Location: Corn Insects and Crop Genetics Research
2020 Annual Report
Objectives
Objective 1: Develop improved maize phenotyping methods based on process-based crop growth models and high throughput phenotyping methods.
Subobjective 1.1: Develop and validate crop growth model calibrations for diverse maize hybrids to predict maize hybrid performance across diverse environments.
Subobjective 1.2: Evaluate high throughput biochemical and metabolic assays for calibration of crop growth models and prediction of maize grain yield.
Subobjective 1.3: Evaluate remote sensing approaches for improving prediction of maize performance and crop growth model calibration.
Objective 2: Understand the molecular genetic control of gametophytic incompatibility.
Subobjective 2.1: Determine if ZmPme3 complements the ga1 allele to restore the female function of Ga1-s.
Subobjective 2.2: Determine the biochemical mechanism of pollen exclusion by the Ga1 system using E. coli expressed ZmPME3.
Subobjective 2.3: Identify binding partners of ZmPME3.
Approach
In order to used 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 to 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
Genetic tests for complementation of ga1 (gametophyte factor 1) by Zea mays pectin methylesterase 3 (ZmPME3). In previous work collaborating with researchers from the University of Hawaii, we reported that a gene called ZmPME3 was involved in cross incompatibility, a trait that prevents a plant from outcrossing with another plant to produce seed. In order to demonstrate the role of ZmPME3 conclusively, we created transgenic maize plants carrying ZmPME3 to see if they gained the cross- incompatibility trait. The transgenic plants were tested by making a cross. The result of the cross suggested that ZmPME3 did not work as predicted. This may be because the transgenic plants did not have enough copies of the transgene to be successful, so this year we repeated the experiment with plants with more copies of ZmPME3. This work is important because it will show conclusively whether ZmPME3 causes cross incompatibly which can be used to increase genetic purity of maize varieties.
Characterize cell walls treated with pectin methylesterase (PME). For maize to produce seeds, pollen from one plant must fertilize an egg in another plant. This requires a pollen tube to grow from where the pollen lands on the plant to an ovary containing egg. The scientific community has evidence that an enzyme called PME is involved in pollen tube growth. To understand its function, we produced a PME encoded by the gene ZmPME3 in the bacterium E. coli as described in the project plan. A novel protein with the same mass as PME accumulated in the bacterial cells. We confirmed that this protein was PME by mass spectrometry and protein sequence analysis. Unfortunately, this protein was not active, probably due to insolubility. We are currently testing methods to solubilize the protein and different expression systems as described in the contingency of our project plan. Other groups have succeeded with expression of similar proteins in Picia pastoris so our next attempt will be to use this system. This work is important because it will allow us to understand how PMEs function to control pollen tube growth, a fundamental biological process that we depend upon for production of food, fiber and fuel.
Comparing pollen exclusion between field corn and popcorn. The gametophyte factor 1 (Ga1) genetic locus is used in popcorn and field corn to increase the genetic purity of grain by preventing unwanted pollen from fertilizing plants in a production field. For example, Ga1 can reduce genetically modified organism (GMO) contamination of grain. In collaboration with two seed companies, we initiated an experiment to compare the ability to prevent unwanted pollinations by field corn hybrids that contain the Ga1-S (Gametophyte factor 1 strong) locus and popcorn hybrids that contain the same locus. Six field corn and six popcorn varieties were planted in the summer of 2019 and their ability to exclude pollen was measured. The experiment will be repeated in the summer of 2020. This experiment may impact regulatory decisions regarding GMO testing of maize field corn hybrids that carry the Ga1 locus. Currently, popcorn does not require GMO testing, while field corn does even though some field corn is protected by Ga1 in the same way that popcorn is. The data from this experiment may allow development of regulations based on the effectiveness of excluding unwanted pollen. This will allow GMO testing resources to be used more efficiently, resulting in increased genetic purity of grain.
Elucidating the genomic context of the Ga1 Locus. The Ga1 genetic locus in maize controls the ability of maize to produce grain, a trait called cross incompatibility. A large segment of the genome surrounding this locus contains inactive genes (pseudogenes) that are related to the active genes at the Ga1 locus. In collaboration with scientists from Iowa State University, we initiated a new computational project to analyze the genome structure around the Ga1 locus in 20 diverse varieties including the popcorn variety HP301. This allowed us to identify structural differences between genomes and analyze the phylogenetic relationships among pseudogenes in varieties with different structures. The goal of this work is to test the hypothesis that the function of the Ga1 locus is responsible for the evolution of this unusual genome structure by creating selective pressure against active Ga1 genes. This may help researchers understand how genome structure changes occur and will lead to a greater understanding of how genomes control biological functions.
Crop model calibration and sensitivity analysis. Process-based crop growth models have contributed extensively to our understanding of management and environmental factors affecting crop growth. However, in maize, these models lack full calibrations for specific hybrids that can be used by public researchers. We have completed full calibrations using the Agricultural Production Systems Simulator (APSIM) modeling platform of 15 publicly available hybrids derived from publicly available maize inbred lines. Crop phenology parameters account for 50% of sensitivity of models to cultivar-specific parameters demonstrating these were the most important parameters. In collaboration with an Iowa State University scientist, our work identified two important limitations in current APSIM model: 1) the model does not accurately account for excess water, and 2) the model over-predicts stalk biomass. These limitations will be addressed in future APSIM model releases. Our work has demonstrated a high correlation between simulated and observed grain yield, demonstrating empirically that we can identify process-based parameters that predict differences in grain yield among maize hybrids. Simulated grain yields among maize hybrids exhibited substantial genotype by environment interaction suggesting that crop model simulations may provide a means to simulate and better understand processes underlying genotype by environment interaction. We expect to publish results soon and make the model calibrations for 15 public maize hybrids available for use in the maize research community.
Accomplishments
1. Process-based crop growth model calibration. Predicting how different crop cultivars will respond to varying environmental, weather, and management conditions remains a significant challenge in agriculture. Variable and unpredictable cultivar response to weather and management creates a significant challenge for producers to consistently choose the best cultivars. ARS researchers at Ames, Iowa, have a collaboration with the Genomes to Fields Initiative (G2F), to contribute to publicly available data sets containing integrated genotype, phenotype, climatic, and soil data from diverse environments and genotypes. Diverse hybrids are grown at a large number of environments to collect agronomic performance data in order to develop modeling approaches to better predict cultivar response to diverse environmental conditions. The results of this collaboration have resulted in publicly available data sets from trials conducted in 2014 through 2018 which contain results of a total of 16 independent trials conducted in Ames, Iowa. These data are a novel resource used by researchers nationally and internationally to improve our ability to predict how crop cultivars respond to diverse environments.
Review Publications
Duangpapeng, P., Lertrat, K., Lomthiasong, K., Aguilar, F., Scott, M.P., Suriharn, B. 2020. Quantitative inheritance of total anthocyanin content in the tassel of small-ear waxy corn (Zea mays var. ceratina). SABRAO J. of Breeding and Genetics. 52(1):30-44.
Abel, C.A., Coates, B.S., Millard, M.J., Williams, W.P., Scott, M.P. 2020. Evaluation of XL370A-derived maize germplasm for resistance to leaf feeding by fall armyworm. Southwestern Entomologist. 45(1):69-74. https://doi.org/10.3958/059.045.0107.
Abel, C.A., Coates, B.S., Scott, M.P. 2019. Evaluation of maize germplasm from Saint Croix for resistance to leaf feeding by fall armyworm. Southwestern Entomologist. 44(1):99-103. https://doi.org/10.3958/059.044.0111.
Ramstein, G.P., Larsson, S.J., Cook, J.P., Edwards, J.W., Ersoz, E.S., Flint Garcia, S.A., Gardner, C.A., Holland, J.B., Lorenz, A.J., Mcmullen, M.D., Millard, M.J., Rocheford, T.R., Tuinstra, M.R., Bradbury, P., Buckler IV, E.S., Romay, M.C. 2020. Dominance effects and functional enrichments improve prediction of agronomic traits in hybrid maize. Genetics. 215:215-230. https://doi.org/10.1534/genetics.120.303025.
Mcfarland, B.A., Alkhalifah, N., Bohn, M., Bubert, J., Buckler IV, E.S., Ciampitti, I., Edwards, J.W., Ertl, D., Gage, J.L., Falcon, C.M., Flint Garcia, S.A., Gore, M., Graham, C., Hirsch, C., Holland, J.B., Hood, E., Hooker, D., Jarquin, D., Kaeppler, S., Knoll, J.E., Kruger, G., Lauter, N.C., Lee, E.C., Lima, D.C., Lorenz, A., Lynch, J.P., Mckay, J., Miller, N.D., Moose, S.P., Murray, S.C., Nelson, R., Poudyal, C., Rocheford, T., Rodriguez, O., Romay, M., Schnable, J.C., Schnable, P.S., Scully, B.T., Sekhon, R., Silverstein, K., Singh, M., Smith, M., Spalding, E.P., Springer, N., Thelen, K., Thomison, P., Tuinstra, M., Wallace, J., Walls, R., Wills, D., Wisser, R.J., Xu, W., Yeh, C., De Leon, N. Maize genomes to fields (G2F): 2014 –2017 field seasons: genotype, phenotype, climatic, soil and inbred ear image datasets. BMC Research Notes. 13,71 (2020). https://doi.org/10.1186/s13104-020-4922-8.
Falcon, C.M., Kaeppler, S.M., Spalding, E.P., Miller, N.D., Haase, N., Alkhalifah, N., Bohn, M., Buckler IV, E.S., Campbell, D.A., Ciampitti, I., Coffey, L., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gore, M.A., Graham, C., Hirsch, C.N., Holland, J.B., Jarquin, D., Knoll, J.E., Lauter, N.C., Lawrence-Dill, C.J., Lee, E.C., Lorenz, A., Lynch, J.P., Murray, S.C., Nelson, R., Romay, M., Rocheford, T., Schnable, P., Scully, B.T., Smith, M.C., Springer, N., Tuinstra, M., Walton, R., Weldekidan, T., Wisser, R.J., Xu, W., De Leon, N. Relative utility of agronomic, phenological, and morphological traits for assessing genotype-by-environment interaction in maize inbreds. Crop Science. 2020; 60:62-81. https://doi.org/10.1002/csc2.20035
