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.

Genomic selection - the prediction of breeding values using DNA polymorphisms - is a disruptive method that has widely been adopted by animal and plant breeders to increase productivity. It was recently shown that other sources of molecular variations such as those resulting from transcripts or metabolites could be used to accurately predict complex traits. These endophenotypes have the advantage of capturing the expressed genotypes and consequently the complex regulatory networks that occur in the different layers between the genome and the phenotype. However, obtaining such omics data at very large scales, such as those typically experienced in breeding, remains challenging. As an alternative, we proposed using near-infrared spectroscopy (NIRS) as a high-throughput, low cost and non-destructive tool to indirectly capture endophenotypic variants and compute relationship matrices for predicting complex traits, and coined this new approach ”phenomic selection” (PS). We tested PS on two species of economic interest (Triticum aestivum L. and Populus nigra L.) using NIRS on various tissues (grains, leaves, wood). We showed that one could reach predictions as accurate as with molecular markers, for developmental, tolerance and productivity traits, even in environments radically different from the one in which NIRS were collected. Our work constitutes a proof of concept and provides new perspectives for the breeding community, as PS is theoretically applicable to any organism at low cost and does not require any molecular information.

Summary• The seasonal timing of growth events is crucial to tree distribution and conservation. The seasonal growth cycle is strongly adapted to the local climate that is changing because of global warming. We studied bud set as one cornerstone of the seasonal growth cycle in an integrative approach.• Bud set was dissected at the phenotypic level into several components, and phenotypic components with most genetic variation were identified. While phenotypic variation resided in the timing of growth cessation, and even so more in the duration from growth cessation to bud set, the timing of growth cessation had a stronger genetic component in both natural and hybrid populations.• Quantitative trait loci (QTL) were identified for the most discriminative phenotypic bud-set components across four poplar pedigrees. The QTL from different pedigrees were recurrently detected in six regions of the poplar genome.• These regions of 1.83-4.25 Mbp in size, containing between 202 and 394 genes, form the basis for further molecular-genetic dissection of bud set.

Bud set, the cornerstone delimiting the seasonal growth period in trees, is the dynamic net result of the often photoperiod-controlled growth cessation and the subsequent bud formation. Here, we show that in hybrid poplar, the critical day length for growth cessation and the duration of bud formation each vary with local climatic conditions in identical genotypes. The detailed dissection of bud set suggests temperature as one additional environmental factor that modifies the sensitivity to day-length signals at growth cessation and influences the duration of bud formation in poplar. The ability of perennial plants to integrate additional environmental signals with photoperiod signaling may add to short-term acclimatization to the predicted longer growing seasons in future climates.

Poplar is the first forest tree genome to be decoded. As an initial step to the comprehensive analysis of poplar proteome, we described reference 2-D-maps for eight tissues/organs of the plant, and the functional characterization of some proteins. A total of 398 proteins were excised from the gels. About 91.2% were identified by nanospray LC-MS/MS, based on comparison with 260,000 Populus sp. ESTs. In comparison, reliable PMFs were obtained for only 51% of the spots by MALDI-TOF-MS, from which 43% (83 spots) positively matched gene models of the Populus trichocarpa genome sequence. Among these 83 spots, 58% matched with the same proteins as identified by LC-MS/MS, 21.7% with unknown function proteins and 19.3% with completely different functions. In the second phase, we studied the effect of drought stress on poplar root and leaf proteomes. The function of up- and down-regulated proteins is discussed with respect to the physiological response of the plants and compared with transcriptomic data. Some important clues regarding the way poplar copes with water deficit were revealed.

Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed‐based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass‐scale deployment of PBCs.

Summary• In order to elucidate the genetic control of resistance to Melampsora laricipopulina leaf rust in hybrid poplars, a Populus deltoides × P. trichocarpa F 1 progeny was analysed for qualitative and quantitative rust resistances.• This progeny was evaluated for three components of quantitative resistance (latent period, uredinia number and uredinia size) to seven M. larici-populina strains in controlled conditions, and for one component of field susceptibility (rust colonization on the most infected leaf).• One qualitative resistance locus inherited from P. deltoides , R 1 , was localized on the genetic map. It segregates 1 : 1 in the F 1 progeny and is effective against four of the studied strains. QTL analysis was performed separately on R 1 and r 1 genotype subsets. An additional detection was conducted on the entire F 1 progeny for the three strains able to overcome R 1 and for MAX2. A total of nine QTLs were detected. Two had large, broad-spectrum effects. One ( R US ) is inherited from the P. trichocarpa parent; the other is inherited from P. deltoides and colocalized with R 1 . Seven QTLs had only limited and specific effects. Significant interaction effects were detected mainly between the two major QTLs.• Implications of these results for durable resistance breeding strategies, and possible benefits from the Populus genome sequence, are discussed.

growth regulators. Another characteristic distinguishing the To initiate somatic embryogenesis in Pinus syl7estris and two species in culture was that in some embryogenic cell lines Pinus pinaster, immature seeds were collected from June to August and the developmental stage of the zygotic embryos of P. syl7estris, somatic embryos matured spontaneously when was determined. Four developmental stages were distinguished initiated and maintained on medium without growth regulators. Some of these embryos developed into plantlets on the and the response of the zygotic embryos at each of the four same medium at the frequency of 40%. Therefore, in P. developmental stages was compared intra-and inter-species. For this study, modified Litvay's medium (LM), with or syl7estris all the stages of somatic embryogenesis were without growth regulators, was chosen. Somatic embryogene-achieved on the medium without growth regulators. However, sis was initiated and maintained on both media but the two in both species, maturation of a large number of somatic species displayed different propensities. In P. syl7estris, the embryos was greatly improved on medium containing high highest initiation frequency was obtained with intact concentration of gellan gum (Gelrite 10 g l − 1 ) and abscisic acid (60 mM). Cotyledonary somatic embryos subsequently megagametophytes containing embryos at the four-cell stage to the stage of cleavage polyembryony (up to 22 and 9%, germinated (72 and 80% for P. syl7estris and P. pinaster, respectively). The culture medium had no significant effect on respectively) and developed into plantlets (48 and 29%, for P. syl7estris and P. pinaster, respectively). This represents a the initiation and proliferation of embryogenic cultures. In P. pinaster, however, the best response occurred from excised significant improvement in plantlet recovery from somatic zygotic embryos at the stage prior to elongation of cotyledon embryos of both species. primordia (up to 40% explants responded), on medium with