12. Cappa, E.P., Chen, C., Klutsch, J.G. et al. Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine. BMC Genomics 23, 536 (2022). https://doi.org/10.1186/s12864-022-08747-7
Genomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to identify alleles or genomic regions of complex traits in forest trees species. Here, 1490 interior lodgepole pine (Pinus contorta Dougl. ex. Loud. var. latifolia Engelm) trees from four open-pollinated progeny trials were genotyped with 25,099 SNPs, and phenotyped for 15 growth, wood quality, pest resistance, drought tolerance, and defense chemical (monoterpenes) traits. The main objectives of this study were to: (1) identify genetic markers associated with these traits and determine their genetic architecture, and to compare the marker detected by single- (ST) and multiple-trait (MT) GWA models; (2) evaluate and compare the accuracy and control of bias of the genomic predictions for these traits underlying different ST and MT parametric and non-parametric GP methods. GWA, ST and MT analyses were compared using a linear transformation of genomic breeding values from the respective genomic best linear unbiased prediction (GBLUP) model. GP, ST and MT parametric and non-parametric (Reproducing Kernel Hilbert Spaces, RKHS) models were compared in terms of prediction accuracy (PA) and control of bias.
MT-GWA analyses identified more significant associations than ST. Some SNPs showed potential pleiotropic effects. Averaging across traits, PA from the studied ST-GP models did not differ significantly from each other, with generally a slight superiority of the RKHS method. MT-GP models showed significantly higher PA (and lower bias) than the ST models, being generally the PA (bias) of the RKHS approach significantly higher (lower) than the GBLUP.
The power of GWA and the accuracy of GP were improved when MT models were used in this lodgepole pine population. Given the number of GP and GWA models fitted and the traits assessed across four progeny trials, this work has produced the most comprehensive empirical genomic study across any lodgepole pine population to date.
11. Pest defenses under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations. Proceedings of the Royal Society B: Biological Sciences https://doi.org/10.17863/CAM.86267
Whilst droughts, intensified by climate change, have been affecting forests worldwide, pest epidemics are a major source of uncertainty for assessing drought impacts on forest trees. Thus far, little information has documented the adaptability and evolvability of traits related to drought and pests simultaneously. We conducted common-garden experiments to investigate how several phenotypic traits (i.e., height growth, drought avoidance based on water-use efficiency inferred from δ13C, and pest resistance based on defense traits) interact in five mature lodgepole pine populations established in four progeny trials in western Canada. The relevance of interpopulation variation in climate sensitivity highlighted that seed-source warm populations had greater adaptive capability than cold populations. In test sites, warming generated taller trees with higher δ13C and increased the evolutionary potential of height growth and δ13C across populations. We found, however, no pronounced gradient in defenses and their evolutionary potential along populations or test sites. Response to selection was weak in defenses across test sites, but high for height growth particularly at warm test sites. Response to selection of δ13C varied depending on its selective strength relative to height growth. We conclude that warming could promote the adaptability and evolvability of growth response and drought avoidance with a limited evolutionary influence from pest (biotic) pressures.
10. Cappa EP, Klutsch JG, Sebastian-Azcona J, Ratcliffe B, Wei X, Da Ros L, Liu Y, Chen C, Benowicz A, Sadoway S, Mansfield SD, Erbilgin N, Thomas BR, El-Kassaby YA. (2022) Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program. PLOS ONE 17(3): e0264549. https://doi.org/10.1371/journal.pone.0264549
Tree improvement programs often focus on improving productivity-related traits; however, under present climate change scenarios, climate change-related (adaptive) traits should also be incorporated into such programs. Therefore, quantifying the genetic variation and correlations among productivity and adaptability traits, and the importance of genotype by environment interactions, including defense compounds involved in biotic and abiotic resistance, is essential for selecting parents for the production of resilient and sustainable forests. Here, we estimated quantitative genetic parameters for 15 growth, wood quality, drought resilience, and monoterpene traits for Picea glauca (Moench) Voss (white spruce). We sampled 1,540 trees from three open-pollinated progeny trials, genotyped with 467,224 SNP markers using genotyping-by-sequencing (GBS). We used the pedigree and SNP information to calculate, respectively, the average numerator and genomic relationship matrices, and univariate and multivariate individual-tree models to obtain estimates of (co)variance components. With few site-specific exceptions, all traits examined were under genetic control. Overall, higher heritability estimates were derived from the genomic- than their counterpart pedigree-based relationship matrix. Selection for height, generally, improved diameter and water use efficiency, but decreased wood density, microfibril angle, and drought resistance. Genome-based correlations between traits reaffirmed the pedigree-based correlations for most trait pairs. High and positive genetic correlations between sites were observed (average 0.68), except for those pairs involving the highest elevation, warmer, and moister site, specifically for growth and microfibril angle. These results illustrate the advantage of using genomic information jointly with productivity and adaptability traits, and defense compounds to enhance tree breeding selection for changing climate.
9. Cappa, E.P., Ratcliffe, B., Chen, C., Thomas, B.R., Liu, Y., Klustch, J., Wei, X., Azcona, J. S., Benowicz, A., Sadoway, S., Erbilgin, N., El-Kassaby, Y.A. Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP. Heredity (2022). https://doi.org/10.1038/s41437-022-00508-2
Modeling environmental spatial heterogeneity can improve the efficiency of forest tree genomic evaluation. Furthermore, genotyping costs can be lowered by reducing the number of markers needed. We investigated the impact on variance components, breeding value accuracy, and bias of two phenotypic data adjustments (experimental design and autoregressive spatial models), and a relationship matrix calculated from a subset of markers selected for their ability to infer ancestry. Using a multiple-trait multiple-site single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) approach, four scenarios (2 phenotype adjustments × 2 marker sets) were applied to diameter at breast height (DBH), height (HT), and resistance to western gall rust (WGR) in four open-pollinated progeny trials of lodgepole pine, with 1490 (out of 11,188) trees genotyped with 25,099 SNPs. As a control, we fitted the conventional ABLUP model using pedigree information. The highest heritability estimates were achieved for the ABLUP followed closely by the ssGBLUP with the full marker set and using the spatial phenotype adjustments. The highest predictive ability was obtained by using a reduced marker subset (8000 SNPs) when either the spatial (DBH: 0.429, and WGR: 0.513) or design (HT: 0.467) phenotype corrections were used. No significant difference was detected in prediction bias among the six fitted models, and all values were close to 1 (0.918–1.014). Results demonstrated that selecting informative markers, such as those capturing ancestry, can improve the predictive ability. The use of spatial correlation structure increased traits’ heritability and reduced prediction bias, while increases in predictive ability were trait-dependent.
8. Wei, X., Benowicz, A., Sebastian-Azcona, J., & Thomas, B. R. (2022). Genetic variation in leaf traits and gas exchange responses to vapour pressure deficit in contrasting conifer species. Functional Ecology, 00, 1–11. https://doi.org/10.1111/1365-2435.14007
1. Mechanistically predicting the evolutionary response of tree species to climate change requires an understanding of genetic variation in relevant traits. Here we compared the phenotypic and genetic variation in the Leaf Economics Spectrum (LES) traits and the response of gas exchange to vapour pressure deficit (VPD) in lodgepole pine (Pico) and white spruce (Pigl), an early and a late successional species dominating the boreal forests of western Canada.
2. We measured gas exchange, foliar nitrogen and lamina mass to area ratio in 697 c. 30- year- old trees in two field progeny trials. We analysed the response of gas exchange rates to VPD using a novel quantitative genetic model, the function- valued trait approach.
3. Pico showed greater phenotypic variation in the LES traits and greater genetic variation in photosynthetic rate than Pigl, but the species showed no significant difference in their phenotypic correlations between the LES traits. Pico showed a less sensitive stomatal response to VPD than Pigl and no significant genetic variation in stomatal sensitivity. In contrast, Pigl showed a positive correlation between the genetic values of stomatal sensitivity to VPD and stomatal con-ductance under low VPD.
4. Our study region is projected to see an increase in VPD with climate change; the less sensitive and genetically diverse stomatal response to VPD in Pico could make this species more vulnerable to climate-change-induced droughts.
KEYWORDSclimate change, function-valued trait, genetic variation, lodgepole pine, stomatal conductance, succession, vapour pressure deficit, white spruce
7. Wang, S., An, H., Chang, W-Y., Gaston, C., Thomas, B.R. Economic potential of adopting genomic technology in Alberta’s tree improvement sector. The Forestry Chronicle. 2021. Vol 97, No 3. https://doi.org/10.5558/tfc2021-024
The adoption of genomic technology and the use of improved seeds are expected to improve timber productivity in Alberta. However, this improvement will need to take place within the confines of the public-private nature of the sector
where 93% of the total forest area is publicly owned. The purpose of this study is to explore the extent to which a timber harvest policy known as the allowable cut effect can affect the welfare outcomes of adopting genomics-assisted tree breeding. Using the forest industry of Alberta as the empirical setting, the economic returns to the adoption of this new breeding technology in lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) and white spruce (Picea glauca (Moench) Voss) are calculated by estimating a timber supply model and a spatial equilibrium model. Under certain pol- icy and technology improvement scenarios, the economic returns are negative, which would result in non-adoption of the technology. However, under other feasible conditions, the payoffs of genomics-assisted tree breeding research are large and positive. These results illustrate the important role that government policies can have on the returns to adopting new technologies.
6. Letitia M. Da Ros, Barb R. Thomas, Shawn D. Mansfield, Wood quality trait associations with climate: Room for improvement in two northern commercial tree species?, Forest Ecology and Management, Volume 497, 2021, 119492, ISSN 0378-1127, https://doi.org/10.1016/j.foreco.2021.119492
Climate driven tree mortality threatens the current performance and productivity of the temperate boreal forests. For economically important tree species, progeny trials provide an opportunity to assess variability in wood quality and growth traits and their associations with climatic stressors, such as water availability. Data from 3,152 34-year-old white spruce and lodgepole pine progeny, representing 120 half-sib families, were used to test the selective pressure of aridity on wood density and wood microfibril angle, two attributes that contribute to wood performance. Tree increment cores were further evaluated for correlations between time of transition out of juvenile wood production and the environment. Aridity at seed point of origin had minimal to no selective pressure on overall wood density or microfibril angle in the breeding populations represented in this study. Aridity at the progeny test sites had a greater effect on spruce wood density, however, similar effects on pine could not be assessed as sites were too climatically similar. Transition out of juvenile wood production was not found to be influenced by genetic differences across families in either species examined. These determinations are pivotal for breeding programs which seek to use heritable and economically important traits to select for adaptability in a changing climate.
Keywords: Tree improvement; Transition age; Climate change; Lodgepole pine; White spruce; Aridity; Drought tolerance
5. Ullah, A., Klutsch, J. G., & Erbilgin, N. (2021). Production of complementary defense metabolites reflects a co-evolutionary arms race between a host plant and a mutualistic bark beetle-fungal complex. Plant, Cell & Environment, 1– 14. https://doi.org/10.1111/pce.14100
Intra-specific variation in conifers has been extensively studied with respect to defense against herbivores and pathogens. While studies have shown the ability of individual or specific mixtures of compounds to influence insects and microbes, research testing biologically relevant mixtures of defense compounds reflecting intra-specific variation amongst tree populations to enemy complexes is needed. We characterized the variations in lodgepole pine monoterpenes from a progeny trial in western Canada and grouped trees in four clusters using their monoterpene profiles. We then selected 11 representative families across four clusters and amended their entire monoterpene profiles (with the exception of β-phellandrene) in media to determine how representative families affect the performance of the mountain pine beetle or its fungal symbiont. We placed adult beetles or inoculated fungus on the amended media and measured beetle performance and fungal growth as a proxy to host suitability. We found that different clusters or families differentially influenced beetle or fungal responses. However, monoterpene profiles of trees suitable to the beetle or the fungus were dissimilar. These outcomes reflect a co-evolutionary arms-race between the host and the bark beetle-fungus complex, which has resulted in the production of complementary defense metabolites among different pine populations to enhance tree survival.
4. Jennifer G. Klutsch, Chen X. Kee, Eduardo P. Cappa, Blaise Ratcliffe, Barb R. Thomas, and Nadir Erbilgin "Increment Coring Induced Traumatic Resin Ducts in White Spruce But Not in Lodgepole Pine," Tree-Ring Research 76(1), 54-58, (21 January 2020). https://doi.org/10.3959/TRR2019-5
Received: 26 March 2019; Accepted: 12 October 2019; Published: 21 January 2020
Injury from sampling increment cores may induce defense responses in trees, which may vary between species and reflect differing defense allocation strategies against attack by insects and pathogens. We recorded presence of systemic induction of traumatic resin ducts from early-season increment coring in mature white spruce (Picea glauca) and lodgepole pine (Pinus contorta var. latifolia) trees. In the year of coring, traumatic resin ducts formed three months later, 20 cm below the initial coring site in the xylem of white spruce and showed little variation in response among the spruce families. In contrast, lodgepole pine did not form traumatic resin ducts in trees cored earlier in the growing season. Although traumatic resin ducts are induced by biotic and abiotic disturbances, we found a species-specific defense response to increment coring in two common boreal forest tree species.
3. Wei-Yew Chang, Chris Gaston, Julie Cool, Barb R Thomas, A financial analysis of using improved planting stock of white spruce and lodgepole pine in Alberta, Canada: genomic selection versus traditional breeding, Forestry: An International Journal of Forest Research, Volume 92, Issue 3, July 2019, Pages 297–310, https://doi.org/10.1093/forestry/cpz011
Genomics-assisted tree breeding (GATB) is an emerging biotechnology method that has the potential to produce improved planting stock in selected traits, such as greater volume or higher wood quality, more quickly and effectively compared with traditional field-based breeding (TB) methods. In this study, we conducted an ex-ante stand-level financial benefit-cost analysis that is linked to a provincial tree growth and yield projection model to investigate the potential financial benefits of using improved white spruce (Picea glauca (Moench) Voss) and lodgepole pine (Pinus contorta Dougl. var. latifolia Engelm.) planting stock identified via alternative tree improvement strategies (i.e. GATB vs. TB methods) for forest companies in the province of Alberta, Canada. With consideration of major tree breeding and establishment costs, expected sawlog price premiums at harvest, a shorter breeding cycle time, and additional genetic gain in volume achieved from using the GATB method relative to the TB method in the financial analysis; this study found that the use of GATB-selected third-generation planting stock was difficult to justify economically alone compared with TB-selected seedlings under the current sawlog market value and the current planting rate with improved stock in the province. However, results of our sensitivity analysis also revealed that the GATB method is: (1) more financially supported at lower discount rates; (2) strongly supported through decreased seedling costs with increased areas planted with improved stock; and (3) strongly supported through an increase in log price premiums at harvest resulting from potentially better wood quality and higher volume production relative to TB-selected stock. The findings of this study highlight several important market and biophysical factors that forest managers should take into account when adopting biotechnology in forestry.
2. Sun S, Miao Z, Ratcliffe B, Campbell P, Pasch B, El-Kassaby YA, et al. (2019) SNP variable selection by generalized graph domination. PLoS ONE 14(1): e0203242. https://doi.org/10.1371/journal.pone.0203242
Background: High-throughput sequencing technology has revolutionized both medical and biological research by generating exceedingly large numbers of genetic variants. The resulting datasets share a number of common characteristics that might lead to poor generalization capacity. Concerns include noise accumulated due to the large number of predictors, sparse information regarding the p≫n problem, and overfitting and model mis-identification resulting from spurious collinearity. Additionally, complex correlation patterns are present among variables. As a consequence, reliable variable selection techniques play a pivotal role in predictive analysis, generalization capability, and robustness in clustering, as well as interpretability of the derived models.
Methods and findings: K-dominating set, a parameterized graph-theoretic generalization model, was used to model SNP (single nucleotide polymorphism) data as a similarity network and searched for representative SNP variables. In particular, each SNP was represented as a vertex in the graph, (dis)similarity measures such as correlation coefficients or pairwise linkage disequilibrium were estimated to describe the relationship between each pair of SNPs; a pair of vertices are adjacent, i.e. joined by an edge, if the pairwise similarity measure exceeds a user-specified threshold. A minimum k-dominating set in the SNP graph was then made as the smallest subset such that every SNP that is excluded from the subset has at least k neighbors in the selected ones. The strength of k-dominating set selection in identifying independent variables, and in culling representative variables that are highly correlated with others, was demonstrated by a simulated dataset. The advantages of k-dominating set variable selection were also illustrated in two applications: pedigree reconstruction using SNP profiles of 1,372 Douglas-fir trees, and species delineation for 226 grasshopper mouse samples. A C++ source code that implements SNP-SELECT and uses Gurobi optimization solver for the k-dominating set variable selection is available (https://github.com/transgenomicsosu/SNP-SELECT).
1. Chang, W.-Y., Wang, S., Gaston, C., Cool, J., An, H. and Thomas, B. 2019. Economic evaluations of tree improvement for planted forests: A systematic review. BioProducts Business: 4(1), 2019, pp 1-14. https://doi.org/10.22382/bpb-2019-001
This paper reviews the literature on the economic evaluations of tree improvement for planted forests and investigates whether or not using improved reforestation stock from tree improvement programs is a good investment. The main findings from systematic web-based searches show that (1) tree improvement is an effective tool to improve forest productivity and to realize financial returns; (2) economic gains from wood production with selection for breeding traits (e.g., high-volume yield or height growth) are the main reasons forest managers adopt new biotechnologies in tree improvement; (3) cost-benefit analysis is the primary empirical approach for estimating the economic effects of tree improvement for planted forests; and (4) there is very little literature on estimating the non-market benefits (e.g., improved watershed protection, amenities, or conservation of genetic diversity) that tree improvement brings, using non-market valuation techniques. The recent introduction of new biotechnologies in tree improvement, such as genomics-assisted tree breeding (GATB), can achieve genetic gains in selected traits more quickly and effectively than traditional breeding approaches, providing economic incentives for forest managers to use better quality stock for planted forests. Therefore, we suggest that future research should (1) consider the additional benefit, extra research and development costs, and time saved by applying new biotechnologies in tree improvement (e.g., GATB) in the cost-benefit analysis; (2) investigate the trade-offs between timber volume and wood quality traits and assess the economic effects of new biotechnologies in tree improvement along different stages of the forestry supply chain; and (3) explicitly account for the non-market trait values for the targeted breeding traits (e.g., drought/pest resistance) so that tree improvement programs can contribute to sustainable production systems. Economic analyses along these lines could help policy makers, forest managers, and forest company owners better understand the trade-offs of alternative breeding objectives and make economically efficient investment decisions for planted forests.