High-dimensional and high throughput genomic, field performance, and environmental data are becoming increasingly available to crop breeding programs, and their integration can facilitate genomic prediction within and across environments and provide insights into the genetic architecture of complex traits and the nature of genotype-by-environment interactions. To partition trait variation into additive and dominance (main effect) genetic and corresponding genetic-by-environment variances, and to identify specific environmental factors that influence genotype-by-environment interactions, we curated and analyzed genotypic and phenotypic data on 1918 maize (Zea mays L.) hybrids and environmental data from 65 testing environments. For grain yield, dominance variance was similar in magnitude to additive variance, and genetic-by-environment variances were more important than genetic main effect variances. Models involving both additive and dominance relationships best fit the data and modeling unique genetic covariances among all environments provided the best characterization of the genotype-by-environment interaction patterns. Similarity of relative hybrid performance among environments was modeled as a function of underlying weather variables, permitting identification of weather covariates driving correlations of genetic effects across environments. The resulting models can be used for genomic prediction of mean hybrid performance across populations of environments tested or for environment-specific predictions. These results can also guide efforts to incorporate high-throughput environmental data into genomic prediction models and predict values in new environments characterized with the same environmental characteristics.

Genomic prediction provides an efficient alternative to conventional phenotypic selection for developing improved cultivars with desirable characteristics. New and improved methods to genomic prediction are continually being developed that attempt to deal with the integration of data types beyond genomic information. Modern automated weather systems offer the opportunity to capture continuous data on a range of environmental parameters at specific field locations. In principle, this information could characterize training and target environments and enhance predictive ability by incorporating weather characteristics as part of the genotype-by-environment (G×E) interaction component in prediction models. We assessed the usefulness of including weather data variables in genomic prediction models using a naïve environmental kinship model across 30 environments comprising the Genomes to Fields (G2F) initiative in 2014 and 2015. Specifically four different prediction scenarios were evaluated (i) tested genotypes in observed environments; (ii) untested genotypes in observed environments; (iii) tested genotypes in unobserved environments; and (iv) untested genotypes in unobserved environments. A set of 1,481 unique hybrids were evaluated for grain yield. Evaluations were conducted using five different models including main effect of environments; general combining ability (GCA) effects of the maternal and paternal parents modeled using the genomic relationship matrix; specific combining ability (SCA) effects between maternal and paternal parents; interactions between genetic (GCA and SCA) effects and environmental effects; and finally interactions between the genetics effects and environmental covariates. Incorporation of the genotype-by-environment interaction term improved predictive ability across all scenarios. However, predictive ability was not improved through inclusion of naive environmental covariates in G×E models. More research should be conducted to link the observed weather conditions with important physiological aspects in plant development to improve predictive ability through the inclusion of weather data.

Objectives: Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F's genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014-2017. Data description:Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported. The 2014 and 2015 datasets are updated versions from the previously released files [1] while 2016 and 2017 datasets are newly available to the public.

Crop simulation models are used at the field scale to estimate crop yield potential, optimize current management, and benchmark input-use efficiency. At issue is the ability of crop models to predict local and regional actual yield and total production without need of site-year specific calibration of internal parameters associated with fundamental physiological processes. In this study, a well-validated maize simulation model was used to estimate yield potential for 45 locations across the U.S. Corn Belt, including both irrigated and rainfed environments, during four years (2011-2014) that encompassed diverse weather conditions. Simulations were based on measured weather data, dominant soil properties, and key management practices at each location (including sowing date, hybrid maturity, and plant density). The same set of internal model parameters were used across all site-years. Simulated yields were upscaled from locations to larger spatial domains (county, agricultural district, state, and region), following a bottom-up approach based on a climate zone scheme and distribution of maize harvested area. Simulated yields were compared against actual yields reported at each spatial level, both in absolute terms as well as deviations from long-term averages. Similar comparisons were performed for total maize production, estimated as the product of simulated yields and official statistics on maize harvested area in each year. At county-level, the relationship between simulated and actual yield was better described by a curvilinear model, with decreasing agreement at higher yields (>12 Mg ha-1). Comparison of actual and simulated yield anomalies, as estimated from the yearly yield deviations from the long-term actual and simulated average yield, indicated a linear relationship at county-level. In both cases (absolute yields and yield anomalies comparisons), the agreement increased with increasing spatial aggregation (from county to region). An approach based on long-term actual and simulated yields and year-specific simulated yield allowed estimation of actual yield with a high degree of accuracy at county level (RMSE ≤ 18%), even in years with highly favorable weather or severe drought. Estimates of total production, which are of greatest interest to buyers and sellers in the market, were also in close agreement with actual production (RMSE ≤ 22%). The approach proposed here to estimate yield and production can complement other approaches that rely on surveys, field crop cuttings, and empirical statistical methods and serve as basis for in-season yield and production forecasts.

We demonstrate that the integrated sub-wavelength aperture probe designed for THz near-field scanning probe microscopy can be used to map surface plasmon waves at THz frequencies. Observed near-field images of metallic patterns reveal surface plasmon waves superimposed over THz transmission images. We discuss the coupling mechanism for the surface waves and arrive to an important conclusion that the detected surface wave images represent the spatial derivative of the surface plasmon electric field. The relationship between the electric field and the measured signal is confirmed experimentally by mapping surface waves in bow-tie antennas. This study explains previously observed effects in THz near-field microscopy and provides a framework for analysis of near-field images.