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Additional file 1: Table 1S. Bread wheat cultivars used in this experiment. Table 2S. Bread wheat landraces used in this experiment.

Additional file 2: Fig. 1S. Density histogram of 25 morpho-physiological characteristics in an association panel consisting of 292 Iranian bread wheat accessions under normal and salinity conditions. Abbreviations: Electrolyte leakage (ELI); SPAD; shoot fresh weight (SFW); shoot dry weight (SDW); relative water content (RWC); root fresh weight (RFW); root dry weight (RDW); root volume (RV); shoot height (SH); root height (RH); chlorophyll a (Chl a); chlorophyll b (Chl b); total chlorophyll (total Chl); carotenoid (Car); protein; proline; catalase (CAT); guaiacol peroxidase (GPX); malondialdehyde (MDA); Shoot Na (Na-s); Root Na (Na-r); Shoot K (K-s); Root K (K-r); Shoot K/Na (K/Na-s); root K/Na (K/Na-r). Figure 2S. The number of subpopulations in the wheat panel based on ΔK values (a), A structure plot of 298 wheat cultivars and landraces determined by K = 3 (b).

Future climate change has been predicted to disrupt local adaptation in many perennial plants, such as forest trees, but the magnitude and location of these effects are thus far poorly understood. Here, we assess local adaptation to current climate in European aspen (Populus tremula) by using environmental association analyses to identify genetic variants associated with two representative climate variables describing current day variation in temperature and precipitation. We also analysed patterns of genetic differentiation between southern and northern populations and observe that regions of high genetic differentiation are enriched for SNPs that are significantly associated with climate. Using variants associated with climate, we examined patterns of isolation by distance and environment and used spatial modelling to predict the geographic distribution of genomic variation in response to two scenarios of future climate change. We show that climate conditions at a northern reference site will correspond to climate conditions experienced by current day populations located 4–8 latitude degrees further south. By assessing the relationship between phenotypic traits and vegetative fitness, we also demonstrate that southern populations harbour genetic variation that likely would be adaptive further north under both climate change scenarios. Current day populations at the lagging edge of the distribution in Sweden can therefore serve as sources for introducing adaptive alleles onto northern populations, but the likelihood of this largely depends on naturally occurring levels of gene flow.

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Additional file 3.

Additional file 1.

Additional file1: Table S1: Schematic of crosses and numbers of individuals produced by a cross between the parent individuals. Mothers are on the left (yellow) and fathers on top (blue). The parents in bold and all offspring are present in the Krusenberg field trial. Table S2: Monthly mean temperature and rainfall information for years 2017 and 2018. Table S3: Drawings, pictures and descriptions of the 6 stages of bud burst. The table is reproduced as given to the field scorers with drawing of stage 3 and pictures of stages 5 and 6 missing. Drawings reproduced on permission of the owner Alfas Pliura of Lithuanian Research Centre for Agriculture and Forestry. Table S4: Autumn coloration scoring scheme for 2017-2018. Original 2017 and 2018 describe the original scoring systems used in the corresponding years. converted 2017 shows, which stages the original 2017 scores correspond in the 2018 scoring system. Table S5: Phytotron simulated seasons temperature, light conditions and humidity information. The simulated winter shaded in gray. During late July and early August of 2018, a breakdown of the climate chambers occurred causing the simulated winter (marked with *) to be interrupted by high temperatures before resumption of simulated winter temperatures. Table S6: Sequencing breadth and depth coverage of the 121 sequenced individuals. Values have been rounded to three decimals. Genotyped parent and non-parent non-offspring individuals shaded with gray. Table S7: Heritabilites of chosen traits. Broad sense heritability is calculated using the Cullis method. * evident overfitting. Table S8: GO -term enrichment analysis results. Table S9: Hypergeometric test results. Results are rounded to 3 decimals. Table S10: All candidate genes identified within 10 kbp of significant slopes. Table S11: Shared candidate genes between our results and Evans et al. (2014) and McKown et al. (2014). Figure S1: Pearson’s correlation between BLUP and mean values of A) bud burst initation in year 2017 (BB2-17), B) autumn coloring initiation in year 2018 (CO3-18), C) bud set completion (BS7) and D) diameter at breast height (DBH-17). * p < 2.2-16. Figure S2: Spearman’s correlation matrix and heatmap of all our chosen 23 traits. Figure S3: Logarithmic p-value Manhattan plot. Figure S4: Logarithmic p-value QQ-plot. Figure S5: Level of LD as function of distance. Figure S6: Venn diagram of candidate genes for both year for A) bud burst initiation (BB2), B) bud burs completion (BB4) C) autumn coloring initiation (CO3), D) autumn coloring completion (CO8) E) leaf shed initiation (LS2) and F) leaf shed completion (LS5).

Entering and exiting winter dormancy presents important trade-offs between growth and survival at northern latitudes and many forest trees display local adaptation across latitude. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth. We performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment. We uncovered 629 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. A comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis that autumn phenology transitions. &nbsp

Supporting methods, figures, tables, and references

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

Norway spruce (Picea abies) is an important boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics controlling important wood quality traits in Norway spruce. We performed a functional genome-wide association mapping of 17 wood quality traits in Norway spruce using 178101 single-nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood quality traits were defined using functional modelling of wood properties across annual growth rings. Association mapping was performed using a multilocus LASSO penalized regression method and we detected a total of 51 significant SNPs from 39 candidate genes that are involved in wood formation. Our study represents the first functional multi-locus genome-wide association mapping (AM) in Norway spruce. The results advance our understanding of the genetics influencing wood traits, identify novel candidate genes for further functional studies and support current Norway spruce breeding efforts.

Correspondance: Molecular Ecology Resources Primer Development Consortium, E-mail: editorial.office@molecolres.com; International audience; This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides

Understanding the genetics of lifetime fitness is crucial to understand a species’ ecological preferences and ultimately predict its ability to cope with novel environmental conditions. Yet, there is a dearth of information regarding the impact of the ecological variance experienced by natural populations on expressed phenotypic and fitness differences. Here, we follow the natural dynamics of experimental A. thaliana populations over 5 successive plantings whose timing was determined by the natural progression of the plant’s life cycle and disentangle the environmental and genetic factors that drive plant ecological performance at a given locality. We show that, at the intermediate latitude where the experiment was conducted, a given genotype can experience different life cycles across successive seasons. Lifetime fitness across these seasons varied strongly, with a fall planting yielding 36-fold higher fitness compared to a spring planting. In addition, the actual life-stage at which plant overwinter oscillated across years, depending on the timing of the end of the summer season. We observed a rare but severe fitness differential after inadequate early flowering in one of the five planting. Substrate variation played a comparatively minor role, but also contributed to modulate the magnitude of fitness differentials between genotypes. Finally, reciprocal introgressions on chromosome 4 demonstrated that the fitness effect of a specific chromosomal region is strongly contingent on micro-geographic and seasonal fluctuations. Our study contributes to emphasize the extent to which the fitness impact of phenotypic traits and the genes that encode them in the genome can fluctuate. Experiments aiming at dissecting the molecular basis of local adaptation must apprehend the complexity introduced by temporal fluctuations because they massively affect the expression of phenotype and fitness differences.

Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P