Biophysical and economic implications for agriculture of +1.5° and +2.0°C global warming using AgMIP Coordinated Global and Regional Assessments.

This study presents results of the Agricultural Model Intercomparison and Improvement Project (AgMIP) Coordinated Global and Regional Assessments (CGRA) of +1.5° and +2.0°C global warming above pre-industrial conditions. This first CGRA application provides multi-discipline, multi-scale, and multi-model perspectives to elucidate major challenges for the agricultural sector caused by direct biophysical impacts of climate changes as well as ramifications of associated mitigation strategies. Agriculture in both target climate stabilizations is characterized by differential impacts across regions and farming systems, with tropical maize Zea mays experiencing the largest losses, while soy Glycine max mostly benefits. The result is upward pressure on prices and area expansion for maize and wheat Triticum aestivum, while soy prices and area decline (results for rice Oryza sativa are mixed). An example global mitigation strategy encouraging bioenergy expansion is more disruptive to land use and crop prices than the climate change impacts alone, even in the +2.0°C scenario which has a larger climate signal and lower mitigation requirement than the +1.5°C scenario. Coordinated assessments reveal that direct biophysical and economic impacts can be substantially larger for regional farming systems than global production changes. Regional farmers can buffer negative effects or take advantage of new opportunities via mitigation incentives and farm management technologies. Primary uncertainties in the CGRA framework include the extent of CO2 benefits for diverse agricultural systems in crop models, as simulations without CO2 benefits show widespread production losses that raise prices and expand agricultural area.

Multimodel ensembles of wheat growth: many models are better than one.

Crop models of crop growth are increasingly used to quantify the impact of global changes due to climate or crop management. Therefore, accuracy of simulation results is a major concern. Studies with ensembles of crop models can give valuable information about model accuracy and uncertainty, but such studies are difficult to organize and have only recently begun. We report on the largest ensemble study to date, of 27 wheat models tested in four contrasting locations for their accuracy in simulating multiple crop growth and yield variables. The relative error averaged over models was 24-38% for the different end-of-season variables including grain yield (GY) and grain protein concentration (GPC). There was little relation between error of a model for GY or GPC and error for in-season variables. Thus, most models did not arrive at accurate simulations of GY and GPC by accurately simulating preceding growth dynamics. Ensemble simulations, taking either the mean (e-mean) or median (e-median) of simulated values, gave better estimates than any individual model when all variables were considered. Compared to individual models, e-median ranked first in simulating measured GY and third in GPC. The error of e-mean and e-median declined with an increasing number of ensemble members, with little decrease beyond 10 models. We conclude that multimodel ensembles can be used to create new estimators with improved accuracy and consistency in simulating growth dynamics. We argue that these results are applicable to other crop species, and hypothesize that they apply more generally to ecological system models.

Putting mechanisms into crop production models.

Crop growth models dynamically simulate processes of C, N and water balance on daily or hourly time-steps to predict crop growth and development and at season-end, final yield. Their ability to integrate effects of genetics, environment and crop management have led to applications ranging from understanding gene function to predicting potential impacts of climate change. The history of crop models is reviewed briefly, and their level of mechanistic detail for assimilation and respiration, ranging from hourly leaf-to-canopy assimilation to daily radiation-use efficiency is discussed. Crop models have improved steadily over the past 30-40 years, but much work remains. Improvements are needed for the prediction of transpiration response to elevated CO2 and high temperature effects on phenology and reproductive fertility, and simulation of root growth and nutrient uptake under stressful edaphic conditions. Mechanistic improvements are needed to better connect crop growth to genetics and to soil fertility, soil waterlogging and pest damage. Because crop models integrate multiple processes and consider impacts of environment and management, they have excellent potential for linking research from genomics and allied disciplines to crop responses at the field scale, thus providing a valuable tool for deciphering genotype by environment by management effects.

Runoff transport of pyrethroids from a residential lawn in central California.

An irrigation runoff study on a residential lawn was conducted in California, northeast of Sacramento, during the summer and fall of 2008 to investigate the contribution of turf uses of pyrethroids to residues in Californian urban creek sediments. This study examined how over irrigation (i.e., irrigation that produces runoff) in the summer season may transport recently applied pyrethroids. The study included liquid and granular applications of both bifenthrin [(2-methyl-3-phenyl-phenyl) methyl 3-(2-chloro-3,3,3-trifluoro-prop-1-enyl)-2,2-dimethyl-cyclopropane-1-carboxylate] and beta-cyfluthrin [Cyano(4-fluoro-3-phenoxyphenyl)methyl 3-(2,2-dichloroethenyl)-2,2-dimethyl-cyclopropanecarboxylate]. Generally, runoff did not occur at irrigation rates of 2.03 cm/h (0.8 in/h) but did occur when the irrigation rates were increased to about 3.81 cm/h (1.5 in/h), generating chemical losses in the first runoff event of up to 0.58 and 0.08% of applied for beta-cyfluthrin and bifenthrin, respectively. Chemical runoff losses dropped significantly between over-irrigation events with the third over-irrigation event chemical runoff losses representing 0.026 and 0.015% of applied for beta-cyfluthrin and bifenthrin, respectively. Runoff losses were generally less for liquid formulations than granular formulations but within a factor of three. Additionally, the study included a simulated winter rainstorm 8 wk after application. The low runoff losses from turf seen in this study suggest that other sources could be contributing to observed residues in urban streams. Other sources could include pyrethroids ending up on impervious surfaces, such as concrete driveways from off-target applications to turf, spills, and other poor handling practices, or pyrechroids applied directly to impervious surfaces for insect control.

Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean.

Multienvironment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET data sets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for > 70 years in the United States and Canada, consisting of 20-50 entries each year at 10-20 locations. The CDBN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association studies (GWAS) using best linear unbiased predictions derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2 million SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. Mash found two large genomic regions with effects on multiple phenotypes, supporting a hypothesis of pleiotropic or linked effects that were likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that statistical genomics approaches can be used on MET phenotypic data to discover significant genetic effects and to define genomic regions associated with crop improvement.

Next generation of elevated [CO2] experiments with crops: a critical investment for feeding the future world.

A rising global population and demand for protein-rich diets are increasing pressure to maximize agricultural productivity. Rising atmospheric [CO(2)] is altering global temperature and precipitation patterns, which challenges agricultural productivity. While rising [CO(2)] provides a unique opportunity to increase the productivity of C(3) crops, average yield stimulation observed to date is well below potential gains. Thus, there is room for improving productivity. However, only a fraction of available germplasm of crops has been tested for CO(2) responsiveness. Yield is a complex phenotypic trait determined by the interactions of a genotype with the environment. Selection of promising genotypes and characterization of response mechanisms will only be effective if crop improvement and systems biology approaches are closely linked to production environments, that is, on the farm within major growing regions. Free air CO(2) enrichment (FACE) experiments can provide the platform upon which to conduct genetic screening and elucidate the inheritance and mechanisms that underlie genotypic differences in productivity under elevated [CO(2)]. We propose a new generation of large-scale, low-cost per unit area FACE experiments to identify the most CO(2)-responsive genotypes and provide starting lines for future breeding programmes. This is necessary if we are to realize the potential for yield gains in the future.

Simulating the influence of vernalization, photoperiod and optimum temperature on wheat developmental rates.

BACKGROUND AND AIMS: Accurately representing development is essential for applying crop simulations to investigate the effects of climate, genotypes or crop management. Development in wheat (Triticum aestivum, T. durum) is primarily driven by temperature, but affected by vernalization and photoperiod, and is often simulated by reducing thermal-time accumulation using vernalization or photoperiod factors or limiting accumulation when a lower optimum temperature (T(optl)) is exceeded. In this study T(optl) and methods for representing effects of vernalization and photoperiod on anthesis were examined using a range of planting dates and genotypes. METHODS: An examination was made of T(optl) values of 15, 20, 25 and 50 degrees C, and either the most limiting or the multiplicative value of the vernalization and photoperiod development rate factors for simulating anthesis. Field data were from replicated trials at Ludhiana, Punjab, India with July through to December planting dates and seven cultivars varying in vernalization response. KEY RESULTS: Simulations of anthesis were similar for T(optl) values of 20, 25 and 50 degrees C, but a T(optl) of 15 degrees C resulted in a consistent bias towards predicting anthesis late for early planting dates. Results for T(optl) above 15 degrees C may have occurred because mean temperatures rarely exceeded 20 degrees C before anthesis for many planting dates. For cultivars having a strong vernalization response, anthesis was more accurately simulated when vernalization and photoperiod factors were multiplied rather than using the most limiting of the two factors. CONCLUSIONS: Setting T(optl) to a high value (30 degrees C) and multiplying the vernalization and photoperiod factors resulted in accurately simulating anthesis for a wide range of planting dates and genotypes. However, for environments where average temperatures exceed 20 degrees C for much of the pre-anthesis period, a lower T(optl) (23 degrees C) might be appropriate. These results highlight the value of testing a model over a wide range of environments.

Estimating parametric phenotypes that determine anthesis date in Zea mays: Challenges in combining ecophysiological models with genetics.

Ecophysiological crop models encode intra-species behaviors using parameters that are presumed to summarize genotypic properties of individual lines or cultivars. These genotype-specific parameters (GSP's) can be interpreted as quantitative traits that can be mapped or otherwise analyzed, as are more conventional traits. The goal of this study was to investigate the estimation of parameters controlling maize anthesis date with the CERES-Maize model, based on 5,266 maize lines from 11 plantings at locations across the eastern United States. High performance computing was used to develop a database of 356 million simulated anthesis dates in response to four CERES-Maize model parameters. Although the resulting estimates showed high predictive value (R2 = 0.94), three issues presented serious challenges for use of GSP's as traits. First (expressivity), the model was unable to express the observed data for 168 to 3,339 lines (depending on the combination of site-years), many of which ended up sharing the same parameter value irrespective of genetics. Second, for 2,254 lines, the model reproduced the data, but multiple parameter sets were equally effective (equifinality). Third, parameter values were highly dependent (p<10-6919) on the sets of environments used to estimate them (instability), calling in to question the assumption that they represent fundamental genetic traits. The issues of expressivity, equifinality and instability must be addressed before the genetic mapping of GSP's becomes a robust means to help solve the genotype-to-phenotype problem in crops.

Comparative Aerial and Ground Based High Throughput Phenotyping for the Genetic Dissection of NDVI as a Proxy for Drought Adaptive Traits in Durum Wheat.

High-throughput phenotyping platforms (HTPPs) provide novel opportunities to more effectively dissect the genetic basis of drought-adaptive traits. This genome-wide association study (GWAS) compares the results obtained with two Unmanned Aerial Vehicles (UAVs) and a ground-based platform used to measure Normalized Difference Vegetation Index (NDVI) in a panel of 248 elite durum wheat (Triticum turgidum L. ssp. durum Desf.) accessions at different growth stages and water regimes. Our results suggest increased ability of aerial over ground-based platforms to detect quantitative trait loci (QTL) for NDVI, particularly under terminal drought stress, with 22 and 16 single QTLs detected, respectively, and accounting for 89.6 vs. 64.7% phenotypic variance based on multiple QTL models. Additionally, the durum panel was investigated for leaf chlorophyll content (SPAD), leaf rolling and dry biomass under terminal drought stress. In total, 46 significant QTLs affected NDVI across platforms, 22 of which showed concomitant effects on leaf greenness, 2 on leaf rolling and 10 on biomass. Among 9 QTL hotspots on chromosomes 1A, 1B, 2B, 4B, 5B, 6B, and 7B that influenced NDVI and other drought-adaptive traits, 8 showed per se effects unrelated to phenology.

Corrigendum: Comparative Aerial and Ground Based High Throughput Phenotyping for the Genetic Dissection of NDVI as a Proxy for Drought Adaptive Traits in Durum Wheat.

[This corrects the article DOI: 10.3389/fpls.2018.00893.].

Investigation of the Influence of Leaf Thickness on Canopy Reflectance and Physiological Traits in Upland and Pima Cotton Populations.

Many systems for field-based, high-throughput phenotyping (FB-HTP) quantify and characterize the reflected radiation from the crop canopy to derive phenotypes, as well as infer plant function and health status. However, given the technology's nascent status, it remains unknown how biophysical and physiological properties of the plant canopy impact downstream interpretation and application of canopy reflectance data. In that light, we assessed relationships between leaf thickness and several canopy-associated traits, including normalized difference vegetation index (NDVI), which was collected via active reflectance sensors carried on a mobile FB-HTP system, carbon isotope discrimination (CID), and chlorophyll content. To investigate the relationships among traits, two distinct cotton populations, an upland (Gossypium hirsutum L.) recombinant inbred line (RIL) population of 95 lines and a Pima (G. barbadense L.) population composed of 25 diverse cultivars, were evaluated under contrasting irrigation regimes, water-limited (WL) and well-watered (WW) conditions, across 3 years. We detected four quantitative trait loci (QTL) and significant variation in both populations for leaf thickness among genotypes as well as high estimates of broad-sense heritability (on average, above 0.7 for both populations), indicating a strong genetic basis for leaf thickness. Strong phenotypic correlations (maximum r = -0.73) were observed between leaf thickness and NDVI in the Pima population, but not the RIL population. Additionally, estimated genotypic correlations within the RIL population for leaf thickness with CID, chlorophyll content, and nitrogen discrimination ([Formula: see text] = -0.32, 0.48, and 0.40, respectively) were all significant under WW but not WL conditions. Economically important fiber quality traits did not exhibit significant phenotypic or genotypic correlations with canopy traits. Overall, our results support considering variation in leaf thickness as a potential contributing factor to variation in NDVI or other canopy traits measured via proximal sensing, and as a trait that impacts fundamental physiological responses of plants.

Erratum: The uncertainty of crop yield projections is reduced by improved temperature response functions.

This corrects the article DOI: 10.1038/nplants.2017.102.

Erratum: The uncertainty of crop yield projections is reduced by improved temperature response functions.

This corrects the article DOI: 10.1038/nplants.2017.102.

Author Correction: The uncertainty of crop yield projections is reduced by improved temperature response functions.

Nature Plants 3, 17102 (2017); published online 17 July 2017; corrected online 27 September 2017.

The uncertainty of crop yield projections is reduced by improved temperature response functions.

Increasing the accuracy of crop productivity estimates is a key element in planning adaptation strategies to ensure global food security under climate change. Process-based crop models are effective means to project climate impact on crop yield, but have large uncertainty in yield simulations. Here, we show that variations in the mathematical functions currently used to simulate temperature responses of physiological processes in 29 wheat models account for >50% of uncertainty in simulated grain yields for mean growing season temperatures from 14 °C to 33 °C. We derived a set of new temperature response functions that when substituted in four wheat models reduced the error in grain yield simulations across seven global sites with different temperature regimes by 19% to 50% (42% average). We anticipate the improved temperature responses to be a key step to improve modelling of crops under rising temperature and climate change, leading to higher skill of crop yield projections.

Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton.

The application of high-throughput plant phenotyping (HTPP) to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010-2012. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL) expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars.

Emerging semantics to link phenotype and environment.

Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.

Development and evaluation of a field-based high-throughput phenotyping platform.

Physiological and developmental traits that vary over time are difficult to phenotype under relevant growing conditions. In this light, we developed a novel system for phenotyping dynamic traits in the field. System performance was evaluated on 25 Pima cotton (Gossypium barbadense L.) cultivars grown in 2011 at Maricopa, Arizona. Field-grown plants were irrigated under well watered and water-limited conditions, with measurements taken at different times on 3 days in July and August. The system carried four sets of sensors to measure canopy height, reflectance and temperature simultaneously on four adjacent rows, enabling the collection of phenotypic data at a rate of 0.84ha h-1. Measurements of canopy height, normalised difference vegetation index and temperature all showed large differences among cultivars and expected interactions of cultivars with water regime and time of day. Broad-sense heritabilities (H2)were highest for canopy height (H2=0.86-0.96), followed by the more environmentally sensitive normalised difference vegetation index (H2=0.28-0.90) and temperature (H2=0.01-0.90) traits. We also found a strong agreement (r2=0.35-0.82) between values obtained by the system, and values from aerial imagery and manual phenotyping approaches. Taken together, these results confirmed the ability of the phenotyping system to measure multiple traits rapidly and accurately.