Genomes to Fields 2022 Maize genotype by Environment Prediction Competition

Dayane Cristina Lima; Jacob D Washburn; José Ignacio Varela; Qiuyue Chen; Joseph L Gage; Maria Cinta Romay; James Holland; David Ertl; Marco Lopez-Cruz; Fernando M Aguate; Gustavo de Los Campos; Shawn Kaeppler; Timothy Beissinger; Martin Bohn; Edward Buckler; Jode Edwards; Sherry Flint-Garcia; Michael A Gore; Candice N Hirsch; Joseph E Knoll; John McKay; Richard Minyo; Seth C Murray; Osler A Ortez; James C Schnable; Rajandeep S Sekhon; Maninder P Singh; Erin E Sparks; Addie Thompson; Mitchell Tuinstra; Jason Wallace; Teclemariam Weldekidan; Wenwei Xu; Natalia de Leon

doi:10.1186/s13104-023-06421-z

Genomes to Fields 2022 Maize genotype by Environment Prediction Competition

BMC Res Notes. 2023 Jul 17;16(1):148. doi: 10.1186/s13104-023-06421-z.

Authors

Dayane Cristina Lima¹, Jacob D Washburn², José Ignacio Varela³, Qiuyue Chen⁴, Joseph L Gage⁴, Maria Cinta Romay⁵, James Holland⁶, David Ertl⁷, Marco Lopez-Cruz⁸, Fernando M Aguate⁸, Gustavo de Los Campos⁹, Shawn Kaeppler³, Timothy Beissinger¹⁰, Martin Bohn¹¹, Edward Buckler¹², Jode Edwards¹³, Sherry Flint-Garcia², Michael A Gore¹⁴, Candice N Hirsch¹⁵, Joseph E Knoll¹⁶, John McKay¹⁷, Richard Minyo¹⁸, Seth C Murray¹⁹, Osler A Ortez²⁰, James C Schnable²¹, Rajandeep S Sekhon²², Maninder P Singh²³, Erin E Sparks²⁴, Addie Thompson²³, Mitchell Tuinstra²⁵, Jason Wallace²⁶, Teclemariam Weldekidan²⁴, Wenwei Xu²⁷, Natalia de Leon³

Affiliations

¹ Department of Agronomy, University of Wisconsin - Madison, Madison, WI, 53706, USA. dclima@wisc.edu.
² USDA-ARS Plant Genetics Research Unit, 205 Curtis Hall, Columbia, MO, 65211, USA.
³ Department of Agronomy, University of Wisconsin - Madison, Madison, WI, 53706, USA.
⁴ Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
⁵ Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
⁶ USDA-ARS Plant Science Research Unit, Raleigh, NC, 27606, USA.
⁷ Iowa Corn Promotion Board, Johnston, IA, 50131, USA.
⁸ Department of Epidemiology and Biostatistics, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA.
⁹ Department of Plant, Soil and Microbial Sciences, Department of Epidemiology and Biostatistics, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA.
¹⁰ Department of Crop Science, Center for Integrated Breeding Research, University of Göttingen, Carl-Sprengel-Weg 1, 37075, Göttingen, Germany.
¹¹ University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
¹² USDA-ARS and Cornell University, Ithaca, NY, 14853, USA.
¹³ USDA ARS CICGRU, 716 Farmhouse Ln, Ames, IA, 50011-1051, USA.
¹⁴ Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
¹⁵ Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA.
¹⁶ USDA-ARS Crop Genetics and Breeding Research Unit, Tifton, GA, 31793, USA.
¹⁷ Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
¹⁸ Department of Horticulture and Crop Science, College of Food, Agricultural, and Environmental Sciences, Ohio State University, Wooster, OH, 44691, USA.
¹⁹ Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.
²⁰ Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA.
²¹ Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
²² Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA.
²³ Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
²⁴ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA.
²⁵ Department of Agronomy, Purdue University, West Lafayette, IN, 49707, USA.
²⁶ Department of Crop & Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
²⁷ Texas A&M University, College Station, TX, 77843, USA.

Abstract

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.

Keywords: Grain yield; Maize; Root mean squared error.

MeSH terms

Edible Grain / genetics
Genome, Plant* / genetics
Genotype
Phenotype
Zea mays* / genetics