White Pine Blister Rust Research Articles

Adaptive monitoring in action: Reconsidering design‐based estimators reveals underestimation of whitebark pine disease prevalence in the Greater Yellowstone Ecosystem

Abstract Identifying and understanding status and trends in ecological indicators motivates continual monitoring over decades. Many programs rely on probability surveys and their companion design‐based estimators for status assessments (e.g. Horvitz–Thompson). Design‐based estimators do not easily extend to trend estimation nor situations with observation errors. Field‐based monitoring efforts inevitably have turnover of field crew members which may affect consistency and accuracy of data collection over time. Additionally, design‐based estimators ignore the complexities of spatial and temporal heterogeneity in an ecological indicator and how this variability may be linked to environmental or biological dynamics. We propose monitoring programs should re‐evaluate their prescribed statistical methods, consider model‐based approaches and adapt their sampling designs as needed to improve inferences. The Greater Yellowstone Ecosystem, home to two of the most iconic U.S. National Parks, has experienced significant declines in whitebark pine Pinus albicaulis communities due to forest pathogens, insect outbreaks, wildland fires and drought. Whitebark pine is a keystone species found in mountainous environments throughout the Western U.S. and Canada. We assessed the design‐based ratio estimator originally recommended for estimating prevalence of white pine blister rust Cronartium ribicola. We compared the design‐based estimator to a model‐based approach that accounts for the sampling design, imperfect detection and allows for infection probabilities to vary over space and time. Ignoring observation errors led to lower estimated prevalence of white pine blister rust in the general population. Using model‐based approaches, we found that the probability of infection has increased since 2004. However, overall prevalence likely has not changed because of the mountain pine beetle Dendroctonus ponderosae‐induced shift towards smaller diameter trees that have a lower probability of infection compared to their larger cohorts. Synthesis and Applications. Using a design‐based approach to detect change in ecological indicators falls short because of the inability to account for observation errors or to explore environmental or biological factors explaining temporal dynamics. Inherently understanding the mechanisms leading to changes in an ecological indicator over time informs potential management actions. Our assessment underscores the need for continued evaluation and updating of a monitoring program's sampling design and analytical procedures to maintain relevancy.

In-vitro anti-fungal assay and association analysis reveal a role for the Pinus monticola PR10 gene (PmPR10-3.1) in quantitative disease resistance to white pine blister rust.

Pathogenesis-related (PR) proteins play important roles in plant defense response. However, functional investigation of PR10 genes is still limited and their physiological roles have not been conclusively characterized in biological processes of conifer trees. Here, we identified multiple novel members in the western white pine (Pinus monticola) PmPR10 family by bioinformatic mining available transcriptomic data. Phylogenetic analysis of protein sequences revealed four PR10 and two PR10-like clusters with a high synteny across different species of five-needle pines. Of 10 PmPR10 genes, PmPR10-3.1 was selected and expressed in Escherichia coli. The purified recombinant protein exhibited inhibitory effects on spore hyphal growth of fungal pathogens Cronartium ribicola, Phoma exigua, and Phoma argillacea by in-vitro anti-fungal analysis. Genetic variation analysis detected a total of 21 single nucleotide polymorphisms (SNPs) within PmPR10-3.1 in a collection of P. monticola seed families. A nonsynonymous SNP (t178g) showed significant association with relative levels of quantitative disease resistance (QDR), explaining about 8.7% of phenotypic variation as the peak value across all SNPs. Our results provide valuable insight into the genetic architecture underlying P. monticola QDR and imply that PmPR10-3.1 may function as an important component in conifer basal immunity for non-specific resistance to a wide spectrum of pathogens.

Infectious Disease, Bark Beetles, and Wildland Fire impacts on Southern Sierra White Pines

Photo 1: The triple treat for southern Sierra white pines. Left: White pine blister rust aeciospores on whitebark pine. Top right: Mountain pine beetle pitch tubes in sugar pine. Bottom right: Wildland fire. Photo credit: Joan Dudney. Photo 2: We surveyed four different white pine species, all susceptible to impacts from blister rust, MPB, and fire. From upper left, whitebark pine (Pinus albicaulis), western white pine (Pinus monticola; lower left), foxtail pine (Pinus balfouriana; center), sugar pine (Pinus lambertiana; right). Photo credit: Joan Dudney. Photo 3: Metal monument maker located at the beginning of the plot (upper left). The beginning of a plot transect (lower left). Example of a journal entry left by Duriscoe’s team (center). Crew assessing a diseased tree (upper right). Crew measuring tree growth, or diameter at breast height (dbh; lower right). Photo credit: Joan Dudney. Photo 4: The crews carried heavy packs and gear through some unanticipated extreme conditions, including dense smoke, lightning storms, flash floods, and steep, cross-country terrain. Photo credit: Joan Dudney. Photo 5: Subalpine white pine forests in the southern Sierra Nevada have much lower levels of MPB, fire, and blister rust compared to lower elevation montane forests. Photo credit: Joan Dudney. These photographs illustrate the article, “Compounding effects of white pine blister rust, mountain pine beetle, and fire threaten four white pine species," by Joan Dudney, Jonathan C. B. Nesmith, Matthew C. Cahill, Jennifer E. Cribbs, Dan M. Duriscoe, Adrian J. Das, Nathan L. Stephenson, and John J. Battles, published in Ecosphere. https://doi.org/10.1002/ecs2.3263.

Using Hyperspectral Imagery to Detect an Invasive Fungal Pathogen and Symptom Severity in Pinus strobiformis Seedlings of Different Genotypes

Finding trees that are resistant to pathogens is key in preparing for current and future disease threats such as the invasive white pine blister rust. In this study, we analyzed the potential of using hyperspectral imaging to find and diagnose the degree of infection of the non-native white pine blister rust in southwestern white pine seedlings from different seed-source families. A support vector machine was able to automatically detect infection with a classification accuracy of 87% (κ = 0.75) over 16 image collection dates. Hyperspectral imaging only missed 4% of infected seedlings that were impacted in terms of vigor according to expert’s assessments. Classification accuracy per family was highly correlated with mortality rate within a family. Moreover, classifying seedlings into a ‘growth vigor’ grouping used to identify the degree of impact of the disease was possible with 79.7% (κ = 0.69) accuracy. We ranked hyperspectral features for their importance in both classification tasks using the following features: 84 vegetation indices, simple ratios, normalized difference indices, and first derivatives. The most informative features were identified using a ‘new search algorithm’ that combines both the p-value of a 2-sample t-test and the Bhattacharyya distance. We ranked the normalized photochemical reflectance index (PRIn) first for infection detection. This index also had the highest classification accuracy (83.6%). Indices such as PRIn use only a small subset of the reflectance bands. This could be used for future developments of less expensive and more data-parsimonious multispectral cameras.

Breeding for Resistance to Tree Pests: Successes, Challenges, and a Guide to the Future

Forests in North America are threatened by a myriad of native and nonnative pests and pathogens, the latter of which are largely introduced via the international trade of raw wood products and live plants. The early twentieth-century arrival of white pine blister rust (WPBR) (Cronartium ribicola) and chestnut blight (Cryphonectria parasitica) on imported seedlings devastated forests across North America. Invasive species notably affect entire genera. For example, WPBR has now infected all North American five-needle pine (Pinus) species across the entire United States, which has affected species of commercial and noncommercial value and threatened sensitive, high-elevation ecosystems (Sniezko et al. 2011, 2014, Sniezko and Koch 2017).

Assessing trends and vulnerabilities in the mutualism between whitebark pine (Pinus albicaulis) and Clark's nutcracker (Nucifraga columbiana) in national parks of the Sierra-Cascade region.

Dispersal of whitebark pine (Pinus albicaulis Engelm.), a keystone species of many high-elevation ecosystems in western North America, depends on Clark's nutcracker (Nucifraga columbiana Wilson), a seed-caching bird with an affinity for whitebark seeds. To the extent that this dependence is mutual, declines in whitebark seed production could cause declines in nutcracker abundance. Whitebark pine is in decline across much of its range due to interacting stressors, including the non-native pathogen white pine blister rust (Cronartium ribicola J. C. Fisch.). We used avian point-count data and tree surveys from four national park units to investigate whether trends in whitebark pine can explain trends in Clark's nutcracker. Spatial trends were modeled using recent data from two parks, while temporal trends were modeled using longer time-series of nutcracker and whitebark data from two additional parks. To assess the potential dependence of nutcrackers on whitebark, we linked a model of nutcracker density (accounting for detection probability) with a model of whitebark trends, using a Bayesian framework to translate uncertainty in whitebark metrics to uncertainty in nutcracker density. In Mount Rainier National Park, temporal models showed dramatic declines in nutcracker density concurrent with significant increases in whitebark crown mortality and trees infected with white pine blister rust. However, nutcrackers did not trend with whitebark metrics in North Cascades National Park Service Complex. In spatial models of data from Yosemite National Park and Sequoia-Kings Canyon National Park, nutcracker density varied not only with local cover of whitebark but also with elevation and, in Sequoia-Kings Canyon, with cover of another species of white pine. Our results add support for the hypothesis that the mutualism between whitebark pine and Clark's nutcracker is vulnerable to disruption by blister rust, and our approach integrates data across monitoring programs to explore trends in species interactions.

Compounding effects of white pine blister rust, mountain pine beetle, and fire threaten four white pine species

AbstractInvasive pathogens and bark beetles have caused precipitous declines of various tree species around the globe. Here, we characterized long‐term patterns of mountain pine beetle (Dendroctonus ponderosae; MPB) attacks and white pine blister rust, an infectious tree disease caused by the pathogen, Cronartium ribicola. We focused on four dominant white pine host species in Sequoia and Kings Canyon National Parks (SEKI), including sugar pine (Pinus lambertiana), western white pine (P. monticola), whitebark pine (P. albicaulis), and foxtail pine (P. balfouriana). Between 2013 and 2017, we resurveyed 152 long‐term monitoring plots that were first surveyed and established between 1995 and 1999. Overall extent (plots with at least one infected tree) of white pine blister rust (blister rust) increased from 20% to 33%. However, the infection rate across all species decreased from 5.3% to 4.2%. Blister rust dynamics varied greatly by species, as infection rate decreased from 19.1% to 6.4% in sugar pine, but increased in western white pine from 3.0% to 8.7%. For the first time, blister rust was recorded in whitebark pine, but not foxtail pine plots. MPB attacks were highest in sugar pines and decreased in the higher elevation white pine species, whitebark and foxtail pine. Both blister rust and MPB were important factors associated with elevated mortality in sugar pines. We did not, however, find a relationship between previous fires and blister rust occurrence. In addition, multiple mortality agents, including blister rust, fire, and MPB, contributed to major declines in sugar pine and western white pine; recruitment rates were much lower than mortality rates for both species. Our results highlighted that sugar pine has been declining much faster in SEKI than previously documented. If blister rust and MPB trends persist, western white pine may follow similar patterns of decline in the future. Given current spread patterns, blister rust will likely continue to increase in higher elevations, threatening subalpine white pines in the southern Sierra Nevada. More frequent long‐term monitoring efforts could inform ongoing restoration and policy focused on threats to these highly valuable and diverse white pines.

Association Mapping and Development of Marker-Assisted Selection Tools for the Resistance to White Pine Blister Rust in the Alberta Limber Pine Populations.

Since its introduction to North America in the early 1900s, white pine blister rust (WPBR) caused by the fungal pathogen Cronartium ribicola has resulted in substantial economic losses and ecological damage to native North American five-needle pine species. The high susceptibility and mortality of these species, including limber pine (Pinus flexilis), creates an urgent need for the development and deployment of resistant germplasm to support recovery of impacted populations. Extensive screening for genetic resistance to WPBR has been underway for decades in some species but has only started recently in limber pine using seed families collected from wild parental trees in the USA and Canada. This study was conducted to characterize Alberta limber pine seed families for WPBR resistance and to develop reliable molecular tools for marker-assisted selection (MAS). Open-pollinated seed families were evaluated for host reaction following controlled infection using C. ribicola basidiospores. Phenotypic segregation for presence/absence of stem symptoms was observed in four seed families. The segregation ratios of these families were consistent with expression of major gene resistance (MGR) controlled by a dominant R locus. Based on linkage disequilibrium (LD)-based association mapping used to detect single nucleotide polymorphism (SNP) markers associated with MGR against C. ribicola, MGR in these seed families appears to be controlled by Cr4 or other R genes in very close proximity to Cr4. These associated SNPs were located in genes involved in multiple molecular mechanisms potentially underlying limber pine MGR to C. ribicola, including NBS-LRR genes for recognition of C. ribicola effectors, signaling components, and a large set of defense-responsive genes with potential functions in plant effector-triggered immunity (ETI). Interactions of associated loci were identified for MGR selection in trees with complex genetic backgrounds. SNPs with tight Cr4-linkage were further converted to TaqMan assays to confirm their effectiveness as MAS tools. This work demonstrates the successful translation and deployment of molecular genetic knowledge into specific MAS tools that can be easily applied in a selection or breeding program to efficiently screen MGR against WPBR in Alberta limber pine populations.

Community Structure and Functional Role of Limber Pine (Pinus flexilis) in Treeline Communities in Rocky Mountain National Park

Research Highlights: Limber pine (Pinus flexilis) is abundant in some alpine treeline ecotone (ATE) communities east of the Continental Divide in Rocky Mountain National Park (RMNP) and the Colorado Front Range. Limber pine may be able to colonize the ATE under changing climate aided by directed seed dispersal by Clark’s nutcrackers (Nucifraga columbiana). Cronartium ribicola, white pine blister rust, is a growing threat to limber pine and may affect its functional role within the ATE. Background and Objectives: The ATE is sensitive, worldwide, to increasing temperature. However, the predicted advance of treeline under a changing climate may be modified by tree species composition and interactions. We aimed to (1) examine the conifer species composition and relative abundances in treeline communities with limber pine; (2) assess which functional roles limber pine assumes in these communities—tree island initiator, tree island component, and/or solitary tree; and (3) determine whether limber pine’s occurrence as a tree island initiator can be predicted by its relative abundance as a solitary tree. Materials and Methods: We selected four study sites in RMNP above subalpine forest limber pine stands. We sampled the nearest tree island to each of forty random points in each study site as well as solitary tree plots. Results: Across study sites, limber pine comprised, on average, 76% of solitary trees and was significantly more abundant as a solitary tree than Engelmann spruce (Picea engelmannii) or subalpine fir (Abies lasiocarpa). Limber pine was a frequent component of multi-tree islands in three study sites, the major component in one study site, and dominated single-tree islands at two study sites. At three of four study sites, no species had significantly greater odds of being a tree island initiator. Limber pine was found less often as a tree island initiator than predicted from its relative abundance as a solitary tree, given the likely role of solitary trees in tree island formation.

Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance.

The genomic architecture and molecular mechanisms controlling variation in quantitative disease resistance loci are not well understood in plant species and have been barely studied in long-generation trees. Quantitative trait loci mapping and genome-wide association studies were combined to test a large single nucleotide polymorphism (SNP) set for association with quantitative and qualitative white pine blister rust resistance in sugar pine. In the absence of a chromosome-scale reference genome, a high-density consensus linkage map was generated to obtain locations for associated SNPs. Newly discovered associations for white pine blister rust quantitative disease resistance included 453 SNPs involved in wide biological functions, including genes associated with disease resistance and others involved in morphological and developmental processes. In addition, NBS-LRR pathogen recognition genes were found to be involved in quantitative disease resistance, suggesting these newly reported genes are qualitative genes with partial resistance, they are the result of defeated qualitative resistance due to avirulent races, or they have epistatic effects on qualitative disease resistance genes. This study is a step forward in our understanding of the complex genomic architecture of quantitative disease resistance in long-generation trees, and constitutes the first step towards marker-assisted disease resistance breeding in white pine species.

In Situ Processing and Efficient Environmental Detection (iSPEED) of tree pests and pathogens using point-of-use real-time PCR.

Global trade and climate change are responsible for a surge in foreign invasive species and emerging pests and pathogens across the world. Early detection and surveillance activities are essential to monitor the environment and prevent or mitigate future ecosystem impacts. Molecular diagnostics by DNA testing has become an integral part of this process. However, for environmental applications, there is a need for cost-effective and efficient point-of-use DNA testing to obtain accurate results from remote sites in real-time. This requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We developed a point-of-use real-time Polymerase Chain Reaction system using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions for on-site applications. We demonstrate the use of this approach with pathogens and pests covering a broad spectrum of known undesirable forest enemies: the fungi Sphaerulina musiva, Cronartium ribicola and Cronartium comandrae, the oomycete Phytophthora ramorum and the insect Lymantria dispar. We obtained positive DNA identification from a variety of different tissues, including infected leaves, pathogen spores, or insect legs and antenna. The assays were accurate and yielded no false positive nor negative. The shelf-life of the lyophilized reactions was confirmed after one year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable instruments demonstrate the suitability of the method, named in Situ Processing and Efficient Environmental Detection (iSPEED), for field testing. This kit fits in a backpack and can be carried to remote locations for accurate and rapid detection of pests and pathogens.

Volatiles of High-Elevation Five-Needle Pines: Chemical Signatures through Ratios and Insight into Insect and Pathogen Resistance.

High-elevation five-needle pine trees are a group of Pinus species in the subgenus Strobus that occur at the edges of plant growth near the alpine tree line. These species are ecologically very important and are also threatened by climate-driven insect outbreaks and an exotic pathogen. Volatile organic compounds (VOCs) play central roles in the environmental adaptation of plants and in their defense against insects and pathogens. For example, the VOCs emitted by some high-elevation five-needle pine species attract female, tree-killing mountain pine beetles (MPB, Dendroctonus ponderosae) in the pioneering phase whereas VOCs from other species strongly repel this foremost herbivore, but the mechanism is unknown. We collected and compared headspace VOCs from foliage of eight species of high-elevation five-needle pines in Europe and North America. Overall, VOCs differed quantitatively among species with few qualitative differences. Despite species emitting essentially the same compounds, Random Forest analysis correctly classified 117 of the 126 trees sampled by using VOCs and identified the most important compounds for species classification and for separating species resistant from those susceptible to MPB or white pine blister rust (Cronartium ribicola). These VOC 'fingerprints' resulted largely from species emitting distinctive ratios of compounds, rather than through presence of species-specific compounds. Importantly, these Pinus species vary greatly in resistance to the main herbivore (MPB) and pathogen (white pine blister rust) causing tree mortality. Thus, these findings provide insights and should guide research into understanding resistance and in developing tools to manage these important trees. For instance, studies into the functions of five-needle pine VOCs in defense against abiotic or biotic stressors should focus on blend ratios rather than on individual compounds.

Paired Stated Preference Methods for Valuing Management of White Pine Blister Rust: Order Effects and Outcome Uncertainty

Paired Stated Preference Methods for Valuing Management of White Pine Blister Rust: Order Effects and Outcome Uncertainty

Whitebark Pine in the National Parks of the Pacific States: An Assessment of Population Vulnerability

Whitebark pine (Pinus albicaulis) is a long-lived tree found in high-elevation forests of western North America that is declining due to the non-native white pine blister rust (Cronartium ribicola) and climate-driven outbreaks of mountain pine beetle (Dendroctonus ponderosae; MPB). The National Park Service established a monitoring program for whitebark pine in seven parks, including Sequoia & Kings Canyon, Yosemite, Lassen Volcanic, Crater Lake, Mount Rainier, Olympic, and North Cascades National Parks. Using these data, we summarized stand structure, presence of blister rust, and MPB prevalence to provide a baseline for future monitoring. Next, we used a stochastic, size-structured population model to speculate on future trends in the seven national park populations under conditions of increased MPB activity and ongoing blister rust infection observed in Crater Lake. We found that blister rust infected 29 to 54% of whitebark pine in all the parks except the two southernmost, Sequoia & Kings Canyon and Yosemite, where infections rates were 0.3% and 0.2%, respectively. The proportion of dead trees in Sequoia & Kings Canyon and Yosemite was low (0 to 1%), while they ranged from 10 to 43% in the other parks. Model projections suggested an average population decline of 25% in the parks over the next century using Crater Lake conditions, declines which are possible if blister rust continues to spread and climate change results in a significant increase in the frequency or severity of MPB outbreaks. Overall, our study describes conditions at seven western parks and illustrates potential rates of whitebark pine decline if pest outbreaks and/or blister rust infections worsen.

Whitebark pine (Pinus albicaulis) growth and defense in response to mountain pine beetle outbreaks

Whitebark pine (Pinus albicaulis) is a critical forest species of Northern Rocky Mountain upper subalpine ecosystems, yet little is known about the physiological response of whitebark pine to disturbance (e.g. fire, bark beetles, and pathogens) across a range of diverse environmental gradients. Resin-based defenses have long been recognized as the primary mechanism by which conifers respond to attack by bark beetles and pathogens and several studies have linked resin duct properties to survivorship during periods of increased beetle activity. However, to our knowledge, no studies have compared axial resin ducts in the secondary xylem of whitebark pine across pairs of living and dead whitebark pine trees to better understand survivorship following multiple disturbances including mountain pine beetle and white pine blister rust. We found a clear distinction in growth and defense characteristics between live and dead whitebark pine. Across our study sites on the Flathead Indian Reservation in northwestern Montana, live whitebark pine produced larger resin ducts with a greater annual investment in resin-based defenses than whitebark pine that died. Resin duct size, duct area, and relative duct area were all greater in live whitebark pine (by 56%, 48%, and 57%, respectively) and these were the most important variables influencing whitebark pine survivorship. In contrast, whitebark pine that had died grew faster over time (22% larger ring widths) than their live counterparts and also produced more resin duct structures (20% more ducts on average). Whitebark pine at our study sites exhibit differing strategies in the allocation of resources toward growth and defense, with the majority of survivors of recent disturbance investing more in defensive structures than growth. Our results support the idea that maintaining genetic variability and the associated suite of differing physiological traits promotes diverse response strategies to a complex array of biophysical and biological stressors that might leave a species vulnerable to extinction across its range.

Characterization of Cronartium ribicola dsRNAs reveals novel members of the family Totiviridae and viral association with fungal virulence

BackgroundMycoviruses were recently discovered in the white pine blister rust (WPBR) fungus Cronartium ribicola (J.C. Fisch.). Detection and characterization of their double stranded RNA (dsRNA) would facilitate understanding of pathogen virulence and disease pathogenesis in WPBR systems.MethodsFull-length cDNAs were cloned from the dsRNAs purified from viral-infected C. ribicola, and their cDNA sequences were determined by DNA sequencing. Evolutionary relationships of the dsRNAs with related mycoviruses were determined by phylogenetic analysis. Dynamic distributions of the viral RNAs within samples of their fungal host C. ribicola were investigated by measurement of viral genome prevalence and viral gene expression.ResultsIn this study we identified and characterized five novel dsRNAs from C. ribicola, designated as Cronartium ribicola totivirus 1–5 (CrTV1 to CrTV5). These dsRNA sequences encode capsid protein and RNA-dependent RNA polymerase with significant homologies to dsRNA viruses of the family Totiviridae. Phylogenetic analysis showed that the CrTVs were grouped into two distinct clades. CrTV2 through CrTV5 clustered within the genus Totivirus. CrTV1 along with a few un-assigned dsRNAs constituted a distinct phyletic clade that is genetically distant from presently known genera in the Totiviridae family, indicating that CrTV1 represents a novel genus in the Totiviridae family. The CrTVs were prevalent in fungal samples obtained from infected western white pine, whitebark pine, and limber pines. Viral RNAs were generally expressed at higher levels during in planta mycelium growth than in aeciospores and urediniospores. CrTV4 was significantly associated with C. ribicola virulent pathotype and specific C. ribicola host tree species, suggesting dsRNAs as potential tools for dissection of pathogenic mechanisms of C. ribicola and diagnosis of C. ribicola pathotypes.ConclusionPhylogenetic and expression analyses of viruses in the WPBR pathogen, C. ribicola, have enchanced our understanding of virus diversity in the family Totiviridae, and provided a potential strategy to utilize pathotype-associated mycoviruses to control fungal forest diseases.

Whitebark Pine in Crater Lake and Lassen Volcanic National Parks: Assessment of Stand Structure and Condition in a Management and Conservation Perspective

Whitebark pine (Pinus albicaulis. Engelm.) is vulnerable to a number of threats including an introduced pathogen (Cronartium ribicola J.C. Fisch.), epidemic levels of native mountain pine beetle (Dendroctonus ponderosae Hopkins), fire suppression, and climate change. To describe the structure of whitebark pine populations in two national parks in the southern Cascades (Crater Lake, Oregon, USA (CRLA) and Lassen Volcanic, California, USA (LAVO) National Parks), we surveyed trees in 30 × 50 × 50 m plots in both parks. We used these plots to describe the extent of white pine blister rust (the disease caused by Cronartium ribicola), mountain pine beetle occurrence, and to elucidate factors influencing the presence of pests and pathogens, cone production, and canopy kill. In each plot, we recorded data related to tree health, including symptoms of blister rust and mountain pine beetle, and reproductive vigor (cone production). In both parks, encroachment from other species, particularly mountain hemlock (Tsuga mertensiana (Bong.) Carrière), was negatively associated with cone production. In CRLA, water stress was a good predictor of blister rust infection and cone production. For CRLA and LAVO, the presence of mountain pine beetle and blister rust was associated with higher canopy kill for whitebark pine. Lastly, we found evidence for a pest-pathogen interaction, mountain pine beetle attack was greater for trees that showed symptoms of blister rust infection in CRLA. Our results indicate that whitebark pine populations in the southern Cascade Range are experiencing moderate levels of blister rust infection compared with other sites across the species range, and that competition from shade-tolerant species may result in an additional threat to whitebark pine in both parks. We present our findings in the context of park management and situate them in range-wide and regional conservation strategies aimed at the protection and restoration of a declining species.

Survival of Whitebark Pine Seedlings Grown from Direct Seeding: Implications for Regeneration and Restoration under Climate Change

Whitebark pine populations are declining nearly range-wide, primarily from the exotic fungal pathogen that causes white pine blister rust (WPBR). Climate change is expected to exacerbate these declines by decreasing climatically suitable areas. Planting WPBR-resistant seedlings is a key restoration action, but it is costly, time consuming, and labor intensive. Direct seeding—sowing seeds rather than planting seedlings—may reduce costs and open remote areas to restoration; however, its efficacy remains largely unexplored. In this case study, we estimated the annual survival rates (ASR) of seedlings grown from directly sown seeds, and the effect of elevation zone and microsite type on survival. For five years we monitored 184 caches containing one or more seedlings within one study area in the Greater Yellowstone Ecosystem. Seed caches were originally stratified between subalpine forest and treeline and among three microsite types defined by a nurse object: Rocks, trees, and no object. To estimate ASR, we selected the most parsimonious model of a set using AICc. ASR was best described by elevation zone and year and ranged from 0.571 to 0.992. The odds of seedling survival were 2.62 times higher at treeline than in subalpine forest and were 4.6 to 36.2 times higher in 2016–2018 than 2014. We estimated the probability that a whitebark pine seed cache would contain one or more living seedlings six years after sowing to be 0.175 and 0.0584 for treeline and subalpine caches, respectively. We estimated that 1410 and 4229 caches ha−1 would need to be sown at treeline and in subalpine forest, respectively, to attain target restoration densities of 247 established trees ha−1. Our findings, although based on one study area, suggest that climate change may be increasing treeline regeneration, and that direct seeding may be a viable restoration option and climate change mitigation tool for whitebark pine.

Climatic Correlates of White Pine Blister Rust Infection in Whitebark Pine in the Greater Yellowstone Ecosystem

Whitebark pine, a foundation species at tree line in the Western U.S. and Canada, has declined due to native mountain pine beetle epidemics, wildfire, and white pine blister rust. These declines are concerning for the multitude of ecosystem and human benefits provided by this species. An understanding of the climatic correlates associated with spread is needed to successfully manage impacts from forest pathogens. Since 2000 mountain pine beetles have killed 75% of the mature cone-bearing trees in the Greater Yellowstone Ecosystem, and 40.9% of monitored trees have been infected with white pine blister rust. We identified models of white pine blister rust infection which indicated that an August and September interaction between relative humidity and temperature are better predictors of white pine blister rust infection in whitebark pine than location and site characteristics in the Greater Yellowstone Ecosystem. The climate conditions conducive to white pine blister rust occur throughout the ecosystem, but larger trees in relatively warm and humid conditions were more likely to be infected between 2000 and 2018. We mapped the infection probability over the past two decades to identify coarse-scale patterns of climate conditions associated with white pine blister rust infection in whitebark pine.

Development and application of marker-assisted selection (MAS) tools for breeding of western white pine (Pinus monticola Douglas ex D. Don) resistance to blister rust (Cronartium ribicola J.C. Fisch.) in British Columbia

Cronartium ribicola causes white pine blister rust (WPBR) on five-needle pines worldwide. After accidental introduction into North America about 100 years ago, this invasive fungus has caused heavy mortality in western white pine (Pinus monticola) and other related five-needle pines across North America. Breeding by selection of rare resistant trees is time-consuming; therefore, genomics-based tools are highly desirable to speed up the breeding process. Our laboratory previously constructed genetic maps for the P. monticola Cr2 locus that confers major gene resistance (MGR) to WPBR and identified several nucleotide-binding site leucine-rich repeat (NBS-LRR) genes as Cr2 positional candidates. In the present study, single nucleotide polymorphism (SNP) loci within Cr2 candidate genes (contig58688 and contig41490) were selected to develop qPCR-based genotyping assays using two SNP genotyping technologies (TaqMan and Kompetitive Allele Specific PCR-KASP). To evaluate the utility and efficiency of these marker-assisted selection (MAS) tools in British Columbia’s (BC’s) breeding program, we analyzed 46 open-pollinated bulk seedlots that were randomly selected across BC’s landscape. SNP genotyping results were highly consistent, with matching rates of over 99% between TaqMan and KASP assays for each specific SNP locus. The Cr2-linked alleles were absent in all genotyped samples for the snp58688-82Y locus and about 86% of all genotyped samples for the snp41490-1778M locus. These results demonstrate that both the TaqMan and KASP SNP genotyping assays are powerful MAS tools with accuracy up to 100% for prediction of Cr2-resistance in wild parental trees, as well as for resistance selection among their progeny following cross-pollination with MGR trees across BC’s landscape.