Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.).

The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.

The ectomycorrhizal fungus Paxillus ammoniavirescens influences the effects of salinity on loblolly pine in response to potassium availability.

Salinity is an increasing problem in coastal areas affected by saltwater intrusion, with deleterious effects on tree health and forest growth. Ectomycorrhizal (ECM) fungi may improve the salinity tolerance of host trees, but the impact of external potassium (K+ ) availability on these effects is still unclear. Here, we performed several experiments with the ECM fungus Paxillus ammoniavirescens and loblolly pine (Pinus taeda L.) in axenic and symbiotic conditions at limited or sufficient K+ and increasing sodium (Na+ ) concentrations. Growth rate, biomass, nutrient content, and K+ transporter expression levels were recorded for the fungus, and the colonization rate, root development parameters, biomass, and shoot nutrient accumulation were determined for mycorrhizal and non-mycorrhizal plants. P. ammoniavirescens was tolerant to high salinity, although growth and nutrient concentrations varied with K+ availability and increasing Na+ exposure. While loblolly pine root growth and development decreased with increasing salinity, ECM colonization was unaffected by pine response to salinity. The mycorrhizal influence on loblolly pine salinity response was strongly dependent on external K+ availability. This study reveals that P. ammoniavirescens can reduce Na+ accumulation of salt-exposed loblolly pine, but this effect depends on external K+ availability.

Increased leaf area index and efficiency drive enhanced production under elevated atmospheric [CO2 ] in a pine-dominated stand showing no progressive nitrogen limitation.

Enhancement of net primary production (NPP) in forests as atmospheric [CO2 ] increases is likely limited by the availability of other growth resources. The Duke Free Air CO2 Enrichment (FACE) experiment was located on a moderate-fertility site in the southeastern US, in a loblolly pine (Pinus taeda L.) plantation with broadleaved species growing mostly in mid-canopy and understory. Duke FACE ran from 1994 to 2010 and combined elevated [CO2 ] (eCO2 ) with nitrogen (N) additions. We assessed the spatial and temporal variation of NPP response using a dataset that includes previously unpublished data from 6 years of the replicated CO2 × N experiment and extends to 2 years beyond the termination of enrichment. Averaged over time (1997-2010), NPP of pine and broadleaved species were 38% and 52% higher under eCO2 compared to ambient conditions. Furthermore, there was no evidence of a decline in enhancement over time in any plot regardless of its native site quality. The relation between spatial variation in the response and native site quality was suggested but inconclusive. Nitrogen amendments under eCO2 , in turn, resulted in an additional 11% increase in pine NPP. For pine, the eCO2 -induced increase in NPP was similar above- and belowground and was driven by both increased leaf area index (L) and production efficiency (PE = NPP/L). For broadleaved species, coarse-root biomass production was more than 200% higher under eCO2 and accounted for the entire production response, driven by increased PE. Notably, the fraction of annual NPP retained in total living biomass was higher under eCO2 , reflecting a slight shift in allocation fraction to woody mass and a lower mortality rate. Our findings also imply that tree growth may not have been only N-limited, but perhaps constrained by the availability of other nutrients. The observed sustained NPP enhancement, even without N-additions, demonstrates no progressive N limitation.

Influence of juvenile wood proportion on density and modulus of elasticity in softwood boards for structural use: a preliminary study.

Juvenile wood (JW) can influence the performance of structural boards since it presents lower physical and mechanical properties. This study aimed evaluate the influence of JW proportion on density and modulus of elasticity (MOE) on boards for structural use. Pinus taeda logs 30 years old, had growth rings manually counted (on the pith to bark direction), and the first six rings were painted with color red (0-6), followed by blue (6.1-12), orange (12.1-18), green (18.1-24), and yellow (over 24.1), successively, and cut into boards. The proportion of each color was obtained by analysis of the transversal areas of boards with software. MOE was obtained by a nondestructive test. Multiple linear regression models were applied with 5% of significance. The estimated MOE indicates that boards with at least 57% of orange and green colors (between 12.1 - 24 years old) can achieve the minimum MOE value for using as structural as well as boards without red color but with the presence of green and yellow can have MOE bigger than 7000 MPa. The study indicates a behavior tendency about which proportion and mixed colors can affect the MOE of the board to be classified as structural.

Efficacy of four systemic insecticides for reducing Nantucket pine tip moth (Rhyaciona frustrana) (Lepidoptera: Tortricidae) infestation levels and improving growth metrics in loblolly pines.

The Nantucket pine tip moth (NPTM) (Rhyacionia frustrana Comstock) is a native, regeneration pest of young loblolly pines (Pinus taeda L.), causing shoot dieback, tree deformity, and growth and volume declines. Soil applications of systemic insecticides may be an effective strategy to suppress NPTM populations. The study objective was to assess the efficacy of four systemic insecticide treatments (chlorantraniliprole, dinotefuran, fipronil, and imidacloprid) for two growing seasons in outplanted bareroot and containerized seedling trials. Response variables included NPTM infestation rates, along with tree height, groundline diameter, volume index, and stem form. Infestation rates significantly decreased for each systemic insecticide treatment during the first year compared to controls, although dinotefuran and imidacloprid provided season-long control in one trial. Chlorantraniliprole reduced NPTM infestation rates for two growing seasons in both trials. While imidacloprid treatments did not alter growth metrics except for one comparison, fipronil and dinotefuran treatments improved several growth metrics. Chlorantraniliprole consistently improved growth metrics throughout the study.

Dirt cheap: an experimental test of controls on resource exchange in an ectomycorrhizal symbiosis.

To distinguish among hypotheses on the importance of resource-exchange ratios in outcomes of mutualisms, we measured resource (carbon (C), nitrogen (N), and phosphorus (P)) transfers and their ratios, between Pinus taeda seedlings and two ectomycorrhizal (EM) fungal species, Rhizopogon roseolus and Pisolithus arhizus in a laboratory experiment. We evaluated how ambient light affected those resource fluxes and ratios over three time periods (10, 20, and 30 wk) and the consequences for plant and fungal biomass accrual, in environmental chambers. Our results suggest that light availability is an important factor driving absolute fluxes of N, P, and C, but not exchange ratios, although its effects vary among EM fungal species. Declines in N : C and P : C exchange ratios over time, as soil nutrient availability likely declined, were consistent with predictions of biological market models. Absolute transfer of P was an important predictor of both plant and fungal biomass, consistent with the excess resource-exchange hypothesis, and N transfer to plants was positively associated with fungal biomass. Altogether, light effects on resource fluxes indicated mixed support for various theoretical frameworks, while results on biomass accrual better supported the excess resource-exchange hypothesis, although among-species variability is in need of further characterization.

Analysis of the ASR and LP3 homologous gene families reveal positive selection acting on LP3-3 gene.

Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.

Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda).

Biological ageing is connected to life history variation across ecological scales and informs a basic understanding of age-related declines in organismal function. Altered DNA methylation dynamics are a conserved aspect of biological ageing and have recently been modelled to predict chronological age among vertebrate species. In addition to their utility in estimating individual age, differences between chronological and predicted ages arise due to acceleration or deceleration of epigenetic ageing, and these discrepancies are linked to disease risk and multiple life history traits. Although evidence suggests that patterns of DNA methylation can describe ageing in plants, predictions with epigenetic clocks have yet to be performed. Here, we resolve the DNA methylome across CpG, CHG, and CHH-methylation contexts in the loblolly pine tree (Pinus taeda) and construct epigenetic clocks capable of predicting ages in this species within 6% of its maximum lifespan. Although patterns of CHH-methylation showed little association with age, both CpG and CHG-methylation contexts were strongly associated with ageing, largely becoming hypomethylated with age. Among age-associated loci were those in close proximity to malate dehydrogenase, NADH dehydrogenase, and 18S and 26S ribosomal RNA genes. This study reports one of the first epigenetic clocks in plants and demonstrates the universality of age-associated DNA methylation dynamics which can inform conservation and management practices, as well as our ecological and evolutionary understanding of biological ageing in plants.

Spatial Distribution and Retention in Loblolly Pine Seedlings of Exogenous dsRNAs Applied through Roots.

Exogenously applied double-stranded RNA (dsRNA) can induce potent host specific gene knockdown and mortality in insects. The deployment of RNA-interference (RNAi) technologies for pest suppression is gaining traction in both agriculture and horticulture, but its implementation in forest systems is lagging. While numerous forest pests have demonstrated susceptibility to RNAi mediated gene silencing, including the southern pine beetle (SPB), Dendroctonus frontalis, multiple barriers stand between laboratory screening and real-world deployment. One such barrier is dsRNA delivery. One possible delivery method is through host plants, but an understanding of exogenous dsRNA movement through plant tissues is essential. Therefore, we sought to understand the translocation and persistence of dsRNAs designed for SPB throughout woody plant tissues after hydroponic exposure. Loblolly pine, Pinus taeda, seedlings were exposed to dsRNAs as a root soak, followed by destructive sampling. Total RNA was extracted from different tissue types including root, stem, crown, needle, and meristem, after which gel electrophoresis confirmed the recovery of the exogenous dsRNAs, which were further verified using Sanger sequencing. Both techniques confirmed the presence of the exogenously applied target dsRNAs in each tissue type after 1, 3, 5, and 7 d of dsRNA exposure. These findings suggest that root drench applications of exogenous dsRNAs could provide a viable delivery route for RNAi technology designed to combat tree feeding pests.

Beyond carbon flux partitioning: Carbon allocation and nonstructural carbon dynamics inferred from continuous fluxes.

Carbon (C) allocation and nonstructural carbon (NSC) dynamics play essential roles in plant growth and survival under stress and disturbance. However, quantitative understanding of these processes remains limited. Here we propose a framework where we connect commonly measured carbon cycle components (eddy covariance fluxes of canopy CO2 exchange, soil CO2 efflux, and allometry-based biomass and net primary production) by a simple mass balance model to derive ecosystem-level NSC dynamics (NSCi ), C translocation (dCi ), and the biomass production efficiency (BPEi ) in above- and belowground plant (i = agp and bgp) compartments. We applied this framework to two long-term monitored loblolly pine (Pinus taeda) plantations of different ages in North Carolina and characterized the variations of NSC and allocation in years under normal and drought conditions. The results indicated that the young stand did not have net NSC flux at the annual scale, whereas the mature stand stored a near-constant proportion of new assimilates as NSC every year under normal conditions, which was comparable in magnitude to new structural growth. Roots consumed NSC in drought and stored a significant amount of NSC post drought. The above- and belowground dCi and BPEi varied more from year to year in the young stand and approached a relatively stable pattern in the mature stand. The belowground BPEbgp differed the most between the young and mature stands and was most responsive to drought. With the internal C dynamics quantified, this framework may also improve biomass production estimation, which reveals the variations resulting from droughts. Overall, these quantified ecosystem-scale dynamics were consistent with existing evidence from tree-based manipulative experiments and measurements and demonstrated that combining the continuous fluxes as proposed here can provide additional information about plant internal C dynamics. Given that it is based on broadly available flux data, the proposed framework is promising to improve the allocation algorithms in ecosystem C cycle models and offers new insights into observed variability in soil-plant-climate interactions.

Spatial variability in tree-ring carbon isotope discrimination in response to local drought across the entire loblolly pine natural range.

Considering the temporal responses of carbon isotope discrimination (Δ13C) to local water availability in the spatial analysis of Δ13C is essential for evaluating the contribution of environmental and genetic facets of plant Δ13C. Using tree-ring Δ13C from years with contrasting water availability at 76 locations across the natural range of loblolly pine, we decomposed site-level Δ13C signals to maximum Δ13C in well-watered conditions (Δ13Cmax) and isotopic drought sensitivity (m) as a change in Δ13C per unit change of Palmer's Drought Severity Index (PDSI). Site water status, especially the tree lifetime average PDSI, was the primary factor affecting Δ13Cmax. The strong spatial correlation exhibited by m was related to both genetic and environmental factors. The long-term average water availability during the period relevant to trees as indicated by lifetime average PDSI correlated with Δ13Cmax, suggesting acclimation in tree gas-exchange traits, independent of incident water availability. The positive correlation between lifetime average PDSI and m indicated that loblolly pines were more sensitive to drought at mesic than xeric sites. The m was found to relate to a plant's stomatal control and may be employed as a genetic indicator of efficient water use strategies. Partitioning Δ13C to Δ13Cmax and m provided a new angle for understanding sources of variation in plant Δ13C, with several fundamental and applied implications.

Improving the representation of forests in hydrological models.

Forests play a critical role in the hydrologic cycle, impacting the surface and groundwater dynamics of watersheds through transpiration, interception, shading, and modification of the atmospheric boundary layer. It is therefore critical that forest dynamics are adequately represented in watershed models, such as the widely applied Soil and Water Assessment Tool (SWAT). SWAT's default parameterization generally produces unrealistic forest growth predictions, which we address here through an improved representation of forest dynamics using species-specific re-parameterizations. We applied this methodology to the two dominant pine species in the southeastern U.S., loblolly pine (Pinus taeda L.) and slash pine (Pinus elliotti). Specifically, we replaced unrealistic parameter values related to tree growth with physically meaningful parameters derived from publicly available remote-sensing products, field measurements, published literature, and expert knowledge. Outputs of the default and re-parameterized models were compared at four pine plantation sites across a range of management, soil, and climate conditions. Results were validated against MODIS-derived leaf area index (LAI) and evapotranspiration (ET), as well as field observations of total biomass. The re-parameterized model outperformed the default model in simulating LAI, biomass accumulation, and ET at all sites. The two parametrizations also resulted in substantially different mean annual water budgets for all sites, with reductions in water yield ranging from 13 to 45% under the new parameterization, highlighting the importance of properly parameterizing forest dynamics in watershed models. Importantly, our re-parameterization methodology does not require alteration to the SWAT code, allowing it to be readily adapted and applied in ongoing and future watershed modeling studies.

The response of coarse root biomass to long-term CO2 enrichment and nitrogen application in a maturing Pinus taeda stand with a large broadleaved component.

Elevated atmospheric CO2 (eCO2 ) typically increases aboveground growth in both growth chamber and free-air carbon enrichment (FACE) studies. Here we report on the impacts of eCO2 and nitrogen amendment on coarse root biomass and net primary productivity (NPP) at the Duke FACE study, where half of the eight plots in a 30-year-old loblolly pine (Pinus taeda, L.) plantation, including competing naturally regenerated broadleaved species, were subjected to eCO2 (ambient, aCO2 plus 200 ppm) for 15-17 years, combined with annual nitrogen amendments (11.2 g N m-2 ) for 6 years. Allometric equations were developed following harvest to estimate coarse root (>2 mm diameter) biomass. Pine root biomass under eCO2 increased 32%, 1.80 kg m-2 above the 5.66 kg m-2 observed in aCO2 , largely accumulating in the top 30 cm of soil. In contrast, eCO2 increased broadleaved root biomass more than twofold (aCO2 : 0.81, eCO2 : 2.07 kg m-2 ), primarily accumulating in the 30-60 cm soil depth. Combined, pine and broadleaved root biomass increased 3.08 kg m-2 over aCO2 of 6.46 kg m-2 , a 48% increase. Elevated CO2 did not increase pine root:shoot ratio (average 0.24) but increased the ratio from 0.57 to 1.12 in broadleaved species. Averaged over the study (1997-2010), eCO2 increased pine, broadleaved and total coarse root NPP by 49%, 373% and 86% respectively. Nitrogen amendment had smaller effects on any component, singly or interacting with eCO2 . A sustained increase in root NPP under eCO2 over the study period indicates that soil nutrients were sufficient to maintain root growth response to eCO2 . These responses must be considered in computing coarse root carbon sequestration of the extensive southern pine and similar forests, and in modelling the responses of coarse root biomass of pine-broadleaved forests to CO2 concentration over a range of soil N availability.

NLR diversity and candidate fusiform rust resistance genes in loblolly pine.

Resistance to fusiform rust disease in loblolly pine (Pinus taeda) is a classic gene-for-gene system. Early resistance gene mapping in the P. taeda family 10-5 identified RAPD markers for a major fusiform rust resistance gene, Fr1. More recently, single nucleotide polymorphism (SNP) markers associated with resistance were mapped to a full-length gene model in the loblolly pine genome encoding for a nucleotide-binding site leucine-rich repeat (NLR) protein. NLR genes are one of the most abundant gene families in plant genomes and are involved in effector-triggered immunity. Inter- and intraspecies studies of NLR gene diversity and expression have resulted in improved disease resistance. To characterize NLR gene diversity and discover potential resistance genes, we assembled de novo transcriptomes from 92 loblolly genotypes from across the natural range of the species. In these transcriptomes, we identified novel NLR transcripts that are not present in the loblolly pine reference genome and found significant geographic diversity of NLR genes providing evidence of gene family evolution. We designed capture probes for these NLRs to identify and map SNPs that stably cosegregate with resistance to the SC20-21 isolate of Cronartium quercuum f.sp. fusiforme (Cqf) in half-sib progeny of the 10-5 family. We identified 10 SNPs and 2 quantitative trait loci associated with resistance to SC20-21 Cqf. The geographic diversity of NLR genes provides evidence of NLR gene family evolution in loblolly pine. The SNPs associated with rust resistance provide a resource to enhance breeding and deployment of resistant pine seedlings.

Prediction ability of genome-wide markers in Pinus taeda L. within and between population is affected by relatedness to the training population and trait genetic architecture.

Genomic prediction has the potential to significantly increase the rate of genetic gain in tree breeding programs. In this study, a clonally replicated population (n = 2063) was used to train a genomic prediction model. The model was validated both within the training population and in a separate population (n = 451). The prediction abilities from random (20% vs 80%) cross validation within the training population were 0.56 and 0.78 for height and stem form, respectively. Removal of all full-sib relatives within the training population resulted in ∼50% reduction in their genomic prediction ability for both traits. The average prediction ability for all 451 individual trees was 0.29 for height and 0.57 for stem form. The degree of genetic linkage (full-sib family, half sib family, unrelated) between the training and validation sets had a strong impact on prediction ability for stem form but not for height. A dominant dwarfing allele, the first to be reported in a conifer species, was discovered via genome-wide association studies on linkage Group 5 that conferred a 0.33-m mean height reduction. However, the QTL was family specific. The rapid decay of linkage disequilibrium, large genome size, and inconsistencies in marker-QTL linkage phase suggest that large, diverse training populations are needed for genomic selection in Pinus taeda L.

Effect of Loblolly Pine (Pinus taeda L.) Hemicellulose Structure on the Properties of Hemicellulose-Polyvinyl Alcohol Composite Film.

Hemicellulose is the second most abundant natural polysaccharide and a promising feedstock for biomaterial synthesis. In the present study, the hemicellulose of loblolly pine was obtained by the alkali extraction-graded ethanol precipitation technique, and the hemicellulose-polyvinyl alcohol (hemicellulose-PVA) composite film was prepared by film casting from water. Results showed that hemicellulose with a low degree of substitution is prone to self-aggregation during film formation, while hemicellulose with high branching has better compatibility with PVA and is easier to form a homogeneous composite film. In addition, the higher molecular weight of hemicellulose facilitates the preparation of hemicellulose-PVA composite film with better mechanical properties. More residual lignin in hemicellulose results in the better UV shielding ability of the composite film. This study provides essential support for the efficient and rational utilization of hemicellulose.

Genomic prediction for fusiform rust disease incidence in a large cloned population of Pinus taeda.

In this study, 723 Pinus taeda L. (loblolly pine) clonal varieties genotyped with 16920 SNP markers were used to evaluate genomic selection for fusiform rust disease caused by the fungus Cronartium quercuum f. sp. fusiforme. The 723 clonal varieties were from five full-sib families. They were a subset of a larger population (1831 clonal varieties), field-tested across 26 locations in the southeast US. Ridge regression, Bayes B, and Bayes Cπ models were implemented to study marker-trait associations and estimate predictive ability for selection. A cross-validation scenario based on a random sampling of 80% of the clonal varieties for the model building had higher (0.71-0.76) prediction accuracies of genomic estimated breeding values compared with family and within-family cross-validation scenarios. Random sampling within families for model training to predict genomic estimated breeding values of the remaining progenies within each family produced accuracies between 0.38 and 0.66. Using four families out of five for model training was not successful. The results showed the importance of genetic relatedness between the training and validation sets. Bayesian whole-genome regression models detected three QTL with large effects on the disease outcome, explaining 54% of the genetic variation in the trait. The significance of QTL was validated with GWAS while accounting for the population structure and polygenic effect. The odds of disease incidence for heterozygous AB genotypes were 10.7 and 12.1 times greater than the homozygous AA genotypes for SNP11965 and SNP6347 loci, respectively. Genomic selection for fusiform rust disease incidence could be effective in P. taeda breeding. Markers with large effects could be fit as fixed covariates to increase the prediction accuracies, provided that their effects are validated further.

Benefits provided by four ectomycorrhizal fungi to Pinus taeda under different external potassium availabilities.

Ectomycorrhizal fungi contribute to the nutrition of many woody plants, including those in the Pinaceae family. Loblolly pine (Pinus taeda L.), a native species of the Southeastern USA, can be colonized by multiple species of ectomycorrhizal fungi. The role of these symbionts in P. taeda potassium (K+) nutrition has not been previously investigated. Here, we assessed the contribution of four ectomycorrhizal fungi, Hebeloma cylindrosporum, Paxillus ammoniavirescens, Laccaria bicolor, and Suillus cothurnatus, in P. taeda K+ acquisition under different external K+ availabilities. Using a custom-made two-compartment system, P. taeda seedlings were inoculated with one of the four fungi, or kept non-colonized, and grown under K+-limited or -sufficient conditions for 8 weeks. Only the fungi had access to separate compartments in which rubidium, an analog tracer for K+, was supplied before harvest. Resulting effects of the fungi were recorded, including root colonization, biomass, and nutrient concentrations. We also analyzed the fungal performance in axenic conditions under varying supply of K+ and sodium. Our study revealed that these four ectomycorrhizal fungi are differentially affected by external K+ and sodium variations, that they are not able to provide similar benefits to the host P. taeda in our growing conditions, and that rubidium may be used with some limitations to estimate K+ transport from ectomycorrhizal fungi to colonized plants.

Coarse Woody Debris Decomposition Assessment Tool: Model validation and application.

Coarse woody debris (CWD) is a significant component of the forest biomass pool; hence a model is warranted to predict CWD decomposition and its role in forest carbon (C) and nutrient cycling under varying management and climatic conditions. A process-based model, CWDDAT (Coarse Woody Debris Decomposition Assessment Tool) was calibrated and validated using data from the FACE (Free Air Carbon Dioxide Enrichment) Wood Decomposition Experiment utilizing pine (Pinus taeda), aspen (Populous tremuloides) and birch (Betula papyrifera) on nine Experimental Forests (EF) covering a range of climate, hydrology, and soil conditions across the continental USA. The model predictions were evaluated against measured FACE log mass loss over 6 years. Four widely applied metrics of model performance demonstrated that the CWDDAT model can accurately predict CWD decomposition. The R2 (squared Pearson's correlation coefficient) between the simulation and measurement was 0.80 for the model calibration and 0.82 for the model validation (P<0.01). The predicted mean mass loss from all logs was 5.4% lower than the measured mass loss and 1.4% lower than the calculated loss. The model was also used to assess the decomposition of mixed pine-hardwood CWD produced by Hurricane Hugo in 1989 on the Santee Experimental Forest in South Carolina, USA. The simulation reflected rapid CWD decomposition of the forest in this subtropical setting. The predicted dissolved organic carbon (DOC) derived from the CWD decomposition and incorporated into the mineral soil averaged 1.01 g C m-2 y-1 over the 30 years. The main agents for CWD mass loss were fungi (72.0%) and termites (24.5%), the remainder was attributed to a mix of other wood decomposers. These findings demonstrate the applicability of CWDDAT for large-scale assessments of CWD dynamics, and fine-scale considerations regarding the fate of CWD carbon.

Major QTL confer race-nonspecific resistance in the co-evolved Cronartium quercuum f. sp. fusiforme-Pinus taeda pathosystem.

Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. Unlike the major epidemics of agricultural crops, the co-evolved pine-rust pathosystem is characterized by steady-state dynamics and high levels of genetic diversity within environments. This poses a unique challenge and opportunity for the deployment of large-effect resistance genes. We used trait dissection to study the genetic architecture of disease resistance in two P. taeda parents that showed high resistance across multiple environments. Two mapping populations (full-sib families), each with ~1000 progeny, were challenged with a complex inoculum consisting of 150 pathogen isolates. High-density linkage mapping revealed three major-effect QTL distributed on two linkage groups. All three QTL were validated using a population of 2057 cloned pine genotypes in a 6-year-old multi-environmental field trial. As a complement to the QTL mapping approach, bulked segregant RNAseq analysis revealed a small number of candidate nucleotide binding leucine-rich repeat genes harboring SNP associated with disease resistance. The results of this study show that in P. taeda, a small number of major QTL can provide effective resistance against genetically diverse mixtures of an endemic pathogen. These QTL vary in their impact on disease liability and exhibit additivity in combination.