2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative.

OBJECTIVES: This release note describes the Maize GxE project datasets within the Genomes to Fields (G2F) Initiative. The Maize GxE project aims to understand genotype by environment (GxE) interactions and use the information collected to improve resource allocation efficiency and increase genotype predictability and stability, particularly in scenarios of variable environmental patterns. Hybrids and inbreds are evaluated across multiple environments and phenotypic, genotypic, environmental, and metadata information are made publicly available. DATA DESCRIPTION: The datasets include phenotypic data of the hybrids and inbreds evaluated in 30 locations across the US and one location in Germany in 2020 and 2021, soil and climatic measurements and metadata information for all environments (combination of year and location), ReadMe, and description files for each data type. A set of common hybrids is present in each environment to connect with previous evaluations. Each environment had a collaborator responsible for collecting and submitting the data, the GxE coordination team combined all the collected information and removed obvious erroneous data. Collaborators received the combined data to use, verify and declare that the data generated in their own environments was accurate. Combined data is released to the public with minimal filtering to maintain fidelity to the original data.

Genomes to Fields 2022 Maize genotype by Environment Prediction Competition.

OBJECTIVES: The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data. DATA DESCRIPTION: This resource used data from the Maize GxE project within the G2F Initiative [1]. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022. Also, soil, weather, environmental covariates data and metadata information for all environments (combination of year and location). Competitors also had access to ReadMe files which described all the files provided. The Maize GxE is a collaborative project and all the data generated becomes publicly available [2]. The dataset used in the 2022 Prediction Competition was curated and lightly filtered for quality and to ensure naming uniformity across years.

2018-2019 field seasons of the Maize Genomes to Fields (G2F) G x E project.

OBJECTIVES: This report provides information about the public release of the 2018-2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments and makes available phenotypic, genotypic, environmental, and metadata information. The initiative understands the necessity to characterize and deploy public sources of genetic diversity to face the challenges for more sustainable agriculture in the context of variable environmental conditions. DATA DESCRIPTION: Datasets include phenotypic, climatic, and soil measurements, metadata information, and inbred genotypic information for each combination of location and year. Collaborators in the G2F initiative collected data for each location and year; members of the group responsible for coordination and data processing combined all the collected information and removed obvious erroneous data. The collaborators received the data before the DOI release to verify and declare that the data generated in their own locations was accurate. ReadMe and description files are available for each dataset. Previous years of evaluation are already publicly available, with common hybrids present to connect across all locations and years evaluated since this project's inception.

Biochar as a negative emission technology: A synthesis of field research on greenhouse gas emissions.

Biochar is one of the few nature-based technologies with potential to help achieve net-zero emissions agriculture. Such an outcome would involve the mitigation of greenhouse gas (GHG) emission from agroecosystems and optimization of soil organic carbon sequestration. Interest in biochar application is heightened by its several co-benefits. Several reviews summarized past investigations on biochar, but these reviews mostly included laboratory, greenhouse, and mesocosm experiments. A synthesis of field studies is lacking, especially from a climate change mitigation standpoint. Our objectives are to (1) synthesize advances in field-based studies that have examined the GHG mitigation capacity of soil application of biochar and (2) identify limitations of the technology and research priorities. Field studies, published before 2022, were reviewed. Biochar has variable effects on GHG emissions, ranging from decrease, increase, to no change. Across studies, biochar reduced emissions of nitrous oxide (N2 O) by 18% and methane (CH4 ) by 3% but increased carbon dioxide (CO2 ) by 1.9%. When biochar was combined with N-fertilizer, it reduced CO2 , CH4 , and N2 O emissions in 61%, 64%, and 84% of the observations, and biochar plus other amendments reduced emissions in 78%, 92%, and 85% of the observations, respectively. Biochar has shown potential to reduce GHG emissions from soils, but long-term studies are needed to address discrepancies in emissions and identify best practices (rate, depth, and frequency) of biochar application to agricultural soils.

Yield prediction through integration of genetic, environment, and management data through deep learning.

Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare the efficacy of 2 model development methods, and contextualize model performance using conventional linear and machine learning models. We examine the usefulness of incorporating interactions between disparate data types. We find deep learning and best linear unbiased predictor (BLUP) models with interactions had the best overall performance. BLUP models achieved the lowest average error, but deep learning models performed more consistently with similar average error. Optimizing deep neural network submodules for each data type improved model performance relative to optimizing the whole model for all data types at once. Examining the effect of interactions in the best-performing model revealed that including interactions altered the model's sensitivity to weather and management features, including a reduction of the importance scores for timepoints expected to have a limited physiological basis for influencing yield-those at the extreme end of the season, nearly 200 days post planting. Based on these results, deep learning provides a promising avenue for the phenotypic prediction of complex traits in complex environments and a potential mechanism to better understand the influence of environmental and genetic factors.

Mycotoxin Co-Occurrence in Michigan Harvested Maize Grain.

Mycotoxins are secondary metabolites produced by fungi that, depending on the type and exposure levels, can be a threat to human and animal health. When multiple mycotoxins occur together, their risk effects on human and animal health can be additive or synergistic. Little information is known about the specific types of mycotoxins or their co-occurrence in the state of Michigan and the Great Lakes region of the United States. To understand the types, incidences, severities, and frequency of co-occurrence of mycotoxins in maize grain (Zea mays L.), samples were collected from across Michigan over two years and analyzed for 20 different mycotoxins. Every sample was contaminated with at least four and six mycotoxins in 2017 and 2018, respectively. Incidence and severity of each mycotoxin varied by year and across locations. Correlations were found between mycotoxins, particularly mycotoxins produced by Fusarium spp. Environmental differences at each location played a role in which mycotoxins were present and at what levels. Overall, data from this study demonstrated that mycotoxin co-occurrence occurs at high levels in Michigan, especially with mycotoxins produced by Fusarium spp., such as deoxynivalenol.