Genomic prediction is used to parameterize canopy growth of a process-based whole-plant model. The updated model formalizes components of genotype by environment interaction (G×E).
Abstract
Dynamic ...process-based plant models capture complex physiological response across time, carrying the potential to extend simulations out to novel environments and lend mechanistic insight to observed phenotypes. Despite the translational opportunities for varietal crop improvement that could be unlocked by linking natural genetic variation to first principles-based modeling, these models are challenging to apply to large populations of related individuals. Here we use a combination of model development, experimental evaluation, and genomic prediction in Brassica rapa L. to set the stage for future large-scale process-based modeling of intraspecific variation. We develop a new canopy growth submodel for B. rapa within the process-based model Terrestrial Regional Ecosystem Exchange Simulator (TREES), test input parameters for feasibility of direct estimation with observed phenotypes across cultivated morphotypes and indirect estimation using genomic prediction on a recombinant inbred line population, and explore model performance on an in silico population under non-stressed and mild water-stressed conditions. We find evidence that the updated whole-plant model has the capacity to distill genotype by environment interaction (G×E) into tractable components. The framework presented offers a means to link genetic variation with environment-modulated plant response and serves as a stepping stone towards large-scale prediction of unphenotyped, genetically related individuals under untested environmental scenarios.
Mountain pine beetle outbreaks in western North America have led to extensive forest mortality, justifiably generating interest in improving our understanding of how this type of ecological ...disturbance affects hydrological cycles. While observational studies and simulations have been used to elucidate the effects of mountain beetle mortality on hydrological fluxes, an ecologically mechanistic model of forest evapotranspiration (ET) evaluated against field data has yet to be developed. In this work, we use the Terrestrial Regional Ecosystem Exchange Simulator (TREES) to incorporate the ecohydrological impacts of mountain pine beetle disturbance on ET for a lodgepole pine‐dominated forest equipped with an eddy covariance tower. An existing degree‐day model was incorporated that predicted the life cycle of mountain pine beetles, along with an empirically derived submodel that allowed sap flux to decline as a function of temperature‐dependent blue stain fungal growth. The eddy covariance footprint was divided into multiple cohorts for multiple growing seasons, including representations of recently attacked trees and the compensatory effects of regenerating understory, using two different spatial scaling methods. Our results showed that using a multiple cohort approach matched eddy covariance‐measured ecosystem‐scale ET fluxes well, and showed improved performance compared to model simulations assuming a binary framework of only areas of live and dead overstory. Cumulative growing season ecosystem‐scale ET fluxes were 8 – 29% greater using the multicohort approach during years in which beetle attacks occurred, highlighting the importance of including compensatory ecological mechanism in ET models.
Key Points
Evapotranspiration in a forest impacted by beetle disturbance is modeled using ecological mechanisms and evaluated against field data
Simulations incorporated beetle life cycle, fungal growth, and xylem occlusion in trees, as well as a regenerating understory
The multicohort approach showed improved performance over simulations that assumed only live and dead overstory
The year 2015 marks the 50th anniversary of Water Resources Research (WRR), which was founded in 1965. More than 15,000 papers have been published in WRR since its inception, and these papers have ...been cited more than 430,000 times. The history of hydrology and the water sciences are also reflected in WRR, which has served as a premier publication outlet and instigator of scientific growth over the last 50 years. The legacy of WRR provides a strong scientific foundation for the hydrology community to rise to the challenges of sustainable water resources management in a future where dramatic environmental change and increasing human population are expected to stress the world's water resources from local to global scales.
Key Points:
History of Water Resources Research
Research trends in hydrology over the last 50 years
Some bibliometrics of Water Resources Research
This study compares eddy‐covariance measurements of carbon dioxide fluxes at six northern temperate and boreal peatland sites in Canada and the northern United States of America, representing both ...bogs and fens. The two peatland types had opposite responses of gross ecosystem photosynthesis (GEP) and ecosystem respiration (ER) to inter‐annual fluctuations in water table level. At fens, wetter conditions were correlated with lower GEP and ER, while at bogs wetter conditions were correlated with higher GEP and ER. We hypothesize that these contrasting responses are due to differences in the relative contributions of vascular plants and mosses. The coherence of our results between sites representing a range of average environmental conditions indicates ecosystem‐scale differences in resilience to hydrological changes that should be taken into account when considering the future of peatland ecosystem services such as carbon sequestration under changing environmental conditions.
Model–data comparisons of plant physiological processes provide an understanding of mechanisms underlying vegetation responses to climate. We simulated the physiology of a piñon pine–juniper woodland ...(Pinus edulis–Juniperus monosperma) that experienced mortality during a 5 yr precipitation-reduction experiment, allowing a framework with which to examine our knowledge of drought-induced tree mortality. We used six models designed for scales ranging from individual plants to a global level, all containing state-of-the-art representations of the internal hydraulic and carbohydrate dynamics of woody plants. Despite the large range of model structures, tuning, and parameterization employed, all simulations predicted hydraulic failure and carbon starvation processes co-occurring in dying trees of both species, with the time spent with severe hydraulic failure and carbon starvation, rather than absolute thresholds per se, being a better predictor of impending mortality. Model and empirical data suggest that limited carbon and water exchanges at stomatal, phloem, and below-ground interfaces were associated with mortality of both species. The model–data comparison suggests that the introduction of a mechanistic process into physiology-based models provides equal or improved predictive power over traditional process-model or empirical thresholds. Both biophysical and empirical modeling approaches are useful in understanding processes, particularly when the models fail, because they reveal mechanisms that are likely to underlie mortality. We suggest that for some ecosystems, integration of mechanistic pathogen models into current vegetation models, and evaluation against observations, could result in a breakthrough capability to simulate vegetation dynamics.
With the increased practice of preventative healthcare to help reduce costs worldwide, sensor technology improvement is vital to patient care. Point-of-care (POC) diagnostics can reduce time and ...lower labor in testing, and can effectively avoid transporting costs because of portable designs. Label-free detection allows for greater versatility in the detection of biological molecules. Here, we describe the use of an impedance-based POC biosensor that can detect changes in the surface modification of a micro-fabricated chip using impedance spectroscopy. Gold nanoparticles (GNPs) have been employed to evaluate the sensing ability of our new chip using impedance measurements. Furthermore, we used impedance measurements to monitor surface functionalization progress on the sensor's interdigitated electrodes (IDEs). Electrodes made from aluminum and gold were employed and the results were analyzed to compare the impact of electrode material. GNPs coated with mercaptoundecanoic acid were also used as a model of biomolecules to greatly enhance chemical affinity to the silicon substrate. The portable sensor can be used as an alternative technology to ELISA (enzyme-linked immunosorbent assays) and polymerase chain reaction (PCR)-based techniques. This system has advantages over PCR and ELISA both in the amount of time required for testing and the ease of use of our sensor. With other techniques, larger, expensive equipment must be utilized in a lab environment, and procedures have to be carried out by trained professionals. The simplicity of our sensor system can lead to an automated and portable sensing system.
Agronomists have used statistical crop models to predict yield on a genotype-by-genotype basis. Mechanistic models, based on fundamental physiological processes common across plant taxa, will ...ultimately enable yield prediction applicable to diverse genotypes and crops. Here, genotypic information is combined with multiple mechanistically based models to characterize photosynthetic trait differentiation among genotypes of
. Infrared leaf gas exchange and chlorophyll fluorescence observations are analyzed using Bayesian methods. Three advantages of Bayesian approaches are employed: a hierarchical model structure, the testing of parameter estimates with posterior predictive checks and a multimodel complexity analysis. In all, eight models of photosynthesis are compared for fit to data and penalized for complexity using deviance information criteria (DIC) at the genotype scale. The multimodel evaluation improves the credibility of trait estimates using posterior distributions. Traits with important implications for yield in crops, including maximum rate of carboxylation (
) and maximum rate of electron transport (
) show genotypic differentiation.
shows phenotypic diversity in causal traits with the potential for genetic enhancement of photosynthesis. This multimodel screening represents a statistically rigorous method for characterizing genotypic differences in traits with clear biophysical consequences to growth and productivity within large crop breeding populations with application across plant processes.
Appreciation of peer reviewers for 2015 Montanari, Alberto; Bahr, Jean; Blöschl, Günter ...
Water resources research,
April 2016, Letnik:
52, Številka:
4
Journal Article
Recenzirano
Odprti dostop
On behalf of the journal, AGU, and the scientific community, the editors would like to sincerely thank those who reviewed manuscripts for Water Resources Research in 2015. The hours reading and ...commenting on manuscripts not only improves the manuscripts themselves but it also increases the scientific rigor of future research in the field. Many of those listed below went beyond and reviewed three or more manuscripts for our journal, and those are indicated in italics. The refereeing contributions they made contributed to 3622 individual reviews of 1434 manuscripts. Thank you again. We look forward to a 2016 of exciting advances in the field and communicating those advances to our community and to the broader public.
Scaling transpiration from trees to larger areas is a fundamental problem in ecohydrology. For scaling stand transpiration from sap flux sensors we asked if plot representativeness depended on plot ...size and location, the magnitude of environmental drivers, parameter needs for ecosystem models, and whether the goal was to estimate transpiration per unit ground area (EC), per unit leaf area (EL), or canopy stomatal conductance (GS). Sap flux data were collected in 108 trees with heat dissipation probes, and biometric properties were measured for 752 trees within a 1.44 ha Populus tremuloides stand along an upland‐to‐wetland gradient. EC was estimated for the stand using eight different plot sizes spanning a radius of 2.0–12.0 m. Each estimate of EC was derived from 200 plots placed randomly throughout the stand. We also derived leaf area index (L), canopy closure (PCC), and the canopy average reference stomatal conductance (GSref), which are key parameters used in modeling transpiration and evapotranspiration. With increasing plot size, EC declined monotonically but EL and GSref were largely invariant. Interplot variance of EC also declined with increasing plot size, at a rate that was independent of vapor pressure deficit. Plot representativeness was dependent on location within the stand. Scaling to the stand required three plots spanning the upland to wetland, with one to at most 10 trees instrumented for sap flux. Plots that were chosen to accurately reflect the spatial covariation of L, PCC, and GSref were most representative of the stand.
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