IntroductionClimate change is exerting profound impacts on ecosystems worldwide. In Quebec, Canada, mean annual temperatures are projected to rise by 2°C over the coming decades. In addition, the frequency and intensity of climate extremes are expected to increase, posing significant risks to forest ecosystems and affecting the performance and survival of tree species.MethodsTo assess the potential impacts of climate change on the local adaptation of white spruce, six geographically distant seed sources were evaluated seven years after planting at two test sites with contrasting growing conditions and latitude in Quebec, eastern Canada. Fall phenology was monitored from mid-July to mid-August 2021. For frost tolerance assessment, representative samples were collected in early September. Additionally, two sampling dates at the end of the growing season were used to characterize the dynamics of non-structural carbohydrates (NSC).Results and DiscussionBud set phenology, autumn frost tolerance, and late-season NSC concentrations (fructose, glucose, sucrose, and pinitol) were significantly influenced by test site, seed source, and their interactions. The average bud set initiation occurred one week later at the southern site compared to the northern site, whereas the final stage of bud set was similar between sites. Significant differences among seed sources were observed for certain phenological stages. By early October, all seed sources growing at the southern site showed reduced frost tolerance compared to those at the northern site, with visible needle tissue damage occurring at temperatures below –12°C, highlighting the increased risk of early autumn frost damage at the southern site. Fructose and glucose exhibited contrasting site-specific temporal trends, increasing from September to October at the southern site while decreasing at the northern site. In contrast, sucrose showed the opposite pattern, with the southwestern seed source exhibiting the lowest content, emphasizing the contrasting roles of NSC in sustaining late-season growth under warmer conditions and in regulating dormancy induction and cold hardiness under colder conditions. Overall, our study highlights the crucial role of NSC dynamics in cold tolerance and local adaptation to early autumn frost events. The implications of these findings for assisted migration strategies are discussed.

Abstract Black spruce ( Picea mariana [Mill.] B.S.P.) is an emblematic and ubiquitous species of the North America’s boreal forest. While conifer breeding programs have traditionally focused on growth and wood property traits, the study of climate adaptation traits is becoming increasingly prevalent, given the predicted impact of climate change on North America’s boreal zone. Through this study, we aimed to identify genes associated with climate adaptation in black spruce across Canada. A total of 254 black spruce trees from 30 populations, covering most of the species’ distribution range, were sampled and genotyped for SNPs located in ∼5000 gene loci. Uni- and multivariate Genotype-Environment Association (GEA) approaches, namely LFMM and RDA, as well as an outlier method based on population differentiation ( F ST ) were used to identify genes significantly associated with climatic factors. As such, a total of 77 genes carrying significant candidate SNPs were identified, among which 14 candidates were corroborated by at least two methods. Many of these gene SNPs were also confirmed at a smaller geographic scale, across west - east partitions corresponding to the two main black spruce historical lineages. Notably, significant gene SNPs were more frequently associated to moisture/aridity factors in the western part of the range, and more to temperature factors in the eastern part. The genes carrying these SNPs were also frequently associated to abiotic and biotic stress response. In the context of rapid climate change in the Canadian boreal forest, the results obtained within the framework of this study should support implementing gene conservation efforts while assisting prediction in black spruce breeding programs, which are instrumental to producing adapted planting stock for the large-scale reforestation efforts conducted annually across the Canadian boreal forest.

Genomic selection (GS) is being increasingly used in tree breeding with the aim to accelerate genetic gains by shortening the long breeding cycles. However, high genotyping costs remain a challenge. This study aimed to determine the optimal marker density in genome coverage to maximize GS accuracy and precision of heritability estimates for growth and wood quality traits. Thousands of SNPs representative of the exome of three major spruce species were used: 18,275 SNPs for black spruce (representing 10,894 distinct gene loci), 11,328 SNPs for white spruce (8647 gene loci), and 116,765 SNPs for Norway spruce (20,695 gene loci). For each species, a similar experimental design was used with related full-sib families replicated on two sites, and GBLUP prediction models were developed. The effect of varying the number of SNPs was examined by resampling subsets from 500 to 100,000 SNPs. Results indicated that plateaus in heritability estimates were reached as the marker density increased, stabilizing between 4000 and 8000 SNPs for a spruce genome size of around 2000 centimorgans, a trend consistent across all traits and species. Predictive ability and prediction accuracy both increased with the number of SNPs up to a similar level, beyond which further improvements were marginal. Such minimum marker densities should be financially affordable for most spruce breeding programs, striking a balance between the need for maximizing GS accuracy and that for minimizing genotyping costs. These findings should support the further deployment of GS in conifer breeding programs, with high selection precision and by reducing the financial burden of very high-density SNP coverage, even for conifers characterized by large giga-genomes.

Assisted population migration (APM) has been proposed as a proactive strategy to mitigate the impacts of climate change on the growth performance of northern forest tree populations. However, seed transfer models used to guide seed deployment lack empirical evidence of age independence of seed source growth and survival, and it is not clear whether sources selected for growth will also have acceptable survival. To address these concerns, we used the 410-series white spruce provenance trials in Ontario, Canada, to assess the effect of tree age on seed transfer models and climate transfer distances. Seed transfer models were developed for tree height, survival, and stand basal area (BA) using climate variables including total annual precipitation, mean minimum temperature of the coldest period, and mean minimum temperature of May. Additionally, we examined the genetic and environmental effects of climate on provenance performance. Our results show that the seed transfer model for tree height was stable with tree age, but tree survival and BA were age dependent. Environmental effects explained about twice the variation in growth compared to genetic effects. Height-based critical seed transfer distance was age independent and 28% larger compared to BA-based distance, which was age dependent. Climate change projections suggest that white spruce growth will be enhanced by future warming in the colder, northwestern region of Ontario, but will decline in the warmer, southern part of the province. Our results highlight the importance of APM for seed deployment to maintain or enhance white spruce productivity and resilience under climate warming.

Local adaptation can lead to the intraspecific variation in a species' genetic makeup, shaping both its physiological and morphological traits as well as its molecular responses. In this study, we assessed variation in key functional leaf traits, such as stomata density, carbon and nitrogen content, cuticular wax composition and leaf shapes, within the transcontinental North American Populus tremuloides Michaux (quaking aspen) by sampling individuals from its four major genetic lineages. We also performed a small-scale common garden experiment with imposed higher temperature and drought stress during which we sampled for transcriptomes using RNAseq and performed physiological measurements to obtain insights into the intraspecific responses among aspen lineages to such abiotic stressors. Our findings revealed several differences in functional traits indicative of local adaptation, such as variation in cuticular wax content, petiole lengths and δ13C. Notably, stomatal density was significantly associated with mean annual precipitation. Moreover, genotypes from the most southern lineage (Mexico) exhibited the largest decline in net photosynthesis under drought, suggesting a more conservative water-use strategy. Gene expression analyses revealed numerous differentially expressed genes under different stress conditions and in different lineages, with overlaps with previous gene selection scans, confirming their possible roles in local adaptation. Weighted gene co-expression network analysis further identified 22 co-expressed gene modules, several of which strongly associated with temperature responses and geographic origin of genetic lineage. Our findings highlight substantial intraspecific variation in functional traits and gene expression patterns in P. tremuloides linked to geographical origin and local environmental conditions. Understanding such adaptive variation is crucial for predicting how forest trees may cope with and adapt to the challenges of climate change.

Genomic prediction, also called genomic selection (GS), is being increasingly used in tree breeding with aim to accelerate genetic gains by shortening the long breeding cycles. However, high genotyping costs remain a challenge. This study aimed to determine the optimal marker density in genome coverage, to maximize GS accuracy and precision of heritability estimates for growth and wood quality traits. Thousands of SNPs representative of the exome of three major spruce species were used: 18,275 SNPs for black spruce (representing 10,894 distinct gene loci), 11,328 SNPs for white spruce (8647 gene loci), and 116,765 SNPs for Norway spruce (20,695 gene loci). For each species, a similar experimental design was used with related full-sib families replicated on two sites, and GBLUP prediction models were developed. The effect of varying the number of SNPs was examined by re-sampling subsets from 500 to 100,000 SNPs. Results indicated that plateaus in heritability estimates were reached as the marker density increased, stabilizing between 4000 to 8000 SNPs for a spruce genome size of around 2000 centimogans, a trend consistent across all traits and species. Predictive ability and prediction accuracy both increased with the number of SNPs up to a similar level, beyond which further improvements were marginal. Such optimal marker density should be financially attainable for most spruce breeding programs, striking a balance between the need for maximizing accuracy and that for minimizing genotyping costs. These findings should support the further deployment of GS in conifer breeding programs, with high selection precision and by reducing the financial burden of very high-density SNP coverage, even for conifers characterized by large giga-genomes. ### Competing Interest Statement The authors have declared no competing interest. In order to comply with Intellectual Property Policies (IPP) of participating governmental and private organizations in this work, the supporting phenotyping and genotyping data is not deposited into the public domain. However, data will be shared upon motivated request to the corresponding author after consulting with participating governmental and private organizations involved in this work. This research was supported by multiple funding agencies across Canada and Sweden. The Ministère des Ressources naturelles et des forêts of Québec supported the maintenance of black spruce and white spruce field tests and sampling, while the Canadian Forest Service and the Natural Resources Canada Genomics R&D Initiative contributed resources to data management, computational resources, and analytical support. SNP genotyping for black spruce and white spruce were funded by Genome Canada and Genome Quebec through grants supporting the FastTRAC II genomic project led by J. Bousquet and P. Lenz, and additional support was received through the Canada Research Chair in Forest Genomics (Univ. Laval). For the Norway spruce component of the study, financial support was provided to H.X. Wu by the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas; grant 230-2014-427) and the Swedish Foundation for Strategic Research (SSF; grant RBP14-0040). The Swedish nor the Canadian funders had any role in study design, data collection, analysis, or publication strategy.

Climate change brings new constraints to which trees will have to adapt, including more frequent severe weather events due to climate anomalies. Black spruce and red spruce are phylogenetically close but adapted to different ecological conditions, and they form a natural hybrid zone where their natural distributions come into contact. Thus, they represent an interesting model to study the effect of introgressive hybridization in the context of climate change, given that interspecific gene flow could eventually affect their capacity to adapt where their natural distributions overlap. Using a common garden field test gathering 20-year-old progeny trees resulting from rigorous controlled crosses including previously verified genetic identity of the parents, growth patterns and wood density differences could be observed between species and between them and their F1 hybrids. A dendroecological analytical approach relying on wood cores was used and revealed similar wood responses to climatic variations between species, both through lifespan climate sensitivity and through episodic stress response indexes. They were however differentially expressed in early- and latewood between black spruce and red spruce, differences likely driven by diverging cambial phenology adaptations to different growing season lengths. F1 hybrids exhibited hybrid vigor for lifespan cumulative growth under the test site conditions but showed intermediate values for traits related to climate response. These results may assist the management of forest genetic resources and contribute to a better understanding of the dynamics of adaptation to climate in hybrid zones.

Introgressive hybridization plays a major role in shaping the evolutionary dynamics and adaptive potential of forest trees. In this study, we developed and validated an exome-wide bispecific SNP genotyping array (Pmr25k) for the closely related species black spruce ( Picea mariana ) and red spruce ( Picea rubens ), two ecologically and economically important North American conifers that form a widespread hybrid zone in eastern Canada. Exome capture and sequencing of pooled red spruce samples yielded over 25,000 high-quality SNPs, which were used in conjunction with a previously developed black spruce gene SNP resource of over 97,000 high-quality SNPs, to construct the bispecific genotyping array. The final array comprised 21,573 successfully manufactured SNPs, representing 14,200 distinct gene loci, of which 85% were segregating when both species were considered together. More than 4000 segregating SNPs could also be successfully used and genotyped in each of white spruce ( Picea glauca ) and Norway spruce ( Picea abies ), highlighting the conserved nature of DNA attachment sites and presence of homologous SNPs for many gene loci. The Pmr25k array thus provides an efficient and reliable high-throughput genotyping tool to investigate introgression, genetic adaptation at the gene level, and to assist genomic-based prediction for breeding and conservation efforts in boreal spruces. ### Competing Interest Statement The authors have declared no competing interest.

Adaptive convergence can arise when response to natural selection involves shared molecular or functional mechanisms among multiple taxa. Conifers are archaic species of ancient origin with delayed sexual maturity related to their woody perennial nature. Thus, they represent a relevant plant group to assess if convergence from selection may have become disconnected between molecular and functional levels. In this purpose, transcriptome-wide SNP diversity was assessed in seven partially sympatric and reproductively isolated conifer species (118 individuals from 67 populations) populating the temperate and boreal forests of northeastern North America. SNP diversity was found highly heterogeneous among species, which would relate to variation in species-specific demography and history. Rapidly evolving genes with signatures of positive selection were identified, and their relative abundance among species reflected differences in transcriptome-wide SNP diversity. The analysis of sequence homology also revealed very limited convergence among taxa in spite of sampling same tissues at same age. However, convergence increased gradually at the levels of gene families and biological processes, which were largely related to stress response and regulatory mechanisms in all species. Given their multiple small to large gene families and long time since inception, conifers may have had sufficient gene network flexibility and gene functional redundancy for evolving alternative adaptive genes for similar metabolic responses to environmental selection pressures. Despite a long divergence time of ~350 Mya between conifers and Angiosperms, we also uncovered a set of 17 key genes presumably under positive selection in both lineages.

Past population dynamics during the Pleistocene ice age and the Holocene era have profoundly influenced the genetic structure and diversity of species. Environmental heterogeneity has further shaped local and regional adaptive variation. Here, we ask how historical processes have led to the current genetic diversity of a key North American species across its vast natural range and what genomic signatures indicate regional adaptive divergence and local adaptation. We used sequencing data from 1903 Populus tremuloides Michx. (quaking aspen) trees to assess historical population dynamics and identify genotype -environment associations within and among the species' major genetic lineages. The two northern and western North American aspen lineages exhibited historical population expansion patterns, while the southernmost lineage experienced a historical bottleneck consistent with past glacial oscillations. We found that the earliest split between genetic lineages of P. tremuloides occurred in the southern part of its distribution range. We further identified larger blocks of adaptive SNPs within separate genomic sequence regions on chromosomes 2 and 8 that may exhibit suppressed genetic recombination, contributing to the maintenance of regional and local adaptation in the species. Our study provides key insights into the evolutionary processes affecting adaptive genetic variation and phylogeography at a broad continental and regional scale, with implications for predicting species' responses to future climate change.

To assess the potential impacts of climate change on white spruce local adaptation, six seed sources were evaluated seven years after plantation on two test sites with contrasting growing conditions and latitude in Quebec. Bud set, frost tolerance, and analysis of non-structural carbohydrates (NSC) content showed important effects of test sites, seed sources, and their interactions on bud set phenology and growth. The average bud set initiation occurred one week later in the southern site compared to the northern site, whereas the late stage of bud set was similar between sites. Significant differences were observed between seed sources for some phenological stages. Frost tolerance was significantly lower in the southern site and below -12 C for all seed sources sampled at the beginning of October. The trend in fructose and glucose content was opposite between sites in September. It decreased from September to October in the southern site and increased in the northern site, while sucrose content showed an opposite pattern, with the southwestern seed source harboring the lowest sucrose content. NSC content was also correlated to frost tolerance. Our study highlighted the crucial role of NSC in cold hardiness to early fall frosts and local adaptation. Implications for assisted migration are discussed. ### Competing Interest Statement The authors have declared no competing interest. Natural Sciences and Engineering Research Council of Canada (NSERC) Allaince, ALLRP 560992-20

Understanding how trees adjust their wood structure to increasing climate variability is critical for predicting forest resilience. In this study, we examined intra-annual density fluctuations (IADFs) in the boreal black spruce as indicators of plastic and genetic responses to water stress. IADFs are abrupt deviations in the density of wood formed within a growth ring and reflect temporary disruptions in cambial activity. We assessed their occurrence in 24-year-old trees from controlled-cross families planted in two climatically distinct common gardens in eastern Québec. Using an automated method, we quantified both the frequency and the structural characteristics of IADFs, including their width, height, and area. Our results show that earlywood IADF frequency was strongly correlated with local climate indices related to water deficit, indicating that IADFs are sensitive biomarkers of both current-year and lagged drought conditions. IADF frequency was positively associated with radial growth but negatively with earlywood and total wood density, suggesting a physiological trade-off between maintaining growth under water stress and investing in wood structural properties. Moreover, moderate levels of genetic control indicated that these traits are partially heritable. By integrating IADFs, climatic, and genetic data, our approach provides new insights into how a major boreal tree species modulate wood structure in response to environmental stress. It thus represents a promising framework for studying drought-response and support the selection of more climate-resilient trees.

Increasing the productivity of planted forests may efficiently provide an important part of the world’s growing demand for wood while protecting natural forests. In this study, we developed an integrated modelling framework to evaluate the financial impacts of improving productivity of planted forests by tree breeding. Using this framework, we compared three genetic improvement scenarios of white spruce plantations, a key reforestation species in North America, and evaluated the differences in the derived wood product assortments in terms of quantity, quality, and revenues. Favouring the production of wood volume appears as the best way to enhance financial gains from white spruce plantations in the current market. The scenario that focused on increasing tree height produced a greater volume of wood products and larger lumber pieces, which resulted in the greatest revenues. In comparison, favouring wood stiffness over volume led to poorer results, as the increased product quality was not sufficient to surpass the financial gain associated with greater wood volumes. While we successfully provided an evaluation of the product assortments derived from genetically improved plantations, the proposed framework would benefit from more data input to help maximize financial gains from a range of tree breeding strategies.

Forests face an escalating threat from the increasing frequency of extreme drought events driven by climate change. To address this challenge, it is crucial to understand how widely distributed species of economic or ecological importance may respond to drought stress. In this study, we examined the transcriptome of white spruce (Picea glauca (Moench) Voss) to identify key genes and metabolic pathways involved in the species’ response to water stress. We assembled a de novo transcriptome, performed differential gene expression analyses at four time points over 22 days during a controlled drought stress experiment involving 2-year-old plants and three genetically distinct clones, and conducted gene enrichment analyses. The transcriptome assembly and gene expression analysis identified a total of 33,287 transcripts corresponding to 18,934 annotated unique genes, including 4,425 genes that are uniquely responsive to drought. Many transcripts that had predicted functions associated with photosynthesis, cell wall organization, and water transport were down-regulated under drought conditions, while transcripts linked to abscisic acid response and defense response were up-regulated. Our study highlights a previously uncharacterized effect of drought stress on lipid metabolism genes in conifers and significant changes in the expression of several transcription factors, suggesting a regulatory response potentially linked to drought response or acclimation. Our research represents a fundamental step in unraveling the molecular mechanisms underlying short-term drought responses in white spruce seedlings. In addition, it provides a valuable source of new genetic data that could contribute to genetic selection strategies aimed at enhancing the drought resistance and resilience of white spruce to changing climates.

Severe drought increasingly threatens the resilience, productivity, and distribution of forest biomes worldwide. Understanding the evolution of tree drought resilience over the past century, along with its geographical and taxonomic relationships, is essential for predicting future forest dynamics. Using a tree-ring database from Canadian forests, encompassing 40,147 trees across 4558 plots and 23 species, we analyzed temporal and spatial patterns of drought resilience. We examined how leaf habit, prior drought exposure, and site- and tree-level factors influence growth resistance (immediate drought response), growth recovery (post-drought growth resumption), and overall resilience. Our findings indicate that most major Canadian tree species exhibit low and declining drought resilience. Mean temperature, moisture availability, and elevation emerged as critical factors in shaping tree responses to drought. At high elevation, drought impacts were buffered by cool temperatures, enabling trees to maintain stable growth rates. Deciduous species showed a significant decline in recovery and resilience throughout the 20th century, whereas evergreen species displayed stable but low resilience and recovery. Summer droughts particularly reduced resistance and recovery in deciduous species compared to evergreens. However, prior drought exposure mitigated negative drought responses over a tree's lifetime, suggesting an adaptive capacity in both evergreen and deciduous species. Older forests unaccustomed to severe droughts appear especially vulnerable, potentially leading to shifts in ecosystem composition and reduced biodiversity. The declining resilience of deciduous species, combined with the low resilience of evergreens, suggests major changes for Canadian forests, including reduced productivity and altered species composition. Our results emphasize the importance of proactive forest management strategies to preserve forest productivity and biodiversity in the context of a changing climate.

Nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes form a major line of defense in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis), but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity, and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae, and other gymnosperms were scanned for NLR genes using existing and customized pipelines. The discovered genes were mapped across chromosomes and linkage groups and analyzed phylogenetically for evolutionary history. Conifer genomes are characterized by dense clusters of NLR genes, highly localized on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and nonconiferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plant's resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding.

Understanding how trees prioritize carbon gain at the cost of drought vulnerability under severe drought conditions is crucial for predicting which genetic groups and individuals will be resilient to future climate conditions. In this study, we investigated variations in growth, tree-ring anatomy as well as carbon and oxygen isotope ratios to assess the sensitivity and the xylem formation process in response to an episode of severe drought in 29 mature white spruce (Picea glauca [Moench] Voss) families grown in a common garden trial. During the drought episode, the majority of families displayed decreased growth and exhibited either sustained or increased intrinsic water-use efficiency (iWUE), which was largely influenced by reduced stomatal conductance as revealed by the dual carbon‑oxygen isotope approach. Different water-use strategies were detected within white spruce populations in response to drought conditions. Our results revealed intraspecific variation in the prevailing physiological mechanisms underlying drought response within and among populations of Picea glauca. The presence of different genetic groups reflecting diverse water-use strategies within this largely-distributed conifer is likely to lessen the negative effects of drought and decrease the overall forest ecosystems' sensitivity to it.

Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5 / Ugt5b and β glu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce ( Picea glauca ) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of β glu-1 -like, Ugt5 -like genes and single-copy genes on 38 Norway spruce ( Picea abies ) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of β glu-1 and Ugt5 genes. We observed very large copy numbers of β glu-1 , with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of β glu-1 in P. glauca but not P. abies . Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.

Genomic selection (GS) is increasingly used in tree breeding because of the possibility to hasten breeding cycles, increase selection intensity or facilitate multi-trait selection, and to obtain less biased estimates of quantitative genetic parameters such as heritability. However, tree breeders are aiming to obtain accurate estimates of such parameters and breeding values while optimizing sampling and genotyping costs. We conducted a metadata analysis of results from 28 GS studies totalling 115 study-traits. We found that heritability estimates obtained using DNA marker-based information for a variety of traits and species were not significantly related to variation in the total number of markers ranging from about 1500 to 116 000, nor by the marker density, ranging from about 1 to 60 markers/centimorgan, nor by the status number of the breeding populations ranging from about 10 to 620, nor by the size of the training set ranging from 236 to 2458. However, the predictive accuracy of breeding values was generally higher when the status number of the breeding population was smaller, which was expected given the higher level of relatedness in small breeding populations, and the increased ability of a given number of markers to trace the long-range linkage disequilibrium in such conditions. According to expectations, the predictive accuracy also increased with the size of the training set used to build marker-based models. Genotyping arrays with a few to many thousand markers exist for several tree species and with the actual costs, GS could thus be efficiently implemented in many more tree breeding programs, delivering less biased genetic parameters and more accurate estimates of breeding values.

In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-seq and genotyping array SNP data for 528 individuals from 2 full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and Picea glauca based on 27,052 markers and 11,609 gene sequences. Altogether, these 2 linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed, herein, open new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.