Environment-Specific Genomic Prediction Ability in Maize Using Environmental Covariates Depends on Environmental Similarity To Training Data

Technology advances have made possible the collection of a wealth of genomic, environmental, and phenotypic data for use in plant breeding. Incorporation of environmental data into environment-specific genomic prediction (GP) is hindered in part because of inherently high data dimensionality. Computationally efficient approaches to combining genomic and environmental information may facilitate extension of GP models to new environments and germplasm, and better understanding of genotype-by-environment (G × E) interactions. Using genomic, yield trial, and environmental data on 1,918 unique hybrids evaluated in 59 environments from the maize Genomes to Fields project, we determined that a set of 10,153 SNP dominance coefficients and a 5-day temporal window size for summarizing environmental variables were optimal for GP using only genetic and environmental main effects. Adding marker-by-environment variable interactions required dimension reduction, and we found that reducing dimensionality of the genetic data while keeping the full set of environmental covariates was best for environment-specific GP of grain yield, leading to an increase in prediction ability of 2.7% to achieve a prediction ability of 80% across environments when data were masked at random. We then measured how prediction ability within environments was affected under stratified training-testing sets to approximate scenarios commonly encountered by plant breeders, finding that incorporation of marker-by-environment effects improved prediction ability in cases where training and test sets shared environments, but did not improve prediction in new untested environments. The environmental similarity between training and testing sets had a greater impact on the efficacy of prediction than genetic similarity between training and test sets.

Combining Therapeutic Drug Monitoring and Pharmacokinetic Modelling Deconvolutes Physiological and Environmental Sources of Variability in Clozapine Exposure

Background: Clozapine is a key antipsychotic drug for treatment-resistant schizophrenia but exhibits highly variable pharmacokinetics and a propensity for serious adverse effects. Currently, these challenges are addressed using therapeutic drug monitoring (TDM). This study primarily sought to (i) verify the importance of covariates identified in a prior clozapine population pharmacokinetic (popPK) model in the absence of environmental covariates using physiologically based pharmacokinetic (PBPK) modelling, and then to (ii) evaluate the performance of the popPK model as an adjunct or alternative to TDM-guided dosing in an active TDM population. Methods: A popPK model incorporating age, metabolic activity, sex, smoking status and weight was applied to predict clozapine trough concentrations (Cmin) in a PBPK-simulated population and an active TDM population comprising 142 patients dosed to steady state at Flinders Medical Centre in Adelaide, South Australia. Post hoc analyses were performed to deconvolute the impact of physiological and environmental covariates in the TDM population. Results: Analysis of PBPK simulations confirmed age, cytochrome P450 1A2 activity, sex and weight as physiological covariates associated with variability in clozapine Cmin (R2 = 0.7698; p = 0.0002). Prediction of clozapine Cmin using a popPK model based on these covariates accounted for <5% of inter-individual variability in the TDM population. Post hoc analyses confirmed that environmental covariates accounted for a greater proportion of the variability in clozapine Cmin in the TDM population. Conclusions: Variability in clozapine exposure was primarily driven by environmental covariates in an active TDM population. Pharmacokinetic modelling can be used as an adjunct to TDM to deconvolute sources of variability in clozapine exposure.

Ecology of Gamebirds in Namha National Protected Area, Lao People’s Democratic Republic

Using camera-trap data, we describe the ecology and occupancy of several species of gamebirds while assessing associations at Namha National Protected Area (Lao People’s Democratic Republic). We detected three species of Arborophila Partridges, albeit in low numbers. Red Junglefowl Gallus gallus show typical diurnal activity, and we provide a record of a male–female pair commensally associated with a boar Sus scrofa. Silver Pheasants Lophura nycthemera have sex ratios slightly favoring females, and are mostly solitary; we provide novel findings of male age structure and rectrix molt. Gray Peacock Pheasants Polyplectron bicalcaratum sex ratios also favor females; males are recorded displaying as early as late February, while daily activity is somewhat bimodal, and we provide novel findings of male age structure. Analysis of the association between occupancy and 14 environmental covariates indicated that Silver Pheasant and Gray Peacock-Pheasant were associated with rougher terrain, and Red Junglefowl had higher occupancy far from well-groomed trails used for tourism. We discuss our results by comparing and contrasting our findings with other studies, and consider implications for conservation in the region.

Ground Observations and Environmental Covariates Integration for Mapping of Soil Salinity: A Machine Learning-Based Approach

Soil salinization is a severe danger to agricultural activity in arid and semi-arid areas, reducing crop production and contributing to land destruction. This investigation aimed to utilize machine learning algorithms to predict spatial soil salinity (dS m−1) by combining environmental covariates derived from remotely sensed (RS) data, a digital elevation model (DEM), and proximal sensing (PS). The study is located in an arid region, southern Iran (52°51′–53°02′E; 28°16′–28°29′N), in which we collected 300 surface soil samples and acquired the spectral data with RS (Sentinel-2) and PS (electromagnetic induction instrument (EMI) and portable X-ray fluorescence (pXRF)). Afterward, we analyzed the data using five machine learning methods as follows: random forest—RF, k-nearest neighbors—kNN, support vector machines—SVM, partial least squares regression—PLSR, artificial neural networks—ANN, and the ensemble of individual models. To estimate the electrical conductivity of the saturated paste extract (ECe), we built three scenarios, including Scenario (1): Synthetic Soil Image (SySI) bands and salinity indices derived from it; Scenario (2): RS data, PS data, topographic attributes, and geology and geomorphology maps; and Scenario (3): the combination of Scenarios (1) and (2). The best prediction accuracy was obtained for the RF model in Scenario (3) (R2 = 0.48 and RMSE = 2.49), followed by Scenario (2) (RF model, R2 = 0.47 and RMSE = 2.50) and Scenario (1) for the SVM model (R2 = 0.26 and RMSE = 2.97). According to ensemble modeling, a combined strategy with the five models exceeded the performance of all the single ones and predicted soil salinity in all scenarios. The results revealed that the ensemble modeling method had higher reliability and more accurate predictive soil salinity than the individual approach. Relative improvement (RI%) showed that the R2 index in the ensemble model improved compared to the most precise prediction for the Scenarios (1), (2), and (3) with 120.95%, 56.82%, and 66.71%, respectively. We applied the best model in each scenario for mapping the soil salinity in the selected area, which indicated that ECe tended to increase from the northwestern to south and southeastern regions. The area with high ECe was located in the regions that mainly had low elevations and playa. The areas with low ECe were located in the higher elevations with steeper slopes and alluvial fans, and thus, relief had great importance. This study provides a precise, cost-effective, and scientific base prediction for decision-making purposes to map soil salinity in arid regions.

Novel Tools for Adjusting Spatial Variability in the Early Sugarcane Breeding Stage

The detection of spatial variability in field trials has great potential for accelerating plant breeding progress due to the possibility of better controlling non-genetic variation. Therefore, we aimed to evaluate a digital soil mapping approach and a high-density soil sampling procedure for identifying and adjusting spatial dependence in the early sugarcane breeding stage. Two experiments were conducted in regions with different soil classifications. High-density sampling of soil physical and chemical properties was performed in a regular grid to investigate the structure of spatial variability. Soil apparent electrical conductivity (ECa) was measured in both experimental areas with an EM38-MK2® sensor. In addition, principal component analysis (PCA) was employed to reduce the dimensionality of the physical and chemical soil data sets. After conducting the PCA and obtaining different thematic maps, we determined each experimental plot’s exact position within the field. Tons of cane per hectare (TCH) data for each experiment were obtained and analyzed using mixed linear models. When environmental covariates were considered, a previous forward model selection step was applied to incorporate the variables. The PCA based on high-density soil sampling data captured part of the total variability in the data for Experimental Area 1 and was suggested to be an efficient index to be incorporated as a covariate in the statistical model, reducing the experimental error (residual variation coefficient, CVe). When incorporated into the different statistical models, the ECa information increased the selection accuracy of the experimental genotypes. Therefore, we demonstrate that the genetic parameter increased when both approaches (spatial analysis and environmental covariates) were employed.

National-Scale Cropland Mapping Based on Phenological Metrics, Environmental Covariates, and Machine Learning on Google Earth Engine

Many challenges prevail in cropland mapping over large areas, including dealing with massive volumes of datasets and computing capabilities. Accordingly, new opportunities have been opened at a breakneck pace with the launch of new satellites, the continuous improvements in data retrieval technology, and the upsurge of cloud computing solutions such as Google Earth Engine (GEE). Therefore, the present work is an attempt to automate the extraction of multi-year (2016–2020) cropland phenological metrics on GEE and use them as inputs with environmental covariates in a trained machine-learning model to generate high-resolution cropland and crop field-probabilities maps in Morocco. The comparison of our phenological retrievals against the MODIS phenology product shows very close agreement, implying that the suggested approach accurately captures crop phenology dynamics, which allows better cropland classification. The entire country is mapped using a large volume of reference samples collected and labelled with a visual interpretation of high-resolution imagery on Collect-Earth-Online, an online platform for systematically collecting geospatial data. The cropland classification product for the nominal year 2019–2020 showed an overall accuracy of 97.86% with a Kappa of 0.95. When compared to Morocco’s utilized agricultural land (SAU) areas, the cropland probabilities maps demonstrated the ability to accurately estimate sub-national SAU areas with an R-value of 0.9. Furthermore, analyzing cropland dynamics reveals a dramatic decrease in the 2019–2020 season by 2% since the 2018–2019 season and by 5% between 2016 and 2020, which is partly driven by climate conditions, but even more so by the novel coronavirus disease 2019 (COVID-19) that impacted the planting and managing of crops due to government measures taken at the national level, like complete lockdown. Such a result proves how much these methods and associated maps are critical for scientific studies and decision-making related to food security and agriculture.

Associations between environmental covariates and temporal changes in malaria incidence in high transmission settings of Uganda: a distributed lag nonlinear analysis

Background Environmental factors such as temperature, rainfall, and vegetation cover play a critical role in malaria transmission. However, quantifying the relationships between environmental factors and measures of disease burden relevant for public health can be complex as effects are often non-linear and subject to temporal lags between when changes in environmental factors lead to changes in malaria incidence. The study investigated the effect of environmental covariates on malaria incidence in high transmission settings of Uganda. Methods This study leveraged data from seven malaria reference centres (MRCs) located in high transmission settings of Uganda over a 24-month period. Estimates of monthly malaria incidence (MI) were derived from MRCs’ catchment areas. Environmental data including monthly temperature, rainfall, and normalized difference vegetation index (NDVI) were obtained from remote sensing sources. A distributed lag nonlinear model was used to investigate the effect of environmental covariates on malaria incidence. Results Overall, the median (range) monthly temperature was 30 °C (26–47), rainfall 133.0 mm (3.0–247), NDVI 0.66 (0.24–0.80) and MI was 790 per 1000 person-years (73–3973). Temperature of 35 °C was significantly associated with malaria incidence compared to the median observed temperature (30 °C) at month lag 2 (IRR: 2.00, 95% CI: 1.42–2.83) and the increased cumulative IRR of malaria at month lags 1–4, with the highest cumulative IRR of 8.16 (95% CI: 3.41–20.26) at lag-month 4. Rainfall of 200 mm significantly increased IRR of malaria compared to the median observed rainfall (133 mm) at lag-month 0 (IRR: 1.24, 95% CI: 1.01–1.52) and the increased cumulative IRR of malaria at month lags 1–4, with the highest cumulative IRR of 1.99(95% CI: 1.22–2.27) at lag-month 4. Average NVDI of 0.72 significantly increased the cumulative IRR of malaria compared to the median observed NDVI (0.66) at month lags 2–4, with the highest cumulative IRR of 1.57(95% CI: 1.09–2.25) at lag-month 4. Conclusions In high-malaria transmission settings, high values of environmental covariates were associated with increased cumulative IRR of malaria, with IRR peaks at variable lag times. The complex associations identified are valuable for designing strategies for early warning, prevention, and control of seasonal malaria surges and epidemics.