American white oak (Quercus alba L.) is a keystone hardwood species with substantial ecological, economic, and cultural value across eastern North American forests. However, its long generation time, delayed reproductive maturity, recalcitrant acorns, regeneration limitations, and complex genotype-by-environment interactions have slowed genetic improvement and climate-resilient deployment. This review synthesizes current knowledge on Q. alba genetics, genomics, quantitative breeding, and conservation, integrating direct evidence from Q. alba with comparative insights from other white oaks (Quercus sect. Quercus) and broader tree improvement systems. Available evidence indicates that white oaks maintain substantial standing genetic variation and geographically structured adaptive diversity, while growth, phenology, and related traits often show moderate genetic control. Nevertheless, polygenic trait architectures, environmental heterogeneity, rapid linkage disequilibrium decay, and limited species-specific validation constrain the direct operational use of genomic signals for selection and seed deployment. We propose an implementation-focused framework that combines range-wide germplasm sampling, multi-environment provenance and progeny trials, spatially adjusted mixed models, genomic prediction, genotype-environment association analyses, and climate-informed seed transfer strategies. Emerging resources, including haplotype-resolved genomes, structural-variant analysis, pangenomics, metabolomics, microbiome-informed phenotyping, and genome editing, may further support white oak improvement but require rigorous validation in Q. alba populations and field trials. We argue that genomic and biotechnological tools should complement, rather than replace, conventional quantitative breeding and long-term field evaluation. A coordinated breeding and restoration strategy that balances genetic gain, adaptive diversity, and climate resilience will be essential for sustaining the productivity, ecological function, and long-term persistence of Q. alba forests under future environmental change.

Longleaf pine (Pinus palustris; figs. 1 through 5) is an iconic tree species native to the southeastern United States. Before the arrival of non-Indigenous settlers, longleaf pine occurred as the dominant tree species across an estimated 29.9 million ha (73.9 million acres) of fire-maintained forests, woodlands, and savannas, and another 7.3 million ha (18 million acres) as a codominant in mixtures with other fire-adapted tree species (Frost, 1993). Over the next three centuries, a combination of anthropogenic factors decimated longleaf pine and its associated ecosystem (Frost, 2006). Longleaf pine was initially harvested by settlers to clear land for agriculture and provide material for housing and fencing. In the early to mid-19th century, vast areas of longleaf pine were killed in turpentine orchards to supply the naval stores industry. Near the turn of the 20th century, steam-powered technology drove decades of extensive logging throughout much of the remaining longleaf pine woodlands. Recovery from exploitation was hindered by regeneration failures deriving from local seed source limitations, seedling depredation from introduced hogs, fire exclusion, and land use conversion. Longleaf pine continued to decline gradually until the 1990s, when existing extent reached its nadir of approximately 1.2 million ha (3 million acres) (Outcalt and Sheffield, 1996). Subsequently, concerns over the loss of habitat for several endemic flora and fauna prompted extensive investment and research into restoring the longleaf pine ecosystem (Landers et al., 1995). Contemporary restoration efforts have succeeded in stemming the loss of longleaf pine extent and have even produced a modest recovery. However, at the current estimated extent of 1.8 million ha (4.4 million acres), restoration remains a work in progress (Oswalt and Guldin, 2021). Longleaf pine is preferentially grown for its ecological, economic, and social values. Ecologically, longleaf pine is considered a foundational species in southeastern woodlands for its role in promoting understory flammability (Varner et al., 2021a). Longleaf pine is also well adapted to resist disturbances such as drought and wind, which are common throughout the region (Rutledge et al., 2021; Samuelson et al., 2019). From an economic perspective, longleaf pine is often commercially grown for sawtimber or utility poles, while its straw is highly sought as groundcover in the landscaping industry (Dickens et al., 2012; South, 2006). Beyond its ecological and economic importance, longleaf pine is viewed by many throughout the region as a cultural symbol connecting humans to their local environment (Gordon et al., 2020).

Fusiform rust, caused by Cronartium quercuum f. sp. fusiforme (Cqf), is the most severe disease of planted southern pines in the south-eastern United States. Despite the critical role pathogen genomics play in disease outcomes, the population structure and genetic variability of Cqf remain poorly characterised. To address this gap, we generated a high-quality chromosome-scale genome assembly of Cqf and leveraged this resource to perform the population genomic analyses of 274 haploid pycniospore samples derived from controlled inoculations with geographically diverse aeciospore collections. The assembled Cqf genome (87.03 Mbp across 19 contigs) displayed high completeness (BUSCO: 91.1%) and structural continuity (Scaffold N50: 5.4 Mbp), establishing a robust reference for population-genetic analysis. PCA, DAPC and ADMIXTURE revealed a pronounced east-west structure indicating five genetically distinct metapopulations (Western Gulf, Upper Central Gulf, Lower Central Gulf, Lower Atlantic Coast/Eastern Piedmont, Mid-Atlantic Coast). AMOVA revealed that high levels of variation exist in Cqf, with the greatest proportion of genetic variation occurring in local populations (85.5%) with moderate differentiation among regional metapopulations (Phi = 0.117). Sliding-window F ST analyses highlighted the genomic regions of elevated differentiation, including loci encoding candidate secreted effector proteins. Genetic diversity metrics revealed evidence of non-random mating in some regions. These results refine the understanding of Cqf population structure, confirm the relevance of USDA Resistance Screening Center geographic zones and provide novel genomic resources to support breeding for durable fusiform rust resistance in southern pines.

Understanding the adaptation to extreme weather events in long-lived conifers while maintaining a competitive growth rate has become increasingly critical for tree improvement focused on successful reforestation and ecosystem restoration. We investigated the genetic parameters of shortleaf pine ( Pinus echinata Mill), a wide-ranging but declining conifer of the southern USA, by analyzing survival, height and diameter growth, stem taper, and ice storm damage using progeny trial data collected through typical economic rotation ages (30 to 40 years). We evaluated 15 progeny trials representing 330 full-sib families formed by a series of disconnected half-diallel crosses among 150 parents originating from three seed-source regions (East Ouachita, West Ouachita, and Ozark) within two environmental zones (Ouachita Mountains and Ozark Plateau) and tested in each zone. Both individual tree- and family-based statistical models provided robust genetic parameter estimates. Narrow-sense heritability of tree height increment from age-5 years to the rotation-age measurement reached 0.38 across the trials that were not impacted by a particularly severe, mid-rotation ice storm. Only negligible dominance genetic and genotype-by-environment variance for growth traits were observed in these trials. Low to moderate genetic control (narrow-sense heritability of 0.1–0.4) suggests that appreciable genetic gain of stem volume (function of tree height and stem diameter) and stem taper are achievable. Genetic correlations were generally favorable among traits, although when not, “correlation breaker” parents could be identified and selected to obtain gain in both volume and tolerance (i.e., resiliency) to ice damage. Despite variations in the impact of the severe ice storm across the trials, our results revealed significant and biologically important levels of genetic control for all traits. Trials that were most severely affected by the severe ice storm presented a unique opportunity for selecting individuals with increased tolerance to ice damage. No discernable trade-off between growth and tolerance to ice damage was found, as faster growing genotypes tended to recover from ice storm damage quickly, thereby maintaining their growth and size advantage in the stands. Overall, our results underscore the potential of tree improvement for enhancing the genetic potential of shortleaf pine and contributing to the success of ongoing reforestation and ecosystem restoration efforts across the southern USA.

More than a century after two introduced pathogens killed billions of American chestnut trees, introgression of resistance alleles from Chinese chestnuts has contributed to the recovery of self-sustaining populations. However, progress has been slow because of the complex genetic architecture of resistance. To better understand blight resistance, we compared reference genomes, gene expression responses, and stem metabolite profiles of the resistant Chinese and susceptible American chestnut species. To accelerate resistance breeding, we conducted large-scale phenotyping and genotyping in hybrids of these species. Simulation and inoculation experiments suggest that significant resistance gains are possible through selectively breeding trees with an average of 70 to 85% American chestnut ancestry. The resources developed in this work are foundational for breeding to create diverse restoration populations with sufficient disease resistance and competitive growth.

White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data. Despite strongly conserved chromosome synteny and genome size across Quercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species - as are the chromosomal locations of R gene clusters - but, gene number within clusters is more labile. We found that Q. alba has high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus. The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution in Quercus.

Changing climate is impacting the health and sustainability of forests throughout the world. It is important for forest resource managers to have abundant and accurate information about the standing, changing, and adaptive genetic diversity of forest tree populations to successfully manage and restore species impacted by climate change, invasive species, and forest fragmentation. This can only be accomplished if genetic resources are widely available for impacted species. For a small number of commercially important conifer species in North America, such resources have been reasonably well developed. However, for nearly all other conifer species, critical genetic resources are limited or completely absent. The International Union for the Conservation of Nature (IUCN) Red List classification of Near Threatened or worse (Vulnerable, Endangered, Critically Endangered) includes many conifer species in North America. We have compiled an inventory of genetic resources available to researchers for these and other at-risk conifer species. With a few important exceptions, such resources barely exist for nearly all of them. We discuss the importance of genetics for managing and restoring forests under climate change and provide a call to action for researchers and managers to develop and implement a coordinated protocol for conserving and restoring the most at-risk conifers.

### Competing Interest Statement The authors have declared no competing interest.

Chestnut blight (caused by Cryphonectria parasitica), together with Phytophthora root rot (caused by Phytophthora cinnamomi), has nearly extirpated American chestnut (Castanea dentata) from its native range. In contrast to the susceptibility of American chestnut, many Chinese chestnut (C. mollissima) genotypes are resistant to blight. In this research, we performed a series of genome-wide association studies for blight resistance originating from three unrelated Chinese chestnut trees (Mahogany, Nanking and M16) and a Quantitative Trait Locus (QTL) study on a Mahogany-derived inter-species F2 family. We evaluated trees for resistance to blight after artificial inoculation with two fungal strains and scored nine morpho-phenological traits that are the hallmarks of species differentiation between American and Chinese chestnuts. Results support a moderately complex genetic architecture for blight resistance, as 31 QTLs were found on 12 chromosomes across all studies. Additionally, although most morpho-phenological trait QTLs overlap or are adjacent to blight resistance QTLs, they tend to aggregate in a few genomic regions. Finally, comparison between QTL intervals for blight resistance and those previously published for Phytophthora root rot resistance, revealed five common disease resistance regions on chromosomes 1, 5, and 11. Our results suggest that it will be difficult, but still possible to eliminate Chinese chestnut alleles for the morpho-phenological traits while achieving relatively high blight resistance in a backcross hybrid tree. We see potential for a breeding scheme that utilizes marker-assisted selection early for relatively large effect QTLs followed by genome selection in later generations for smaller effect genomic regions.

Quercus alba L., also known as white oak, eastern white oak, or American white oak, is a quintessential North American species within the white oak section (Quercus) of the genus Quercus, subgenus Quercus. This species plays a vital role as a keystone species in eastern North American forests and plays a significant role in local and regional economies. As a long-lived woody perennial covering an extensive natural range, Q. alba’s biology is shaped by a myriad of adaptations accumulated throughout its natural history. Populations of Q. alba are crucial repositories of genetic, genomic, and evolutionary insights, capturing the essence of successful historical adaptations and ongoing responses to contemporary environmental challenges in the Anthropocene. This intersection offers an exceptional opportunity to integrate genomic knowledge with the discovery of climate-relevant traits, advancing tree improvement, forest ecology, and forest management strategies. This review provides a comprehensive examination of the current understanding of Q. alba’s biology, considering past, present, and future research perspectives. It encompasses aspects such as distribution, phylogeny, population structure, key adaptive traits to cyclical environmental conditions (including water use, reproduction, propagation, and growth), as well as the species’ resilience to biotic and abiotic stressors. Additionally, this review highlights the state-of-the-art research resources available for the Quercus genus, including Q. alba, showcasing developments in genetics, genomics, biotechnology, and phenomics tools. This overview lays the groundwork for exploring and elucidating the principles of longevity in plants, positioning Q. alba as an emerging model tree species, ideally suited for investigating the biology of climate-relevant traits.

Climate change poses a significant threat to the resilience and sustainability of forest ecosystems. This study examines the performance of white oak (Quercus alba, L.) across a range of provenances in a common garden planting, focusing on the species’ response to climatic variables and the potential role of assisted migration in forest management. We evaluated the survival and growth rates of white oak provenances originating from various points along a latitudinal gradient over a period of 40 years. These provenances were planted in a common garden situated near the midpoint of this latitudinal gradient, where we also monitored their phenological traits, such as budburst and leaf senescence. The results revealed substantial variation in phenological responses and growth patterns among the provenances, with southern provenances demonstrating faster growth and later senescence relative to local sources, with limited impact on survival. In contrast, the northern provenances demonstrated slower growth, resulting in later-aged competition-induced mortality. The findings highlight the necessity of incorporating genetic diversity into white oak reforestation and conservation strategies, as the local provenance may no longer be the most suitable option for current and future conditions. We advocate for a nuanced approach to forest management that leverages genetic insights to optimize seed source selection for reforestation, fostering resilient forest landscapes in the face of ongoing climate shifts.

Efforts to understand how pollinating insect diversity is distributed across large geographic areas are rare despite the importance of such work for conserving regional diversity. We sampled bees (Hymenoptera: Apoidea), hover flies (Diptera: Syrphidae), and butterflies (Lepidoptera) on nineteen National Forests across the southeastern U.S. and related their diversity to ecoregion, landscape context, canopy openness, and forest composition. Bee richness was negatively correlated with both the amount of conifer forest and the extent of wetlands in the surrounding landscape but was positively correlated with canopy openness. Hover flies and butterflies were less sensitive to landscape context and stand conditions. Pollinator communities differed considerably among ecoregions, with those of the Central Appalachian and Coastal Plain ecoregions being particularly distinct. Bee richness and abundance peaked two months earlier in Central Appalachia than in the Coastal Plain and Southeastern Mixed Forest ecoregions. Our findings suggest that hardwood forests may play a particularly important role in supporting forest-associated bees in the southeastern U.S. and that efforts to create more open forest conditions may benefit this fauna.

The American chestnut (Castanea dentata, 2n = 2x = 24), once known as the “King of the Appalachian Forest”, was decimated by chestnut blight during the first half of the twentieth century by an invasive fungus (Cryphonectria parasitica). The Chinese chestnut (C. mollissima, 2n = 2x = 24), in contrast to American chestnut, is resistant to this blight. Efforts are being made to transfer this resistance to American chestnut through backcross breeding and genetic engineering. Both chestnut genomes have been genetically mapped and recently sequenced to facilitate gene discovery efforts aimed at assisting molecular breeding and genetic engineering. To complement and extend this genomic work, we analyzed the distribution and organization of their ribosomal DNAs (35S and 5S rDNA), and the chromatin composition of the nucleolus organizing region (NOR)-associated satellites. Using fluorescent in situ hybridization (FISH), we have identified two 35S (one major and one minor) and one 5S rDNA sites. The major 35S rDNA sites are terminal and sub-terminal in American and Chinese chestnuts, respectively, originating at the end of the short arm of the chromosome, extending through the secondary constriction and into the satellites. An additional 5S locus was identified in certain Chinese chestnut accessions, and it was linked distally to the major 35S site. The NOR-associated satellite in Chinese chestnut was found to comprise a proximal region packed with 35S rDNA and a distinct distal heterochromatic region. In contrast, the American chestnut satellite was relatively small and devoid of the distal heterochromatic region.

Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. In addition, we probe the genetic diversity of this widespread species and investigate its phylogenetic relationships with other oaks using whole-genome data. Our genome assembly comprises two haplotypes each consisting of 12 chromosomes. We found that the species has high genetic diversity, much of which predates the divergence of Q. alba from other oak species and likely impacts divergence time estimation in Quercus . Our phylogenetic results highlight phylogenetic discordance across the genus and suggest different relationships among North American oaks than have been reported previously. Despite a high preservation of chromosome synteny and genome size across the Quercus phylogeny, certain gene families have undergone rapid changes in size including resistance genes (R genes). The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus and forest trees more generally. Future research will continue to reveal the full scope of genomic diversity across the white oak clade.

Torreya taxifolia Arn. (Florida torreya) is a critically endangered (International Union for Conservation of Nature 3.1) conifer with a very limited native range in the USA, occurring in two counties in Florida and one in Georgia where it persists in ravines along the Apalachicola River. The species suffered a major decline, >> 99% loss, beginning in the 1930s, with a total population estimated at 357,500 in the early 1900s decreasing to 1,000 individuals currently remaining in the wild. The initial decline was attributed to an unknown fungal disease with Fusarium torreyae (T. Aoki, J. A. Smith, L. Mount, Geiser and O'Donnell), identified in 2011 as the causal agent of a canker disease. The objectives of this work were to develop genetic markers to uniquely identify individuals, examine the structure of the in situ population, and use an ex situ germplasm resource to determine if reproduction without fertilization (apomixis) occurs. We developed a panel of microsatellite markers, sampled individuals from three natural in situ populations, and found population structure at all levels tested. The markers were next applied to ex situ mothers, potential fathers, and progeny to investigate the occurrence of apomixis. One of 29 progeny seedlings tested and its mother had identical multilocus genotypes. The probability of observing this genotype by chance, given the mother and the two possible fathers' genotypes, is approximately one in ten. Based on these data, we cannot reject the hypothesis that apomixis occurs. Our finding of population structure suggests genotypes from as wide an area as possible are required to capture the diversity of the species in conservation efforts. The multiplexed marker panel can be used to identify individual accessions and assist with managing ex situ collections; however, they are not informative enough to clearly differentiate closely related individuals in the ex situ population.

Oak decline is a general term used for the progressive dieback and eventual mortality of oak trees due to many compounding stressors, typically a combination of predisposing, inciting, and contributing factors. While pinpointing individual causes of decline in oak trees is a challenge, past studies have identified site and stand characteristics associated with oak decline. In this study, we developed a risk map of oak decline for the Daniel Boone National Forest (DBNF), combining GIS, remote sensing (RS), and public reporting (citizen science, CS). Starting with ground reports of decline (CS), we developed a site-scale model (GIS and RS) for oak decline based on four previously identified predisposing factors: elevation, slope, solar radiation, and topographic wetness. We found that areas identified in the model as having a high oak decline risk also reflected areas of observed oak decline (CS). We then optimized and expanded this risk model to the entire range of the DBNF, based on both site characteristics (as piloted for the case study site) and stand inventory data. The stand inventory data (including species composition and age) further improved the model, resulting in a risk map at the landscape level. This case study can serve as a planning tool and highlights the potential usefulness of integrating GIS, remote sensing, and citizen science.

Introduced pests (insects and pathogens) have rapidly increased the numbers of at-risk native forest tree species worldwide. Some keystone species have been functionally extirpated, resulting in severe commercial and ecological losses. When efforts to exclude or mitigate pests have failed, researchers have sometimes applied biotechnology tools to incorporate pest resistance in at-risk species to enable their reintroduction. Often erroneously equated solely with genetic engineering, biotechnology also includes traditional and genome informed breeding—and may provide a holistic approach toward applying genomic-based information and interventions to increase tree species’ pest resistance. Traditional tree breeding is responsible for successes to date, but new technologies offer hope to increase the efficiency of such efforts. Remarkable recent progress has been made, and for some at-risk species, novel biotechnological advances put reintroduction within reach. The high costs of reintroduction of at-risk species at necessary scale, however, will initially limit the pursuit to a few species. Successful deployment of pest resistant material may require improved species-specific knowledge and should integrate into and leverage existing reforestation systems, but these operations are sometimes rare where pest threats are greatest. While use of some biotechnologies, such as traditional tree breeding, are commonplace, others such as genetic engineering are controversial and highly regulated, yet may be the only viable means of achieving reintroduction of some at-risk species. Efforts to modify policy toward allowing the use of appropriate biotechnology, especially genetic engineering, have lagged. Provided that risk-benefits are favorable, policy is likely to follow with public opinion; in some countries, society is now increasingly open to using available biotechnologies. Continued engagement using the most recent advances in social science to build public trust, combined with a science-based collaboration among land managers and regulators, will generate the collective momentum needed to motivate policymakers to act rapidly given the speed at which forest health threats unfold and the large areas they affect.

Decades of genetic research and breeding in southern pines, principally focused on loblolly pine (Pinus taeda L.) and slash pine (Pinus elliottii var. elliottii), have resulted in germplasm with improved resistance to the fungal pathogens that cause fusiform rust and pitch canker disease. Fusiform rust resistance is regulated by gene-for-gene, or major gene, resistance. Multiple clusters of major fusiform rust resistance genes (Fr genes) have been genetically mapped in loblolly pine. One candidate Fr gene is predicted to encode a TIR-NBS-LRR protein. This suggests a similar model of NLR evolution to that found in model plants where NLR gene clusters evolve through homologous recombination mediated by transposable elements. In contrast, studies of pitch canker resistance have identified no major resistance genes, supporting a model of quantitative resistance. For loblolly pine, candidate genes involved in resistance to fusiform rust and pitch canker are summarized and functional annotation data are provided along with relevant studies from other Pinus spp. Avenues of future research are discussed including advanced genomic technologies for simultaneously characterizing resistance genes in the host and avirulence genes in the pathogen and the development of prediction models of resistance and virulence from heterogeneous data sources.

We screened and validated microsatellite DNA markers (i.e., simple sequence repeats, SSRs) from transcriptome sequences of white oak (Quercus alba L.).Of 84 PCR primer pairs previously identified and designed, we found 23 pairs that amplified white oak genomic DNA consistently and were polymorphic among three DNA samples.Subsequently, 16 of these 23 primer pairs were amplified across 225 white oak trees sampled from naturally regenerated stands on the Daniel Boone National Forest in southeastern Kentucky.Population estimates of heterozygosity and total and effective allele numbers averaged 66.4%, 11.3, and 5.5, respectively.These 16 SSR markers proved to be highly polymorphic and provided informative data on the genetic diversity of the white oaks within these stands.

Pathogens and pests, native or introduced, can cause high levels of damage and mortality in urban and rural forests. In many cases, little can be done to protect standing trees of the affected species; however, there is a growing recognition that host tree resistance can play a role at countering the long-term impacts of such outbreaks. Leveraging tree resistance for forest health requires a commitment to tree breeding such that resistant genotypes can be identified, propagated, and bred to produce resistant populations for replanting the affected species. Successful resistance breeding programs tend to be results-oriented and organized to deliver resistant populations of seedlings to public and private landowners. Objectives of the initial stages of resistance breeding are to discern whether resistance is present to any degree in the native populations and how it is distributed among these populations across the species' geographic range. In the follow-up stages, the focus shifts to large-scale screening for resistance to identify and select parents for seed production and next-generation breeding. Examples from several successful programs are provided to give students, managers, and decision-makers background on what to expect in starting up and implementing a resistance breeding program.