Research Project: Optimizing Photosynthesis for Global Change and Improved Yield

Location: Global Change and Photosynthesis Research

2019 Annual Report

Objectives
Objective 1: Improve photosynthetic efficiency along with water/nitrogen use efficiency in crops for greater food production and bioenergy crop yields. 1.1 Decrease leaf chlorophyll content to maximize water and nitrogen use efficiency without reduction in the daily integral of canopy carbon. 1.2 Lower energetic costs of photorespiration by installing improved engineered chloroplast photorespiratory bypass pathways. 1.3 Stack best performing reduced chlorophyll and photorespiratory traits to combine efficiencies. 1.4 Determine the heritability of photosynthetic traits in maize, and map QTL for photosynthetic traits and their response to abiotic stress. Objective 2: Identify key regulatory factors controlling carbon and nitrogen assimilation and partitioning in crop plants for improving seed composition and yields. 2.1 Determine the impact of canopy microenvironment on soybean seed composition as affected by canopy position. 2.2 Optimize Rubisco activase (Rca) regulation for dynamic light and temperature environments. Objective 3: Identify new genetic loci for enhancing crop resilience to environmental extremes (higher temperature and increased drought) by determining the major loci and physiological mechanisms that modulate crop performance in response to elevated atmospheric CO2 and tropospheric ozone (GxE). 3.1 Test the response of diverse soybean cultivars to elevated [CO2] and advance genetic populations for mapping CO2 response in soybean. 3.2 Use functional genomic and metabolomic approaches to dissect the mechanistic basis for O3 response in maize. 3.3 Investigate the interactive effects of elevated [O3] and drought stress or high temperature stress on crops. Objective 4: Advance the optimization of central ecosystem services for current and alternative food and bioenergy production systems for carbon, water, nutrient cycling, and energy partitioning, by determining the linkages among genetic, physiological, whole-plant, and ecosystem processes (GxE). 4.1 Quantify direct and indirect ecosystem services for traditional and alternative agroecosystem including but extending beyond harvestable yield. 4.2 Dissociate the impacts of rising temperature and increasing vapor pressure deficit on key ecosystem processes and crop yield. 4.3 Develop techniques for high-throughput phenotyping of leaf and canopy physiological properties to better associate genotype to phenotype. 4.4 Incorporate improved physiological understanding of crop responses to global change and stress conditions into mechanistic crop production models.

Approach
The overall goal of this project is to identify factors affecting food and bioenergy crop production, with an emphasis on photosynthetic performance and intensifying environmental stress. Overall, the experimental approaches combine biophysics, biochemistry, physiology, molecular biology, genetics and genomics. The research will include both laboratory- and field-based studies. Specific approaches for each objective are: Objective 1 – utilize systems biology and transgenic approaches to decrease canopy chlorophyll and reduce flux through photorespiration, as well as to identify genetic variation in photosynthetic traits. Objective 2 – assess the impact of canopy microenvironment on soybean seed composition and engineer Rubisco activase to improve function in dynamic light and temperature environments. Objective 3 – identify genetic loci and the mechanistic basis for enhancing crop responses to global climate change by using free air concentration enrichment and functional genomic and metabolic approaches. Objective 4 – optimize food and bioenergy production systems by high-throughput phenotyping and modeling. Mechanistic crop production models will be developed to improve understanding of carbon, water and nutrient cycling responses to environmental changes.

Progress Report
This is a report for Project 5012-21000-030-00D, which started in June 2018. Research has been initiated for all milestones including improving photosynthetic efficiency in crops, identifying key regulatory factors controlling carbon and nitrogen assimilation and partitioning, identifying new genetic loci for enhancing crop resilience to environmental extremes, and modeling central ecosystem services for current and alternative food and bioenergy production systems. Progress toward improving photosynthetic efficiency was made by testing the heritability of photosynthesis and photosynthetic response to ozone in a half diallel maize population grown at ambient and elevated ozone concentrations at the Soybean Free Air Concentration Enrichment facility. Research discovered that photosynthetic response to ozone pollution was a good predictor of seed yield response to ozone pollution, the heritability of photosynthesis was greater in elevated ozone pollution, and hybrids created from parents Hp301 and NC338 showed greater sensitivity to ozone stress. Carbon and nitrogen partitioning was tested in soybean with and without genetic modification to key Calvin Cycle enzymes grown at ambient and elevated carbon dioxide concentrations, and ambient and elevated temperature at the Soybean Free Air Concentration Enrichment facility. Soybeans were monitored for physiological response and seeds from different layers within the canopy were sampled with the goal of analyzing final yield and seed composition. Progress toward identifying new genetic loci for enhancing crop resilience to environmental extremes came from experiments with near isogenic lines of maize grown at ambient and elevated ozone concentrations and historical soybean cultivars grown at ambient and elevated carbon dioxide concentrations. Significant quantitative trait loci associated with leaf visual damage and photosynthesis in maize were identified. Experiments comparing maize, switchgrass, and sorghum responses to elevated ozone pollution are ongoing. Nine historical soybean cultivars were grown in ambient and elevated carbon dioxide concentrations in the field. Molecular, biochemical, and physiological analysis of these historical lines and their response to carbon dioxide enrichment is ongoing. Advanced ecosystem-scale experiments in diverse bioenergy and cropping systems and construction of in-field gantry systems for high-throughput phenotyping have been established. This research along with advances in modeling contributes to better understanding of ecosystem services provided by annual and perennial cropping systems.

Accomplishments
1. Rising temperatures may safeguard crop nutrition as climate changes. Recent research has shown that rising carbon dioxide levels will likely boost yields but at the cost of nutrition. ARS researchers in Urbana, Illinois, grew soybeans, a major crop for the U.S., in real-world field conditions at the Soybean Free-Air Concentration Experiment (SoyFACE), an agricultural research facility at the University of Illinois that is equipped to increase carbon dioxide and temperature to futuristic levels. The results suggest rising temperatures may benefit seed nutrient content but at the expense of lower yields. Two years of field trials show that increasing temperatures by about 3 degrees Celsius may help preserve seed quality, offsetting the effects of carbon dioxide that make food less nutritious. In soybeans, elevated carbon dioxide levels decreased the amount of iron and zinc in the seed by about 8 to 9 percent, but increased temperatures had the opposite effect. This study shows that a trade-off between optimizing yields for global change and seed nutritional quality may exist, which is an important consideration for future agricultural production related to human nutrition.

2. Uncovering genetic variation in photosynthesis of field-grown maize under ozone pollution. Ozone is a damaging air pollutant to crops, currently costing Midwest U.S. maize producers up to 10% of potential yields. However, there has been little effort to adapt germplasm for ozone tolerance. ARS researchers in Urbana, Illinois, crossed ten diverse inbred maize lines parents with one another to create 45 hybrids, which were tested for ozone response in the field. Results showed that ozone stress altered the heritability of photosynthesis and hybrids created from lines Hp301 and NC338 were particularly sensitive to ozone stress. The research implies that past selection of maize under current ambient ozone levels did not select against alleles that confer sensitivity to ozone pollution. Research was presented at international conferences.

3. Stacking of machine learning algorithms to improve predictions of yield-boosting crop traits. To better predict high-yielding crop traits, methods are required to rapidly and non-destructively analyze key crop traits. ARS researchers in Urbana, Illinois, have stacked together six high-powered, machine learning algorithms that are used to interpret light data reflected from plants. They demonstrated that this technique improved the predictive power of important crop traits related to photosynthesis up to 15 percent, above previous techniques. This work will help to advance the understanding of how crops respond to their environment by allowing researchers and breeders to better understand how crops function in the real world.

4. Elevated ozone concentration reduces photosynthetic carbon gain but does not alter nutrient composition or whole plant biomass in switchgrass. Obtaining renewable energy from biomass feedstocks is projected to reduce reliance on traditional fossil fuels and emissions of greenhouse gases while benefitting economic growth and energy security. Switchgrass is a native perennial warm-season grass and has been recognized as an emerging and promising bioenergy feedstock in the United States. ARS researchers in Urbana, Illinois, used Free Air Concentration Enrichment technology to fumigate switchgrass with elevated ozone concentrations, and measured photosynthetic, growth and nutrient responses to elevated ozone. The study provides evidence that switchgrass exhibits ozone tolerance and suggests that crops such as maize and switchgrass vary in ozone tolerance. Better understanding of variation in bioenergy feedstock responses to air pollution could be used to strategically place bioenergy feedstocks on a dynamic landscape.

Review Publications
South, P.F., Cavanagh, A.P., Liu, H.W., Ort, D.R. 2019. Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field. Science. 363(6422). https://doi.org/10.1126/science.aat9077.
Wedow, J.M., Yendrek, C.R., Mello, T.R., Creste, S., Martinez, C.A., Ainsworth, E.A. 2019. Metabolite and transcript profiling of Guinea grass (Panicum maximum Jacq) response to elevated [CO2] and temperature. Metabolomics. 15:51. https://doi.org/10.1007/s11306-019-1511-8.
Ainsworth, E.A., Lemonnier, P., Wedow, J.M. 2019. The influence of rising tropospheric carbon dioxide and ozone on plant productivity. Plant Biology. 15:51. https://doi.org/10.1111/plb.12973.
Li, S., Courbet, G., Ourry, A., Ainsworth, E.A. 2019. Elevated ozone concentration reduces photosynthetic carbon gain but does not alter leaf structural traits, nutrient composition, or biomass in switchgrass. Plants. 8(4):85. https://doi.org/10.3390/plants8040085.
Ruiz-Vera, U.M., Siebers, M.H., Jaiswal, D., Ort, D.R., Bernacchi, C.J. 2018. Canopy warming accelerates development in soybean and maize, offsetting the delay in soybean reproductive development by elevated CO2 concentrations. Plant, Cell & Environment. 41:2806-2820. https://doi.org/10.1111/pce.13410.
Zhu, P., Jin, Z., Zhuang, Q., Ciais, P., Bernacchi, C.J., Wang, X., Makowski, D., Lobell, D. 2018. The important but weakening maize yield benefit of grain filling prolongation in the US Midwest. Global Change Biology. 24:4718-4730. https://doi.org/10.1111/gcb.14356.
South, P.F., Cavanagh, A.P., Lopez-Calcagno, P.E., Raines, C.A., Ort, D.R. 2018. Optimizing photorespiration for improved crop productivity. Journal of Integrative Plant Biology. https://doi.org/10.1111/jipb.12709.
South, P.F., Lopez-Calgano, P., Raines, C., Fisk, S., Bull, S. 2018. Overexpressing the H-protein of the glycine cleavage system increases biomass yield in glasshouse and field-grown transgenic tobacco plants. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.12953.
Lichiheb, N., Myles, L., Personne, E., Heuer, M., Buban, M., Nelson, A., Kloutsou-Vakakis, S., Rood, M., Joo, E., Miller, J., Bernacchi, C.J. 2019. Implementation of the effect of urease inhibitor on ammonia emissions following urea-based fertilizer application at a Zea mays field in central Illinois: A study with SURFATM-NH3 model. Agricultural and Forest Meteorology. 269-270:78-87. https://doi.org/10.1016/j.agrformet.2019.02.005.
Koehler, I.H., Huber, S.C., Baxter, I.R., Bernacchi, C.J. 2019. Increased temperatures may safeguard the nutritional quality of crops under future elevated CO2 concentrations. Plant Journal. 97(5):872-886. https://doi.org/10.1111/tpj.14166.
Zhu, P., Zhuang, Q., Archontoulis, S., Bernacchi, C.J., Mueller, C. 2019. Dissecting the nonlinear response of maize yield to high temperature stress with model-data integration. Global Change Biology. https://doi.org/10.1111/gcb.14632.
Sorgini, C.A., Barrios-Perez, I., Brown, P.J., Ainsworth, E.A. 2019. Examining genetic variation in maize inbreds and mapping oxidative stress response QTL in B73-Mo17 nearly isogenic lines. Frontiers in Sustainable Food Systems. 3:51. https://doi.org/10.3389/fsufs.2019.00051.
Meacham-Hensold, K., Montes, C.M., Wu, J., Guan, K., Pederson, T., Moore, C., Ainsworth, E.A., Raines, C., Brown, K., Bernacchi, C.J. 2019. High-throughput field phenotyping using hyperspectral reflectance and partial least squares regression (PLSR) reveals genetic modifications to photosynthetic capacity. Remote Sensing of Environment. 231:111176. https://doi.org/10.1016/j.rse.2019.04.029.
Fu, P., Xie, Y., Weng, Q., Myint, S., Meacham-Hensold, K., Bernacchi, C.J. 2019. A physical model-based method for retrieving urban land surface temperatures under cloudy conditions. Remote Sensing of Environment. 230:111191. https://doi.org/10.1016/j.rse.2019.05.010.