Research Project: Improving Maize Production with Crop Growth Models and Cross Compatibility Systems

Location: Corn Insects and Crop Genetics Research

2024 Annual Report

Objectives
Objective 1: Characterize the distribution of the Ga1 and Ga2 gametophytic incompatibility systems in U.S. maize breeding germplasm and the response to changes in temperature on their ability to exclude pollen. Subobjective 1.A: Determine whether alleles capable of overcoming pollen exclusion barriers are present in the U.S. corn breeding germplasm. Subobjective 1.B: Examine the effect of environmental factors on pollen exclusion systems. Objective 2: Develop improved crop growth models using the Agricultural Production Systems Simulator (APSIM) for predicting variation in growth and yield among maize hybrids as affected by varying environmental and management conditions. Subobjective 2.A: Calibrate APSIM to simulate development and growth of total dry matter, grain dry matter, and stalk dry matter across a range of multiple plant densities. Subobjective 2.B: Test plasticity of maize sink during grain filling.

Approach
In order to use hybrid-specific crop growth models to understand factors contributing to genotype by environment interactions, replicated field trials of hybrid corn varieties will be carried out and evaluated for morphological, phonological and chemical traits. Together with environmental data, these data will be used to develop crop growth models with publicly available software. Valuable measures of agronomic performance such as grain yield of the specific hybrids in the study will be predicted. These models will be validated using actual measurements of agronomic performance and used to predict performance in additional environmental conditions. In order to understand molecular genetic control mechanism of gametophytic incompatibility, we will construct a transgene encoding ZmPME3 and use it to complement the ga1 phenotype. A second transgene will be used to mutationally inactivate ZmPME3. All transgenic lines will be evaluated for their ability to exclude unwanted pollen in replicated field trials. In addition, ZmPME will be produced in a bacterial expression system and purified. The activity of the purified protein will be characterized using pectin methylesterase activity assays and the effect of this protein on pollen tube growth will be evaluated in vitro.

Progress Report
Genes that control pollination in maize are useful for preserving genetic purity. Genetic purity is important to growers as it impacts maize market class and the value of their product. In addition, genetic purity is important to organic corn producers, who want to ensure their product is free of genetically modified organisms. To enhance the utility of genes controlling pollination, we need an improved understanding of their distribution in the corn breeding germplasm. In Sub-objective 1A of our research, we initiated a screen of the corn breeding germplasm for the ability to overcome two pollen exclusion systems, Ga1 (Gametophyte factor 1) and Ga2 (Gametophyte factor 2). In this screen, pollen from 96 releases from the Germplasm Enhancement of Maize (GEM) program was put on the silks of plants that are known to have either the Ga1 or the Ga2 pollen exclusion system. If kernels are formed as a result of these pollinations, we conclude that the line being tested is capable of overcoming the pollen exclusion system. Our initial screen identified a small group of varieties that can overcome either the Ga1 or Ga2 systems and these varieties have been put into a pipeline for further characterization. They will first be re-tested to confirm they can overcome a pollen exclusion system. They will then be genotyped and the DNA sequence of known and yet to be sequenced pollen exclusion systems will be determined. These tests will determine if the ability to overcome a pollen control system is due to a new gene or is one that has been identified previously. This information will be useful for understanding the mechanism by which pollination control systems function. Research in Sub-objective 1B examined the impact of environmental conditions on the effectiveness of pollination control systems. Researchers in Ames, Iowa and Raleigh, North Carolina carried out a multi-environment (Iowa, North Carolina and Puerto Rico) field trial that will provide a direct answer to this question. In this trial, a diverse set of inbred lines were each tested for their ability to exclude pollen by applying pollen to the silks and observing whether kernels formed. By testing two different environmental conditions, we will be able to determine if pollen exclusion is controlled by environmental factors. We planned to use a controlled environment study to examine the effect of temperature on pollen exclusion. Our plan was to grow the plants to maturity in a greenhouse and move them to a growth chamber for the controlled-environment parts of the experiment. Since our greenhouse is not functional, we carried out a preliminary study to determine if we could grow plants to maturity entirely in a growth chamber. The tassels did not develop normally in the growth chamber, so we could not carry out the crosses required to do the experiment. We conclude that we will not be able to carry out this experiment entirely in a growth chamber. The research outlined in Objective 2 is to predict environmental and management effects on maize hybrid growth. A large quantity of hybrid seed needed for this objective was produced and is ready for testing. Preliminary experiments were conducted in summer of 2023 and dry matter accumulation in multiple organs as a function of plant density (number of plants per unit area) was analyzed. Preliminary results were used to determine if the design of the experiment includes adequate sampling to achieve the objective. Substantial differences in responses to plant density were observed for dry matter accumulation among maize hybrids and among different organs. The maximum dry-matter accumulation for maize grain, maize stalks, and total plant dry matter varied substantially by plant density, providing insights for future work. One outcome of the preliminary work is that some experimental data may be needed at higher plant densities than currently planned in order to estimate the plant density at which maximum total plant dry matter accumulation (on a per area basis) occurs. We continued cooperation with the Genomes to Fields (G2F) Initiative by providing data for four additional field locations for the 2023-2024 G2F genotype x environment interaction experiments. G2F is a multi-state multi- institution project to study maize genotype x environment interaction that provides access to data on maize hybrid performance and environmental data that would not be possible without multi-institutional collaboration. The collaboration by USDA ARS researchers in Ames strengthens the entire project by providing data from four high quality locations in the center of the U.S. corn belt. Data from the collaboration is eventually released publicly and thus benefits the entire maize research community. We carried out research to develop improved corn varieties for organic production systems, funded by the National Institute of Food and Agriculture (NIFA). This is a cooperative effort involving researchers from USDA-ARS, Iowa State University, the University of Illinois, the University of Wisconsin, and the University of Puerto Rico. Research focuses on varieties with improved genetic purity and nutritional quality and takes advantage of modern breeding tools including genomic selection and a novel organic-friendly doubled haploid method. As part of this research program, we engage midwestern organic farmers and Puerto Rican student interns in an annual “organic corn breeding boot camp” held in conjunction with pollination of our winter nursery in Puerto Rico. Attendees are taught breeding methods in the winter season and then participate in our breeding program in the summer. Student interns from Puerto Rico travel to midwestern research locations where they work on the research project and tour the farms of the boot camp participants they met in Puerto Rico. The boot camp provides a unique opportunity for students, farmers and researchers to learn from each other and contribute to the development of corn varieties that are designed to meet the needs of organic corn producers.

Accomplishments
1. Evolutionary history of the Ga1 locus provides insight into the unusually high genetic diversity of maize. Modern maize contains a tremendous amount of genetic diversity that has allowed plant breeders to make dramatic improvements in agronomic and quality traits but it is not clear where this diversity originated. The Ga1 locus may have played a role in maize domestication by providing the reproductive isolation required for domestication. By analyzing genome sequences of maize wild relatives, ARS reseachers in Ames, Iowa, learned that the Ga1 locus was transferred from an ancient wild relative to modern maize in at least two independent events, with one allele being wide-spread in modern popcorn and a different allele being wide-spread in modern field corn. This information supports a domestication model in which more than one domestication event resulted in transfer of genes from wild relatives to modern maize. This may explain the high level of diversity found in modern maize germplasm. This improved understanding of the origin of maize genetic diversity will improve the efficiency of developing improved maize varieties.

2. A novel experimental approach to studying joint effects of nitrogen fertilizer, plant density, and maize hybrids improves prediction of maize performance and nitrogen fertilizer requirements. Past research has not included the joint effects of nitrogen, plant density, and maize hybrids and has failed to predict the relationship between optimal nitrogen rate and grain yield. By jointly considering the effects of all three variables simultaneously, ARS researchers in Ames, Iowa were able to demonstrate higher grain yield is associated with higher optimal nitrogen rates required with newer hybrids and higher plant densities. The novel approach to model nitrogen response is being applied to additional nitrogen response data to provide more accurate predictions of nitrogen fertilizer requirements and maize grain yield across a broader array of environmental conditions and management approaches. This research has broad implications for producers, production researchers, and breeders who are all trying to optimize production efficiency and optimize the amount of nitrogen fertilizer applied.

Review Publications
Kick, D.R., Wallace, J.G., Schnable, J.C., Kolkmann, J.M., Alaca, B., Beissinger, T.M., Edwards, J.W., Ertl, D., Flint-Garcia, S.A., Gage, J.L., Hirsch, C.N., Knoll, J.E., de Leon, N., Lima, D.C., Moreta, D., Singh, M.P., Thompson, A., Weldekidan, T., Washburn, J.D. 2023. Yield prediction through integration of genetic, environment, and management data through deep learning. G3, Genes/Genomes/Genetics. 13(4). Article jkad006. https://doi.org/10.1093/g3journal/jkad006.
dos Santos, C.L., Miguez, F.E., King, K.A., Ruiz, A., Sciarresi, C., Baum, M.E., Danalatos, G.N., Stallman, M., Wiley, E., Olmedo Pico, L., Thies, A., Puntel, L.A., Topp, C.N., Trifunovic, S., Eudy, D., Mensah, C., Edwards, J.W., Schnable, P.S., Lamkey, K.R., Vyn, T.J., Archontoulis, S.V. 2023. Accelerated leaf appearance and flowering in maize after four decades of commercial breeding. Crop Science. 1-13. https://doi.org/10.1002/csc2.21044.
Bapat, A.R., Moran Lauter, A., Hufford, M.B., Boerman, N.A., Scott, M.P. 2023. The Ga1 locus of the genus Zea is associated with novel genome structures derived from multiple, independent nonhomologous recombination events. G3, Genes/Genomes/Genetics. Article jkad196. https://doi.org/10.1093/g3journal/jkad196.
Ledesma, A., Sales Ribeiro, F., Uberti, A., Edwards, J.W., Hearne, S., Frei, U., Lubberstedt, T. 2023. Molecular characterization of doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic (BSSS) maize population. Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1226072.
Lima, D., Castro, A., Alpers, T., Perkins, A., De Leon, N., Kaeppler, S., Ertl, D., Romay, C., Gage, J., Holland, J.B., Thompson, A., Hirsch, C., Hooker, D., Buckler Iv, E.S., Schnable, J., Wallace, J., Edwards, J.W., Knoll, J.E., Singh, M., Bohn, M., Tuinstra, M., Thomison, P., Sekhon, R., Minyo, R., Murray, S., Flint Garcia, S.A., Weldekidan, T., Beissinger, T., Xu, W. 2023. 2020-2021 Field seasons of maize G x E project within maize genomes to fields initiative. BMC Research Notes. 16, 219 (2023). https://doi.org/10.1186/s13104-023-06430-y.
Lima, D.C., Washburn, J.D., Varela, J.I., Chen, Q., Gage, J.L., Romay, M.C., Holland, J.B., Ertl, D., Lopez-Cruz, M., Aguate, F.M., De Los Campos, G., Kaeppler, S., Beissinger, T., Bohn, M., Buckler IV, E.S., Edwards, J.W., Flint Garcia, S.A., Gore, M.A., Hirsch, C.N., Knoll, J.E., Mckay, J., Minyo, R., Murray, S.C., Ortez, O.A., Schnable, J., Sekhon, R.S., Singh, M.P., Sparks, E.E., Thompson, A., Tuinstra, M., Wallace, J., Weldekidan, T., Xu, W., De Leon, N. 2023. Genomes to fields 2022 maize genotype by environment prediction competition. BMC Research Notes. 16: Article 148. https://doi.org/10.1186/s13104-023-06421-z.
Elli, E.F., Edwards, J.W., Yu, J., Trifunovic, S., Eudy, D.M., Kosola, K.R., Schnable, P.S., Lamkey, K.R., Archontoulis, S.V. 2023. Maize leaf angle genetic gain is slowing down in the last decades. Crop Science. 63(6):3520-3533. https://doi.org/10.1002/csc2.21111.
Yanarella, C.F., Fattel, L., Kristmundsdottir, A.Y., Lopez, M.D., Edwards, J.W., Campbell, D.A., Abel, C.A., Lawrence-Dill, C.J. 2024. Wisconsin diversity panel phenotypes: spoken descriptions of plants and supporting data. BMC Research Notes. 17. Article 33. https://doi.org/10.1186/s13104-024-06694-y.
King, K.A., Archontoulis, S.V., Baum, M., Edwards, J.W. 2023. From a point to a range of optimum estimates for maize plant density and nitrogen rate recommendations. Agronomy Journal. 116(2):598-611. https://doi.org/10.1002/agj2.21516.
Ledesma, A., Santana, A.S., Ribeiro, F.S., Auilar, F.S., Edwards, J.W., Frei, U., Lubberstedt, T. 2023. Genome-wide association analysis of plant architecture traits using doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic maize population. Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1294507.
Bapat, A.R., Scott, M.P. 2024. Pectin methylesterase activities in reproductive tissues of maize plants with different haplotypes of the Ga1 and Ga2 cross incompatibility systems. Plant Reproduction. https://doi.org/10.1007/s00497-024-00502-0.