phenotypic variation. We applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyse this variation across environments and years. We evaluated five categories of fitness-related traits (survival, height, phenology, functional, and biotic-stress response) in a clonal common-garden network planted in contrasted environments (over 20,500 trees). Most of the analysed traits showed evidence of local adaptation based on Qst -Fst comparisons. We further observed a remarkably stable degree of polygenicity, averaging 6% (range of 0%-27%), across traits, environments and years. We detected evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. Because polygenic adaptation can occur rapidly, our results suggest that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, especially in the current context of climate change., This study was funded by the Spanish Ministry of Economy and Competitiveness through projects RTA2010-00120-C02- 02 (CLONAPIN), CGL2011-30182- C02- 01 (AdapCon) and AGL2012-40151- C03- 02 (FENOPIN). The study was also supported by the “Initiative d’Excellence (IdEx) de l’Université de Bordeaux - Chaires d'installation 2015” (EcoGenPin) and the European Union's Horizon 2020 research and innovation programme under grant agreement No 773383 (B4EST)

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios. Measurement(s) growth ring • wood density Technology Type(s) measuring table • calculation Factor Type(s) tree species Sample Characteristic - Organism Betula pendula • Fagus sylvatica • Picea abies • Populus nigra • Pinus pinaster • Pinus sylvestris • Quercus petraea Sample Characteristic - Location Europe Published

International audience; Throughout the Northern Hemisphere, human societies, political systems, and religions have appropriated oaks in symbolic representations. In this review, we explore the possible associations between recent genetic and genomic findings and the symbolic representations of oaks. We first consider the ways in which evolutionary history during the Holocene has tightened links between humans and oaks in Europe, and how this may have led to symbolic representations. We then show how recent findings concerning the structure and evolution of the oak genome have provided additional knowledge about symbolic representations, such as longevity, cohesiveness, and robustness.

Latitudinal and elevational gradients provide valuable experimental settings for studies of the potential impact of global warming on forest tree species. The availability of long-term phenological surveys in common garden experiments for traits associated with climate, such as bud flushing, for sessile oaks (Quercus petraea), provides an ideal opportunity to investigate this impact.We sequenced 18 sessile oak populations, and used available sequencing data for three other closely related European white oak species (Q. pyrenaica, Q. pubescens, Q. robur), to explore the evolutionary processes responsible for shaping the genetic variation across latitudinal and elevational gradients in extant sessile oaks. We used phenotypic surveys in common garden experiments and climatic data for the population of origin, to perform genome-wide scans for population differentiation, genotype-environment (GEA) and genotype-phenotype associations (GPA).The inferred historical relationships betweenQ. petraeapopulations suggest that interspecific gene flow occurred betweenQ. roburandQ. petraeapopulations from cooler or wetter areas. A genome-wide scan of differentiation betweenQ. petraeapopulations identified SNPs displaying strong interspecific relative divergence between these two species. These SNPs followed genetic clines along climatic or phenotypic gradients, providing further support for the likely contribution of introgression to the adaptive divergence ofQ. petraeapopulations.Overall, the results of this study indicate that adaptive introgression ofQ. roburalleles has occurred. We discuss the results of this study in the framework of the post-glacial colonization scenario, in which introgression and diversifying selection have been proposed as essential drivers ofQ. petraeamicroevolution.

Key Message : Needle anatomic plasticity enables fast-growing maritime pine trees to cope with water limitations by enhancing both water-use efficiency and embolism resistance.Abstract : Maritime pine is a major forest tree grown for wood production in Southern Europe. A breeding program for the selection of fast-growing varieties was established in the 1960s, in France. In the context of climate change, the magnitude of phenotypic plasticity is a key issue for the prediction of putative decreases in productivity in the improved genetic material. We characterized the phenotypic plasticity of anatomical and physiological traits in two families with contrasting growth rates, under different water regimes, at the juvenile stage. An analysis of 38 traits showed that the fastest growing family had the greatest phenotypic plasticity for morphological, anatomic, chemical and physiological traits, enabling it to increase its water use efficiency and embolism resistance in response to water deficit. The observed modifications to the extravascular (proportion of spongy parenchyma in needles) and vascular (xylem in the needles and stem) compartments in response to water constraints were consistent with a higher water use efficiency and greater embolism resistance. The ability to optimize meresis and auxesis according to environmental conditions during needle development could be related to growth performance over time in different environmental conditions. These results suggest that selection for growth in maritime pine leads to the selection of individuals with greater phenotypic plasticity related to higher performances in non-limited conditions.

International audience; The pulse of the tree (diurnal cycle of stem radius fluctuations) has been widely studied as a way of analyzing tree responses to the environment, including the phenotypic plasticity of tree-water relationships in particular. However, the genetic basis of this daily phenotype and its interplay with the environment remain largely unexplored. We characterized the genetic and environmental determinants of this response, by monitoring daily stem radius fluctuation (dSRF) on 210 trees from a Eucalyptus urophylla x E. grandis full-sib family over 2 years. The dSRF signal was broken down into hydraulic capacitance, assessed as the daily amplitude of shrinkage (DA), and net growth, estimated as the change in maximum radius between two consecutive days (Delta R). The environmental determinants of these two traits were clearly different: DA was positively correlated with atmospheric variables relating to water demand, while Delta R was associated with soil water content. The heritability for these two traits ranged from low to moderate over time, revealing a time-dependent or environment-dependent complex genetic determinism. We identified 686 and 384 daily quantitative trait loci (QTL) representing 32 and 31 QTL regions for DA and Delta R, respectively. The identification of gene networks underlying the 27 major genomics regions for both traits generated additional hypotheses concerning the biological mechanisms involved in response to water demand and supply. This study highlights that environmentally induced changes in daily stem radius fluctuation are genetically controlled in trees and suggests that these daily responses integrated over time shape the genetic architecture of mature traits.

Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled ‘Genomics and Forest Tree Genetics’ was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.

The presence of heterospecific neighbours can affect damage caused by pest insects on focal plants. However, how plant neighbours influence herbivore performance is poorly understood. We tested the independent and interactive effects of tree species identity and tree neighbour type (conspecific vs. heterospecific) on the performance of a major oak pest, the oak processionary moth larvae (OPM, Thaumetopoea processionea) fed on Quercus robur and Q. petraea. We performed a factorial greenhouse experiment in which we grew two oak saplings per pot, either from the same species or from both species. We quantified growth and mortality of OPM larvae, leaf phenolic compounds, C:N ratio and bud phenology. OPM larvae performed significantly better on Q. petraea than on Q. robur, regardless of plant neighbour type. Phenolic compounds and C:N, but not phenology, differed between oak species and neighbour species identity. Only bud phenology had a significant effect on OPM performance, which was better when young larvae had access to recently unfolded leaves, regardless of oak species and neighbour identity. Although oak neighbour identity altered the expression of leaf traits, this effect had no measurable consequences on OPM performance. However, further studies should consider the effect of oak species neighbour on OPM preferences for either Q. robur or Q. petraea, in pure and mixed stands, before translating current results into recommendations for forest management.Author ContributionTD and BC conceived the study and acquired the data. TD performed experiment and analysed the data. EV, TD and XM performed the chemical analyses. TD and BC drafted the first version of the manuscript and all authors wrote the final version of the manuscript.TD, BC conceived and designed research. TD performed experiment and analysed data. EV, TD, XM performed the chemical analyses. TD, BC wrote the manuscript. All authors read and approved the manuscript.AM and DB conceived and designed research. AM and BB conducted experiments. GR contributed new reagents or analytical tools. AM, BB and GR analysed data. AM wrote the manuscript. All authors read and approved the manuscript.

Forest ecosystems are increasingly challenged by extreme events, e.g. drought, storms, pest and pathogenic fungi outbreaks, causing severe ecological and economical losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e. heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, growth phenology and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), were assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), growth phenology (0.165-0.310) and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021) measured after inoculation under controlled conditions, but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4,227 genome-wide SNPs revealed several loci significantly associated to each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.

International audience; Exotic pathogens cause severe damage in natural populations in the absence of coevolutionary dynamics with their hosts. However, some resistance to such pathogens may occur in naive populations. The objective of this study was to investigate the genetics of this so-called 'exapted' resistance to two pathogens of Asian origin (Erysiphe alphitoides and Phytophthora cinnamomi) in European oak. Host-pathogen compatibility was assessed by recording infection success and pathogen growth in a full-sib family of Quercus robur under controlled and natural conditions. Two high-resolution genetic maps anchored on the reference genome were used to study the genetic architecture of resistance and to identify positional candidate genes. Two genomic regions, each containing six strong and stable quantitative trait loci (QTLs) accounting for 12-19% of the phenotypic variation, were mainly associated with E. alphitoides infection. Candidate genes, especially genes encoding receptor-like-kinases and galactinol synthases, were identified in these regions. The three QTLs associated with P. cinnamomi infection did not colocate with QTLs found for E. alphitoides. These findings provide evidence that exapted resistance to E. alphitoides and P. cinnamomi is present in Q. robur and suggest that the underlying molecular mechanisms involve genes encoding proteins with extracellular signaling functions.

Changes in leaf soluble proteome were explored in 3-month-old plants of metallicolous (M) and nonmetallicolous (NM) Agrostis capillaris L. populations exposed to increasing Cu concentrations (1-50 μM) to investigate molecular mechanisms underlying plant responses to Cu excess and tolerance of M plants. Plants were cultivated on perlite (CuSO4 spiked-nutrient solution). Soluble proteins, extracted by the trichloroacetic acid/acetone procedure, were separated with 2-DE (linear 4-7 pH gradient). Analysis of CCB-stained gels (PDQuest) reproducibly detected 214 spots, and 64 proteins differentially expressed were identified using LC-MS/MS. In both populations, Cu excess impacted both light-dependent (OEE, cytochrome b6-f complex, and chlorophyll a-b binding protein), and -independent (RuBisCO) photosynthesis reactions, more intensively in NM leaves (ferredoxin-NADP reductase and metalloprotease FTSH2). In both populations, upregulation of isocitrate dehydrogenase and cysteine/methionine synthases respectively suggested increased isocitrate oxidation and enhanced need for S-containing amino-acids, likely for chelation and detoxification. In NM leaves, an increasing need for energetic compounds was indicated by the stimulation of ATPases, glycolysis, pentose phosphate pathway, and Calvin cycle enzymes; impacts on protein metabolism and oxidative stress increase were respectively suggested by the rise of chaperones and redox enzymes. Overexpression of a HSP70 may be pivotal for M Cu tolerance by protecting protein metabolism. All MS data have been deposited in the ProteomeXchange with the dataset identifier PXD001930 (http//proteomecentral.proteomexchange.org/dataset/PXD001930).

Key message This review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology. Context A decade after the first forest tree genome sequence was released into the public domain, the rapidly evolving genomics and bioinformatics toolbox has advanced our understanding of the structure, functioning, and evolution of forest tree genomes. Aims and methods This review highlights some of the discoveries and applications that “omics” technologies have made possible for forest trees over the past 10 years. Results In this review, we start by our current understanding of genome evolution and intricacies of gene regulation for reproduction, development, and responses to biotic and abiotic stresses. We then skim over advances in interactome analysis and epigenomics, the knowledge of the extent of genetic variation within and between species, revealing micro- and macro-evolutionary processes and species history, together with the complex architecture of quantitative traits. We finally end with applications in genetic resource conservation and breeding. Conclusion The knowledge gained through the use of these technologies has a huge potential impact for adapting forests to the main challenges they will have to face: changing demand from ecosystem services with potentially conflicting strategies in terms of conservation and use, as well as climate changes and associated threats. Genomics will undoubtedly play a major role over the next decade and beyond, not only to further understand the mechanisms underlying adaptation and evolution but also to develop and implement innovative management and policy actions to preserve the adaptability of natural forests and intensively managed plantations.