@article{ortiz_de smet_sozzani_locke_2024, title={"Field-grown soybean shows genotypic variation in physiological and seed composition responses to heat stress during seed development" (vol 195, 104768, 2022)}, volume={220}, ISSN={["1873-7307"]}, DOI={10.1016/j.envexpbot.2024.105668}, journal={ENVIRONMENTAL AND EXPERIMENTAL BOTANY}, author={Ortiz, Anna C. and De Smet, Ive and Sozzani, Rosangela and Locke, Anna M.}, year={2024}, month={Apr} }
 @article{ethridge_chandra_locke_everman_jordan_owen_leon_2023, title={Changes in the herbicide sensitivity and competitive ability of <i>Abutilon theophrasti</i> over 28 years: Implications for hormesis and weed evolution}, volume={79}, ISSN={1526-498X 1526-4998}, url={http://dx.doi.org/10.1002/ps.7604}, DOI={10.1002/ps.7604}, abstractNote={AbstractBACKGROUNDThe potential of weed species to respond to selection forces affecting the evolution of weedy traits such as competitive ability is poorly understood. This research characterized evolutionary growth changes in a single Abutilon theophrasti Medik. population comparing multiple generations collected from 1988 to 2016. A competition study was performed to understand changes in competitive ability, and a herbicide dose–response study was carried out to assess changes in sensitivity to acetolactate synthase‐inhibiting herbicides and glyphosate over time.RESULTSWhen grown in monoculture, A. theophrasti biomass production per plant increased steadily across year‐lines while leaf number decreased. In replacement experiments, A. theophrasti plants from newer year‐lines were more competitive and produced more biomass and leaf area than the oldest year‐line. No clear differences in sensitivity to imazamox were observed among year‐lines. However, starting in 1995, this A. theophrasti population exhibited a progressive increase in growth in response to a sublethal dose of glyphosate (52 g a.e. ha−1), with the 2009 and 2016 year‐lines having more than 50% higher biomass than the nontreated control.CONCLUSIONThis study demonstrates that weeds can rapidly evolve increased competitive ability. Furthermore, the results indicate the possibility of changes in glyphosate hormesis over time. These results highlight the importance of the role that rapid (i.e., subdecadal) evolution of growth traits might have on the sustainability of weed management strategies. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.}, number={10}, journal={Pest Management Science}, publisher={Wiley}, author={Ethridge, Sandra R. and Chandra, Saket and Locke, Anna M. and Everman, Wesley J. and Jordan, David L. and Owen, Micheal D.K. and Leon, Ramon G.}, year={2023}, month={Jun}, pages={4048–4056} }
 @article{ramanathan_gannon_locke_everman_2023, title={Characterizing atrazine, mesosulfuron-methyl, and topramezone bioavailability in North Carolina soils using greenhouse bioassays}, volume={6}, ISSN={2639-6696}, url={http://dx.doi.org/10.1002/agg2.20371}, DOI={10.1002/agg2.20371}, abstractNote={AbstractHerbicide carryover injury to rotational crops can vary in severity depending on the influence of soil properties on herbicide bioavailability. Greenhouse bioassays were conducted with soybean, radish, and canola to evaluate differences in the bioavailability of three herbicides with carryover risk, atrazine, mesosulfuron‐methyl, and topramezone. Bioassays were conducted in three varying regional soil types with nine herbicide treatment rates including a control. Plant visual injury was evaluated weekly, and aboveground dry biomass was weighed after harvest of soybean 28 days after emergence (DAE) and radish and canola 21 DAE. A log‐logistic dose–response regression model was used to quantify herbicide‐effective concentrations for 30% (EC30), 50% (EC50), and 80% (EC80) visual injury and aboveground dry biomass reduction in each soil type. Relative herbicide‐soil bioavailability was determined through comparisons of herbicide‐effective concentrations among soil types. Pearson correlation revealed that atrazine, mesosulfuron‐methyl, and topramezone EC30 for all species were positively correlated to soil organic matter (OM) content (r = 0.56, 0.48, and 0.40, respectively) and cation exchange capacity (CEC) (r = 0.43, 0.41, and 0.45). Topramezone EC80 for soybean and radish was positively correlated to soil clay content (r = 0.51) and silt content (r = 0.51) and negatively correlated to sand content (r = −0.51) and pH (r = −0.52). Decreased atrazine, mesosulfuron‐methyl, and topramezone bioavailability in soil with high OM and CEC, decreased topramezone bioavailability in coarse‐textured soil and at high soil pH, and differential herbicide sensitivity of crop species can inform grower decisions on herbicide selections and rotational crop plans.}, number={2}, journal={AGROSYSTEMS GEOSCIENCES & ENVIRONMENT}, publisher={Wiley}, author={Ramanathan, Shwetha S. and Gannon, Travis W. and Locke, Anna M. and Everman, Wesley J.}, year={2023}, month={Jun} }
 @article{epie_bauer_stone_locke_2023, title={Density, not tillage, increases soybean protein concentration in some southeastern US environments}, volume={115}, ISSN={0002-1962 1435-0645}, url={http://dx.doi.org/10.1002/agj2.21371}, DOI={10.1002/agj2.21371}, abstractNote={AbstractManagement decisions like planting density and tillage could influence soybean seed composition through their impacts on competition and soil properties. To determine if either of these management decisions could help improve soybean [Glycine max (L.) Merr.] seed quality in the southeastern United States, field experiments were conducted to evaluate the impact of planting density and tillage on seed composition. Five soybean genotypes were examined in multiple environments across three plant densities from 204,000 to 476,000 plants ha−1, and in conventional tillage compared to no‐till. In two of the three environments, seed protein concentration was higher at higher plant densities. Tillage did not affect seed protein concentration, but conventional tillage improved yield when compared with no‐till in two of four environments, resulting in higher protein yield under conventional tillage in these environments. Plant density may be an important management decision to consider for improving soybean seed protein in specific environments in the southeastern United States, and further research could help determine the specific environmental attributes that lead to a density benefit for seed protein.}, number={4}, journal={Agronomy Journal}, publisher={Wiley}, author={Epie, Kenedy Etone and Bauer, Philip J. and Stone, Kenneth C. and Locke, Anna M.}, year={2023}, month={Jun}, pages={1867–1876} }
 @article{van den broeck_bhosale_song_fonseca de lima_ashley_zhu_zhu_van de cotte_neyt_ortiz_et al._2023, title={Functional annotation of proteins for signaling network inference in non-model species}, volume={14}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-023-40365-z}, DOI={10.1038/s41467-023-40365-z}, abstractNote={AbstractMolecular biology aims to understand cellular responses and regulatory dynamics in complex biological systems. However, these studies remain challenging in non-model species due to poor functional annotation of regulatory proteins. To overcome this limitation, we develop a multi-layer neural network that determines protein functionality directly from the protein sequence. We annotate kinases and phosphatases in Glycine max. We use the functional annotations from our neural network, Bayesian inference principles, and high resolution phosphoproteomics to infer phosphorylation signaling cascades in soybean exposed to cold, and identify Glyma.10G173000 (TOI5) and Glyma.19G007300 (TOT3) as key temperature regulators. Importantly, the signaling cascade inference does not rely upon known kinase motifs or interaction data, enabling de novo identification of kinase-substrate interactions. Conclusively, our neural network shows generalization and scalability, as such we extend our predictions to Oryza sativa, Zea mays, Sorghum bicolor, and Triticum aestivum. Taken together, we develop a signaling inference approach for non-model species leveraging our predicted kinases and phosphatases.}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Van den Broeck, Lisa and Bhosale, Dinesh Kiran and Song, Kuncheng and Fonseca de Lima, Cássio Flavio and Ashley, Michael and Zhu, Tingting and Zhu, Shanshuo and Van De Cotte, Brigitte and Neyt, Pia and Ortiz, Anna C. and et al.}, year={2023}, month={Aug} }
 @article{mathers_heitman_huseth_locke_osmond_woodley_2023, title={No-till imparts yield stability and greater cumulative yield under variable weather conditions in the southeastern USA piedmont}, volume={292}, ISSN={0378-4290}, url={http://dx.doi.org/10.1016/j.fcr.2023.108811}, DOI={10.1016/j.fcr.2023.108811}, abstractNote={With projected increases in global temperatures and changes in regional climate, understanding the impact of soil management choices on yield stability is critical for farmer decision-making and agricultural resiliency. No-till and conservation tillage have had variable yield effects depending on crop and location, requiring long-term system-specific studies to gauge potential benefits. Yield and weather data from a 28-year tillage study in the southeastern U.S. piedmont region were analyzed to determine the effect of various conservation tillage practices on maize and soybean productivity and stability under a variety of growth conditions. Growing seasons were grouped by soil moisture and temperature during crop growth stages, and mean crop yields and yield coefficient of variation for the tillage treatments were calculated within the year clusters. Probability density estimates were also used to predict the likelihood of obtaining yields at low and high percentiles. No-till and conservation tillage increased maize yields 42–93% and no-till decreased coefficient of variation of maize yields when soil moisture was low by 10–32%, but had a less pronounced effect on soybean yields. However, the probability of reaching the 90th yield percentile was greater in no-till than conventional tillage in both maize and soybean, by 15% and 10%, respectively. Yield differentiation occurred early in the study, before there was likely substantial differentiation of soil properties from tillage treatments. Previous reports from the site have likewise indicated little differentiation in soil health between tillage systems over the life of the study. Results suggest that surface residue management may be an important driver of system performance, possibly more so than overall soil health.}, journal={Field Crops Research}, publisher={Elsevier BV}, author={Mathers, Cara and Heitman, Joshua and Huseth, Anders and Locke, Anna and Osmond, Deanna and Woodley, Alexander}, year={2023}, month={Mar}, pages={108811} }
 @misc{amin_van den broeck_de smet_locke_sozzani_2023, title={Optimal Brain Dissection in Dense Autoencoders: Towards Determining Feature Importance in -Omics Data}, url={http://dx.doi.org/10.1109/bip60195.2023.10379275}, DOI={10.1109/bip60195.2023.10379275}, abstractNote={Recently, there has been increased interest in ma-chine learning explainability. Understanding the complex relationship between input features of a model and their respective outputs is of increased relevance, especially in biological science. In this paper, we introduce Optimal Brain Dissection (OBD), an innovative methodology designed to examine the importance of first-layer connections in a biology-inspired autoencoder. We incorporated regulator-target interactions within the first autoencoder layer, representing biological regulatory networks, and identified their importance to the reconstruction error, a critical aspect in navigating the complexity of high-dimensional omics data. Through a combination of pruning techniques and counterfactual reasoning, OBD offers a method to quantify feature importance, factoring in both weight magnitude and time-to-laziness. To implement this method, we propose a Dense Autoencoder (DAE) architecture, aiming for increased efficiency and reduced computation. Tailored for omics data, the DAE employs skip concatenations and circumvents non-existent target-target interactions. Our approach aims to understand the relative importance of connections for autoencoder performance, a critical step towards better counter-factual reasoning for neural networks.}, journal={2023 IEEE 5th International Conference on BioInspired Processing (BIP)}, publisher={IEEE}, author={Amin, Fin and Van den Broeck, Lisa and De Smet, Ive and Locke, Anna M. and Sozzani, Rossangela}, year={2023}, month={Nov} }
 @article{ethridge_chandra_everman_jordan_locke_owen_leon_2023, title={Rapid evolution of competitive ability in giant foxtail (<i>Setaria faberi</i>) over 34 years}, volume={71}, ISSN={0043-1745 1550-2759}, url={http://dx.doi.org/10.1017/wsc.2023.1}, DOI={10.1017/wsc.2023.1}, abstractNote={AbstractCompetition between genotypes within a plant population can result in the displacement of the least competitive by more competitive genotypes. Although evolutionary processes in plants may occur over thousands and millions of years, it has been suggested that changes in key fitness traits could occur in as little as decades, with herbicide resistance being a common example. However, the rapid evolution of complex traits has not been proven in weeds. We hypothesized that changes in weed growth and competitive ability can occur in just a few years because of selection in agroecosystems. Seed of multiple generations of a single natural population of the grassy weed giant foxtail (Setaria faberi Herrm.) were collected during 34 yr (i.e., 1983 to 2017). Using a “resurrection” approach, we characterized life-history traits of the different year-lines under noncompetitive and competitive conditions. Replacement-series experiments comparing the growth of the oldest year-line (1983) versus newer year-lines (1991, 1996, 1998, 2009, and 2017) showed that plant competitive ability decreased and then increased progressively in accordance with oscillating selection. The adaptations in competitive ability were reflected in dynamic changes in leaf area and biomass when plants were in competition. The onset of increased competitive ability coincided with the introduction of herbicide-resistant crops in the landscape in 1996. We also conducted a genome-wide association study and identified four loci that were associated with increased competitive ability over time, confirming that this trait changed in response to directional selection. Putative transcription factors and cell wall–associated enzymes were linked to those loci. This is the first study providing direct in situ evidence of rapid directional evolution of competitive ability in a plant species. The results suggest that agricultural systems can exert enough pressure to cause evolutionary adaptations of complex life-history traits, potentially increasing weediness and invasiveness.}, number={1}, journal={Weed Science}, publisher={Cambridge University Press (CUP)}, author={Ethridge, Sandra R. and Chandra, Saket and Everman, Wesley J. and Jordan, David L. and Locke, Anna M. and Owen, Micheal D. K. and Leon, Ramon G.}, year={2023}, month={Jan}, pages={59–68} }
 @article{ethridge_grieger_locke_everman_jordan_leon_2023, title={Views of RNAi approaches for weed management in turfgrass systems}, volume={7}, ISSN={["1550-2759"]}, url={https://doi.org/10.1017/wsc.2023.37}, DOI={10.1017/wsc.2023.37}, abstractNote={AbstractPublic concern regarding the use of herbicides in urban areas (e.g., golf courses, parks, lawns) is increasing. Thus, there is a need for alternative methods for weed control that are safe for the public, effective against weeds, and yet selective to turfgrass and other desirable species. New molecular tools such as ribonucleic acid interference (RNAi) have the potential to meet all those requirements, but before these technologies can be implemented, it is critical to understand the perceptions of key stakeholders to facilitate adoption as well as regulatory processes. With this in mind, turfgrass system managers, such as golf course superintendents and lawn care providers, were surveyed to gain insight into the perception and potential adoption of RNAi technology for weed management. Based on survey results, turfgrass managers believe that cost of weed management and time spent managing weeds are the main challenges faced in their fields. When considering new weed management tools, survey respondents were most concerned about cost, efficacy, and efficiency of a new product. Survey respondents were also optimistic toward RNAi for weed management and would either use this technology in their own fields or be willing to conduct research to develop RNAi herbicides. Although respondents believed that the general public would have some concerns about this technology, they did not believe this to be the most important factor for them when choosing new weed management tools. The need for new herbicides to balance weed control challenges and public demands is a central factor for turfgrass managers’ willingness to use RNAi-based weed control in turfgrass systems. They believe their clientele will be accepting of RNAi tools, although further research is needed to investigate how a wider range of stakeholders perceive RNAi tools for turfgrass management more broadly.}, journal={WEED SCIENCE}, author={Ethridge, Sandra R. and Grieger, Khara and Locke, Anna M. and Everman, Wesley J. and Jordan, David L. and Leon, Ramon G.}, year={2023}, month={Jul} }
 @article{ramanathan_gannon_everman_locke_2022, title={Atrazine, mesosulfuron‐methyl, and topramezone persistence in North Carolina soils}, volume={114}, ISSN={0002-1962 1435-0645}, url={http://dx.doi.org/10.1002/agj2.21041}, DOI={10.1002/agj2.21041}, abstractNote={AbstractInvestigating the effects of soil properties on herbicide persistence can aid in evaluating the carryover potential of herbicides in soil and the consequent injury risk to rotational crops. Laboratory incubation experiments were conducted to quantify the persistence of atrazine, mesosulfuron‐methyl, and topramezone in five regional soils under aerobic conditions at 23 °C. Additionally, mesosulfuron‐methyl persistence was tested at 7 °C, which is representative of regional average winter soil temperature. Herbicide half‐life was calculated with the logarithmic form of first‐order rate of degradation using linear regression and was correlated with soil properties. Half‐lives of atrazine (37–73 d) and topramezone (15–19 d) varied among soil types at 23 °C. Mesosulfuron‐methyl half‐life varied among soils at 7 °C (8.8–9.8 d) and 23 °C (5.4–5.8 d) and between temperatures. Atrazine and topramezone half‐lives were shortest in Candor sand (4% clay, 1.8% organic matter [OM], pH 5.1) and longest in Portsmouth sandy loam (13% clay, 5.3% OM, pH 4.3). Mesosulfuron‐methyl half‐life was longer at lower soil temperature. Half‐lives of atrazine, mesosulfuron‐methyl, and topramezone were correlated with soil OM content (r = .83, −.53, and .63, respectively) and pH (r = −.86, .55, and −.57). Additionally, atrazine and topramezone half‐lives were positively correlated with soil clay content (r = .83 and .71), and mesosulfuron‐methyl half‐life was negatively correlated with temperature (r = −.97). Correlations between soil OM content, clay content, and pH among soil types may have influenced herbicide persistence.}, note={title = {Atrazine, mesosulfuron-methyl, and topramezone persistence in North Carolina soils}, journal = {Agronomy Journal}}, number={2}, journal={Agronomy Journal}, publisher={Wiley}, author={Ramanathan, Shwetha S. and Gannon, Travis W. and Everman, Wesley J. and Locke, Anna M.}, year={2022}, month={Mar}, pages={1068–1079} }
 @article{ethridge_locke_everman_jordan_leon_2022, title={Crop physiological considerations for combining variable-density planting to optimize seed costs and weed suppression}, volume={70}, ISSN={0043-1745 1550-2759}, url={http://dx.doi.org/10.1017/wsc.2022.62}, DOI={10.1017/wsc.2022.62}, abstractNote={AbstractHigh crop densities are valuable to increase weed suppression, but growers might be reluctant to implement this practice due to increased seed cost. Because it is also possible to lower planting densities in areas with no or low weed interference risk, the area allocated to each planting density must be optimized considering seed cost and productivity per plant. In this study, the growth and yield of maize (Zea mays L.), cotton (Gossypium hirsutum L.), and soybean [Glycine max (L.) Merr.] were characterized in response to low planting densities and arrangements. The results were used to develop a bioeconomic model to optimize the area devoted to high- and low-density plantings to increase weed suppression without increasing seed cost. Physiological differences seen in each crop varied with the densities tested; however, maize was the only crop that had differences in yield (per area) between densities. When a model to optimize low and high planting densities was used, maize and cotton showed the most plasticity in yield per planted seed (g seed−1) and area of low density to compensate for high-density area unit. Maize grown at 75% planting density compared with the high-planting density (200%) increased yield (g seed−1) by 229%, return by 43%, and profit by 79% while decreasing the low-density area needed to compensate for high-density area. Cotton planted at 25% planting density compared with the 200% planting density increased yield (g seed−1) by 1,099%, return by 46%, and profit by 62% while decreasing the low-density area needed to compensate for high-density area. In contrast, the high morphological plasticity of soybean did not translate into changes in area optimization, as soybean maintained return, profit, and a 1:1 ratio for area compensation. This optimization model could allow for the use of variable planting at large scales to increase weed suppression while minimizing costs to producers.}, number={6}, journal={Weed Science}, publisher={Cambridge University Press (CUP)}, author={Ethridge, Sandra R. and Locke, Anna M. and Everman, Wesley J. and Jordan, David L. and Leon, Ramon G.}, year={2022}, month={Nov}, pages={687–697} }
 @article{epie_bauer_stone_locke_2022, title={Nitrogen fertilizer effects on soybean physiology, yield components, seed yield and protein content in the Southeastern United States}, volume={46}, ISSN={0190-4167 1532-4087}, url={http://dx.doi.org/10.1080/01904167.2022.2084106}, DOI={10.1080/01904167.2022.2084106}, abstractNote={Abstract Soybean physiology, seed yield and composition can vary greatly and are a function of genetics, environment, and management practices. N fertilizer is not often applied to soybeans, but it can affect yield and seed composition, and the outcome of N fertilization has varied widely among studies. To test if certain physiological responses might be linked with positive agronomic responses to N fertilizer, a field study was conducted in varied environments unique to the Southeast United States (US). Five genotypes from maturity groups V-VII were evaluated. Although the environment and genotype had significant effects on most of the physiological characteristics and yield components measured, nitrogen application interacted significantly with environment for seed protein concentration, seed oil concentration, yield, and percent of nitrogen derived from the atmosphere in leaves during the seed fill period. The direction of the nitrogen effect on protein concentration differed among environments, increasing protein concentration in one environment and reducing protein concentration in another environment. Nitrogen application effects did not vary among the genotypes included in this study. Photosynthetic and nitrogen fixation responses to nitrogen application were not clearly linked with seed protein concentration response. A tailored nitrogen recommendation for environment is the best option for improving seed protein in this region with diverse environmental conditions.}, number={3}, journal={Journal of Plant Nutrition}, publisher={Informa UK Limited}, author={Epie, Kenedy Etone and Bauer, Philip J. and Stone, Kenneth C. and Locke, Anna M.}, year={2022}, month={Jul}, pages={462–472} }
 @article{ethridge_locke_everman_jordan_leon_2022, title={Response of Maize, Cotton, and Soybean to Increased Crop Density in Heterogeneous Planting Arrangements}, volume={12}, ISSN={2073-4395}, url={http://dx.doi.org/10.3390/agronomy12051238}, DOI={10.3390/agronomy12051238}, abstractNote={The reduction of row spacing and increase of crop population density are important tools for maximizing crop yield. For this strategy to be effective, the crop population should not create intraspecific crop competition that penalizes yield. Thus, planting arrangements that increase light interception throughout the canopy without increasing row spacing might be needed to maintain yield. In this study, heterogeneous planting arrangements on evenly spaced rows were analyzed for maize (Zea mays L.), cotton (Gossypium hirsutum L.), and soybean (Glycine max (L.) Merr.). Each crop had four planting arrangements: (1) normal density in all rows, considered the control, (2) doubled density in all rows, (3) a sequential arrangement of normal and tripled densities (each in every other row; NTNT), and (4) normal-tripled-tripled-normal (NTTN). Maize and cotton did not exhibit changes in growth and architecture when comparing uniform and variable planting arrangements. Soybeans were more adaptable and increased biomass production by 44% to 45% in variable arrangements. None of the crops showed differences in yield due to planting arrangement, so the use of rows with different densities might not be needed when using high densities to maximize yield.}, number={5}, journal={Agronomy}, publisher={MDPI AG}, author={Ethridge, Sandra R. and Locke, Anna M. and Everman, Wesley J. and Jordan, David L. and Leon, Ramon G.}, year={2022}, month={May}, pages={1238} }
 @article{ortiz_de smet_sozzani_locke_2022, title={Field-grown soybean shows genotypic variation in physiological and seed composition responses to heat stress during seed development}, volume={195}, ISSN={0098-8472}, url={http://dx.doi.org/10.1016/j.envexpbot.2021.104768}, DOI={10.1016/j.envexpbot.2021.104768}, abstractNote={An average temperature increase between 2.6 and 4.8 °C, along with more frequent extreme temperatures, will challenge crop productivity by the end of the century. To investigate genotypic variation in soybean response to elevated temperature, six soybean (Glycine max) genotypes were subjected to elevated air temperature of + 4.5 °C above ambient for 28 days in open-top field chambers. Gas exchange and chlorophyll fluorescence were measured before and during heating and yield as well as seed composition were evaluated at maturity. Results show that long-term elevated air temperature increased nighttime respiration, increased the maximum velocity of carboxylation by Rubisco, impacted seed protein concentration, and reduced seed oil concentration across genotypes. The genotypes in this study varied in temperature responses for photosynthetic CO2 assimilation, stomatal conductance, photosystem II operating efficiency, quantum efficiency of CO2 assimilation, and seed protein concentration at maturity. These diverse responses among genotypes to elevated air temperature during seed development in the field, reveal the potential for soybean heat tolerance to be improved through breeding and underlines the importance of identifying efficient selection strategies for stress-tolerant crops.}, journal={Environmental and Experimental Botany}, publisher={Elsevier BV}, author={Ortiz, Anna C. and De Smet, Ive and Sozzani, Rosangela and Locke, Anna M.}, year={2022}, month={Mar}, pages={104768} }
 @article{vu_xu_zhu_pan_van zanten_de jong_wang_vanremoortele_locke_van de cotte_et al._2021, title={The membrane-localized protein kinase MAP4K4/TOT3 regulates thermomorphogenesis}, volume={12}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-021-23112-0}, DOI={10.1038/s41467-021-23112-0}, abstractNote={AbstractPlants respond to mild warm temperature conditions by increased elongation growth of organs to enhance cooling capacity, in a process called thermomorphogenesis. To this date, the regulation of thermomorphogenesis has been exclusively shown to intersect with light signalling pathways. To identify regulators of thermomorphogenesis that are conserved in flowering plants, we map changes in protein phosphorylation in both dicots and monocots exposed to warm temperature. We identify MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASE4 (MAP4K4)/TARGET OF TEMPERATURE3 (TOT3) as a regulator of thermomorphogenesis that impinges on brassinosteroid signalling inArabidopsis thaliana. In addition, we show that TOT3 plays a role in thermal response in wheat, a monocot crop. Altogether, the conserved thermal regulation by TOT3 expands our knowledge of thermomorphogenesis beyond the well-studied pathways and can contribute to ensuring food security under a changing climate.}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Vu, Lam Dai and Xu, Xiangyu and Zhu, Tingting and Pan, Lixia and van Zanten, Martijn and de Jong, Dorrit and Wang, Yaowei and Vanremoortele, Tim and Locke, Anna M. and van de Cotte, Brigitte and et al.}, year={2021}, month={May} }
 @article{ramos-giraldo_reberg-horton_locke_mirsky_lobaton_2020, title={Drought Stress Detection Using Low-Cost Computer Vision Systems and Machine Learning Techniques}, volume={22}, ISSN={1520-9202 1941-045X}, url={http://dx.doi.org/10.1109/MITP.2020.2986103}, DOI={10.1109/MITP.2020.2986103}, abstractNote={The real-time detection of drought stress has major implications for preventing cash crop yield loss due to variable weather conditions and ongoing climate change. The most widely used indicator of drought sensitivity/tolerance in corn and soybean is the presence or absence of leaf wilting during periods of water stress. We develop a low-cost automated drought detection system using computer vision coupled with machine learning (ML) algorithms that document the drought response in corn and soybeans field crops. Using ML, we predict the drought status of crop plants with more than 80% accuracy relative to expert-derived visual drought ratings.}, number={3}, journal={IT Professional}, publisher={Institute of Electrical and Electronics Engineers (IEEE)}, author={Ramos-Giraldo, Paula and Reberg-Horton, Chris and Locke, Anna M. and Mirsky, Steven and Lobaton, Edgar}, year={2020}, month={May}, pages={27–29} }
 @article{alam_hummel_yeung_locke_ignacio_baltazar_jia_ismail_septiningsih_bailey‐serres_2020, title={Flood resilience loci <i>SUBMERGENCE 1</i> and <i>ANAEROBIC GERMINATION 1</i> interact in seedlings established underwater}, volume={4}, ISSN={2475-4455 2475-4455}, url={http://dx.doi.org/10.1002/pld3.240}, DOI={10.1002/pld3.240}, abstractNote={AbstractCrops with resilience to multiple climatic stresses are essential for increased yield stability. Here, we evaluate the interaction between two loci associated with flooding survival in rice (Oryza sativa L.). ANAEROBIC GERMINATION 1 (AG1), encoding TREHALOSE 6‐PHOSPHATE PHOSPHATASE 7 (TPP7), promotes mobilization of endosperm reserves to enhance the elongation of a hollow coleoptile in seeds that are seeded directly into shallow paddies. SUBMERGENCE 1 (SUB1), encoding the ethylene‐responsive transcription factor SUB1A‐1, confers tolerance to complete submergence by dampening carbohydrate catabolism, to enhance recovery upon desubmergence. Interactions between AG1/TPP7 and SUB1/SUB1A‐1 were investigated under three flooding scenarios using four near‐isogenic lines by surveying growth and survival. Pyramiding of the two loci does not negatively affect anaerobic germination or vegetative‐stage submergence tolerance. However, the pyramided AG1 SUB1 genotype displays reduced survival when seeds are planted underwater and maintained under submergence for 16 d. To better understand the roles of TPP7 and SUB1A‐1 and their interaction, temporal changes in carbohydrates and shoot transcriptomes were monitored in the four genotypes varying at the two loci at four developmental timeponts, from day 2 after seeding through day 14 of complete submergence. TPP7 enhances early coleoptile elongation, whereas SUB1A‐1 promotes precocious photoautotrophy and then restricts underwater elongation. By contrast, pyramiding of the AG1 and SUB1 slows elongation growth, the transition to photoautotrophy, and survival. mRNA‐sequencing highlights time‐dependent and genotype‐specific regulation of mRNAs associated with DNA repair, cell cycle, chromatin modification, plastid biogenesis, carbohydrate catabolism and transport, elongation growth, and other processes. These results suggest that interactions between AG1/TPP7 and SUB1/SUB1A‐1 could impact seedling establishment if paddy depth is not effectively managed after direct seeding.}, number={7}, journal={Plant Direct}, publisher={Wiley}, author={Alam, Rejbana and Hummel, Maureen and Yeung, Elaine and Locke, Anna M. and Ignacio, John Carlos I. and Baltazar, Miriam D. and Jia, Zhenyu and Ismail, Abdelbagi M. and Septiningsih, Endang M. and Bailey‐Serres, Julia}, year={2020}, month={Jul} }
 @article{locke_ramirez_2020, title={Increased nitrogen fixation and remobilization may increase seed protein without a yield penalty in a soybean introgression line}, volume={35}, ISSN={1542-7528 1542-7536}, url={http://dx.doi.org/10.1080/15427528.2020.1835771}, DOI={10.1080/15427528.2020.1835771}, abstractNote={ABSTRACT Development of soybean [Glycine max (L.) Merr.] varieties with high seed protein concentration are hindered by a negative correlation between seed protein and yield. “Benning HP,” a genotype that breaks this tradeoff, contains an introgressed high-protein allele. Field and growth chamber experiments were conducted to identify N flux(es) that enable Benning HP’s increased seed protein without a yield penalty. When the N source was completely controlled, Benning HP could fix more N than its recurrent parent, but this depended on the rhizobium strain and plant developmental stage. In the field, Benning HP remobilized N from its leaves at a higher rate than its recurrent parent during seed fill in only one of the years studied. These results demonstrate that Benning HP has higher potential N fixation and N remobilization from vegetative tissue compared to its lower protein parent, but the expression of those traits may depend on environment and sink control.}, number={4}, journal={Journal of Crop Improvement}, publisher={Informa UK Limited}, author={Locke, Anna M. and Ramirez, Martha E.}, year={2020}, month={Oct}, pages={486–507} }
 @article{rosas-anderson_sinclair_locke_carter_rufty_2020, title={Leaf gas exchange recovery of soybean from water-deficit stress}, volume={34}, ISSN={1542-7528 1542-7536}, url={http://dx.doi.org/10.1080/15427528.2020.1764429}, DOI={10.1080/15427528.2020.1764429}, abstractNote={ABSTRACT As the risk of drought attributable to climate change increases, the development of high-yielding, drought-adapted cultivars will be critical for minimizing yield losses in crops like soybean (Glycine max (L.) Merr.). In this study, the ability of soybean genotypes to recover transpiration and leaf gas exchange capacity following re-watering from soil drying was investigated. The plants were subjected to controlled water-deficit stress and recovery in growth-chamber experiments. Transpiration was measured on five soybean genotypes and photosynthesis rates on two select genotypes. After water re-supply, transpiration was initially low but increased until a stable rate was reached on day 3, to about 50% to 100% of the rates of reference plants that had not been stressed. The largest difference in maximum transpiration recovery was between the varieties USDA-N8002 and Benning compared to the landrace Geden Shirazu, with Geden Shirazu having the lowest recovery. Photosynthesis and vapor-pressure-deficit response measurements did not show that restricted plant stomatal conductance was responsible for the limitation observed in Geden Shirazu recovery. Since all genotypes showed rapid recovery from water-deficit stress in 3 d, more rapid recovery was not indicated as a major candidate for improving soybean drought tolerance. However, the extent of recovery varied among genotypes and those genotypes that fully recovered to rates of well-watered plants such as Benning and USDA-N8002 would seemingly be advantageous for drought conditions.}, number={6}, journal={Journal of Crop Improvement}, publisher={Informa UK Limited}, author={Rosas-Anderson, Pablo and Sinclair, Thomas R. and Locke, Anna and Carter, Thomas E. and Rufty, Thomas W.}, year={2020}, month={May}, pages={785–799} }
 @misc{ramos-giraldo_reberg-horton_mirsky_lobaton_locke_henriquez_zuniga_minin_2020, title={Low-cost Smart Camera System for Water Stress Detection in Crops}, url={http://dx.doi.org/10.1109/SENSORS47125.2020.9278744}, DOI={10.1109/SENSORS47125.2020.9278744}, abstractNote={The availability of easy-to-use, low-cost, and highly scalable tools makes it possible to achieve rapid and widespread adoption of precision agriculture. In this paper we outline the development of a smart camera system to detect drought stress in corn and soybean crops. The system is comprised of a Raspberry Pi Zero W, Raspberry Pi Camera, WittyPi mini, a cooling and solar power system, temperature sensors both inside and outside of the box, and infrared canopy temperature and light sensors. The system was built to collect data in a configurable time frame and has an embedded machine-learning (ML) processing system. The camera was configured using an Internet of Things (IoT) platform to manage the device and send images to the Cloud. One of the challenges for this system was to effectively implement machine learning models on this limited-resource embedded platform. We achieved an accuracy of 74% with the embedded machine learning algorithm when classifying water stress in soybeans.}, journal={2020 IEEE SENSORS}, publisher={IEEE}, author={Ramos-Giraldo, Paula and Reberg-Horton, S. Chris and Mirsky, Steven and Lobaton, Edgar and Locke, Anna M. and Henriquez, Esleyther and Zuniga, Ane and Minin, Artem}, year={2020}, month={Oct} }
 @article{lee_sung_locke_taliercio_whetten_zhang_carter_burton_mian_2019, title={Registration of USDA‐N6003LP Soybean Germplasm with Low Seed Phytate}, volume={13}, ISSN={1936-5209 1940-3496}, url={http://dx.doi.org/10.3198/jpr2018.09.0064crg}, DOI={10.3198/jpr2018.09.0064crg}, abstractNote={Soybean [Glycine max (L.) Merr.] meal is the main source of protein in poultry and swine rations worldwide. Phytate, the main storage form of phosphorous in soybean meal, is largely indigestible by monogastric animals and, thus, a major concern both for nutrition and for environmental pollution. USDA‐N6003LP (Reg. no. GP‐435, PI 689999) is a low‐phytate (LP) determinate, lodging‐resistant early maturity group (MG) VI soybean germplasm developed and released jointly by the USDA‐ARS and the North Carolina Agricultural Research Service. USDA‐N6003LP is derived from a backcross (BC1) between recurrent parent ‘NC‐Roy’ and LP donor line USDA CX1834. NC‐Roy is a high‐yielding MG VI cultivar adapted to the southern United States. USDA‐N6003LP has 60% lower phytate and 4.8 times higher inorganic phosphorus (Pi) contents in its seed than the seed of NC‐Roy. It matures approximately 5 d earlier and has larger seed size and better lodging resistance (P < 0.05) compared with NC‐Roy. Across 17 environments in the USDA Uniform Soybean Tests, Southern States and over four local yield trials in North Carolina, USDA‐N6003LP yielded 91 and 97% of NC‐Roy, respectively. Field emergences of this line in four tests in NC were 79 to 80% compared with 89 to 90% for NC‐Roy. USDA‐N6003LP is the first early MG VI LP germplasm release with good agronomic performance and relatively normal field emergence. It will be useful as parental stock for soybean breeders interested in developing LP soybean cultivars.}, number={3}, journal={Journal of Plant Registrations}, publisher={Wiley}, author={Lee, Sungwoo and Sung, Mikyung and Locke, Anna and Taliercio, Earl and Whetten, Rebecca and Zhang, Bo and Carter, Thomas E., Jr. and Burton, Joseph W. and Mian, M. A. Rouf}, year={2019}, month={Sep}, pages={427–432} }
 @article{taliercio_scaboo_baxter_locke_2019, title={The Ionome of a Genetically Diverse Set of Wild Soybean Accessions}, volume={59}, ISSN={0011-183X 1435-0653}, url={http://dx.doi.org/10.2135/cropsci2019.02.0079}, DOI={10.2135/cropsci2019.02.0079}, abstractNote={Soybean [Glycine max (L.) Merr.] provides oil and protein for fuel, food, and feed around the world. The limited genetic diversity of domesticated soybean threatens future yield and limits breeders' ability to optimize the nutrient composition of soybean. Glycine soja (L.) Merr. is a wild relative of soybean that is substantially more genetically and phenotypically diverse than domesticated soybean. Breeding advances have overcome many of the challenges of breeding with G. soja. Genomics and publicly available marker data facilitated the identification of a genetically diverse core set from the USDA G. soja germplasm collection and allowed the identification of progeny that capture the valuable genetic diversity present in the wild germplasm. Valuable seed composition traits have been identified among wild soybean accessions. We extend these observations to include the seed ionome of 84 wild soybean accessions. Measurement of the concentrations of 19 elements from wild soybean seeds and 13 G. max accessions from multiple environments show that 17 of the element levels have a range of heritabilities and are substantially influenced by the environment. The average concentrations of many elements were higher in the wild soybean than domesticated soybean and also varied among maturity groups. Genetic markers potentially associated with improved mineral composition of Glycine seed have also been identified. This variation may be sufficient to improve mineral content of soy meal. Notably, S concentrations were higher in G. soja, and S levels correlate with total protein levels and S‐containing amino acids. These observations may be used by breeders to improve seed composition of soybean.}, number={5}, journal={Crop Science}, publisher={Wiley}, author={Taliercio, Earl and Scaboo, Andrew and Baxter, Ivan and Locke, Anna M.}, year={2019}, month={Aug}, pages={1983–1991} }
 @article{locke_slattery_ort_2018, title={Field‐grown soybean transcriptome shows diurnal patterns in photosynthesis‐related processes}, volume={2}, ISSN={2475-4455 2475-4455}, url={http://dx.doi.org/10.1002/pld3.99}, DOI={10.1002/pld3.99}, abstractNote={AbstractMany plant physiological processes have diurnal patterns regulated by diurnal environmental changes and circadian rhythms, but the transcriptional underpinnings of many of these cycles have not been studied in major crop species under field conditions. Here, we monitored the transcriptome of field‐grown soybean (Glycine max) during daylight hours in the middle of the growing season with RNA‐seq. The analysis revealed 21% of soybean genes were differentially expressed over the course of the day. Expression of some circadian‐related genes in field‐grown soybean differed from previously reported expression patterns measured in controlled environments. Many genes in functional groups contributing to and/or depending on photosynthesis showed differential expression, with patterns particularly evident in the chlorophyll synthesis pathway. Gene regulatory network inference also revealed seven diurnally sensitive gene nodes involved with circadian rhythm, transcription regulation, cellular processes, and water transport. This study provides a diurnal overview of the transcriptome for an economically important field‐grown crop and a basis for identifying pathways that could eventually be tailored to optimize diurnal regulation of carbon gain.}, number={12}, journal={Plant Direct}, publisher={Wiley}, author={Locke, Anna M. and Slattery, Rebecca A. and Ort, Donald R.}, year={2018}, month={Dec} }
 @article{heat waves alter reproductive growth in maize without long term effects on photosynthesis and plant water status, url={https://doi.org/10.1016/j.agee.2016.11.008}, DOI={10.1016/j.agee.2016.11.008}, abstractNote={Due to climate change, heat waves are predicted to become more frequent and severe. While long-term studies on temperature stress have been conducted on important crops such as maize (Zea mays), the immediate or long-term effects of short duration but extreme high temperature events during key developmental periods on physiological and yield parameters are unknown. Therefore, heat waves were applied to field-grown maize in east central Illinois using infrared heating technology. The heat waves warmed the canopy approximately 6 °C above ambient canopy temperatures for three consecutive days during vegetative development (Wv1) and during an early reproductive stage (silking; Wv2). Neither treatment affected aboveground vegetative biomass, and Wv1 did not significantly reduce reproductive biomass. However, Wv2 significantly reduced total reproductive biomass by 16% (p < 0.1) due to significant reductions in cob length (p < 0.1), cob mass (p < 0.05), and husk mass (p < 0.05). Although not statistically significant, seed yield was also reduced by 13% (p = 0.15) and kernel number by 10% (p = 0.16) in the Wv2 treatment. Soil water status was unaffected in both treatments, and leaf water potential and midday photosynthesis were only transiently reduced by heating with complete recovery after the treatment period. Therefore, the reduction in Wv2 reproductive biomass was most likely due to greater sensitivity of reproductive structures to direct effects of high temperature stress.} }
 @article{rice sub1a constrains remodeling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery, url={https://doi.org/10.1111/pce.13094}, DOI={10.1111/pce.13094}, abstractNote={AbstractThe rice (Oryza sativa L.) ethylene‐responsive transcription factor gene SUB1A‐1 confers tolerance to prolonged, complete submergence by limiting underwater elongation growth. Upon desubmergence, SUB1A‐1 genotypes rapidly recover photosynthetic function and recommence development towards flowering. The underpinnings of the transition from stress amelioration to the return to homeostasis are not well known. Here, transcriptomic and metabolomic analyses were conducted to identify mechanisms by which SUB1A improves physiological function over the 24 hr following a sublethal submergence event. Evaluation of near‐isogenic genotypes after submergence and over a day of reaeration demonstrated that SUB1A transiently constrains the remodelling of cellular activities associated with growth. SUB1A influenced the abundance of ca. 1,400 transcripts and had a continued impact on metabolite content, particularly free amino acids, glucose, and sucrose, throughout the recovery period. SUB1A promoted recovery of metabolic homeostasis but had limited influence on mRNAs associated with growth processes and photosynthesis. The involvement of low energy sensing during submergence and recovery was supported by dynamics in trehalose‐6‐phosphate and mRNAs encoding key enzymes and signalling proteins, which were modulated by SUB1A. This study provides new evidence of convergent signalling pathways critical to the rapidly reversible management of carbon and nitrogen metabolism in submergence resilient rice.} }
 @article{locke_barding_sathnur_larive_bailey‐serres_2018, title={Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery}, volume={41}, ISSN={0140-7791 1365-3040}, url={http://dx.doi.org/10.1111/pce.13094}, DOI={10.1111/pce.13094}, abstractNote={AbstractThe rice (Oryza sativa L.) ethylene‐responsive transcription factor gene SUB1A‐1 confers tolerance to prolonged, complete submergence by limiting underwater elongation growth. Upon desubmergence, SUB1A‐1 genotypes rapidly recover photosynthetic function and recommence development towards flowering. The underpinnings of the transition from stress amelioration to the return to homeostasis are not well known. Here, transcriptomic and metabolomic analyses were conducted to identify mechanisms by which SUB1A improves physiological function over the 24 hr following a sublethal submergence event. Evaluation of near‐isogenic genotypes after submergence and over a day of reaeration demonstrated that SUB1A transiently constrains the remodelling of cellular activities associated with growth. SUB1A influenced the abundance of ca. 1,400 transcripts and had a continued impact on metabolite content, particularly free amino acids, glucose, and sucrose, throughout the recovery period. SUB1A promoted recovery of metabolic homeostasis but had limited influence on mRNAs associated with growth processes and photosynthesis. The involvement of low energy sensing during submergence and recovery was supported by dynamics in trehalose‐6‐phosphate and mRNAs encoding key enzymes and signalling proteins, which were modulated by SUB1A. This study provides new evidence of convergent signalling pathways critical to the rapidly reversible management of carbon and nitrogen metabolism in submergence resilient rice.}, number={4}, journal={Plant, Cell & Environment}, publisher={Wiley}, author={Locke, Anna M. and Barding, Gregory A., Jr and Sathnur, Sumukh and Larive, Cynthia K. and Bailey‐Serres, Julia}, year={2018}, month={Apr}, pages={721–736} }
 @article{siebers_slattery_yendrek_locke_drag_ainsworth_bernacchi_ort_2017, title={Simulated heat waves during maize reproductive stages alter reproductive growth but have no lasting effect when applied during vegetative stages}, volume={240}, ISSN={0167-8809}, url={http://dx.doi.org/10.1016/j.agee.2016.11.008}, DOI={10.1016/j.agee.2016.11.008}, abstractNote={Due to climate change, heat waves are predicted to become more frequent and severe. While long-term studies on temperature stress have been conducted on important crops such as maize (Zea mays), the immediate or long-term effects of short duration but extreme high temperature events during key developmental periods on physiological and yield parameters are unknown. Therefore, heat waves were applied to field-grown maize in east central Illinois using infrared heating technology. The heat waves warmed the canopy approximately 6 °C above ambient canopy temperatures for three consecutive days during vegetative development (Wv1) and during an early reproductive stage (silking; Wv2). Neither treatment affected aboveground vegetative biomass, and Wv1 did not significantly reduce reproductive biomass. However, Wv2 significantly reduced total reproductive biomass by 16% (p < 0.1) due to significant reductions in cob length (p < 0.1), cob mass (p < 0.05), and husk mass (p < 0.05). Although not statistically significant, seed yield was also reduced by 13% (p = 0.15) and kernel number by 10% (p = 0.16) in the Wv2 treatment. Soil water status was unaffected in both treatments, and leaf water potential and midday photosynthesis were only transiently reduced by heating with complete recovery after the treatment period. Therefore, the reduction in Wv2 reproductive biomass was most likely due to greater sensitivity of reproductive structures to direct effects of high temperature stress.}, journal={Agriculture, Ecosystems & Environment}, publisher={Elsevier BV}, author={Siebers, Matthew H. and Slattery, Rebecca A. and Yendrek, Craig R. and Locke, Anna M. and Drag, David and Ainsworth, Elizabeth A. and Bernacchi, Carl J. and Ort, Donald R.}, year={2017}, month={Mar}, pages={162–170} }
 @article{gray_dermody_klein_locke_mcgrath_paul_rosenthal_ruiz-vera_siebers_strellner_et al._2016, title={Intensifying drought eliminates the expected benefits of elevated carbon dioxide for soybean}, volume={2}, ISSN={2055-0278}, url={http://dx.doi.org/10.1038/nplants.2016.132}, DOI={10.1038/nplants.2016.132}, number={9}, journal={Nature Plants}, publisher={Springer Science and Business Media LLC}, author={Gray, Sharon B. and Dermody, Orla and Klein, Stephanie P. and Locke, Anna M. and McGrath, Justin M. and Paul, Rachel E. and Rosenthal, David M. and Ruiz-Vera, Ursula M. and Siebers, Matthew H. and Strellner, Reid and et al.}, year={2016}, month={Sep} }
 @article{intensifying drought eliminates the expected benefits of elevated carbon dioxide for soybean, url={https://doi.org/10.1038/nplants.2016.132}, DOI={10.1038/nplants.2016.132} }
 @article{locke_ort_2015, title={Diurnal depression in leaf hydraulic conductance at ambient and elevated [CO2] reveals anisohydric water management in field-grown soybean and possible involvement of aquaporins}, volume={116}, ISSN={0098-8472}, url={http://dx.doi.org/10.1016/j.envexpbot.2015.03.006}, DOI={10.1016/j.envexpbot.2015.03.006}, abstractNote={Diurnal cycles of photosynthesis and water use in field-grown soybean (Glycine max) are tied to light intensity and vapor pressure deficit (VPD). At high mid-day VPD, transpiration rates can lead to a decline in leaf water potential (Ψleaf) if leaf hydraulic conductance (Kleaf) is insufficient to supply water to intercellular airspaces in pace with demand. Kleaf is determined by leaf xylem conductivity to water, as well as extra-xylem pathways that are likely mediated by aquaporin water transport proteins. When transpiration demand exceeds the maximum capacity of Kleaf to supply water, high tension in the water column can cause cavitation in xylem, and these emboli-blocked xylem vessels reduce water transport and thus lower Kleaf. Stomatal conductance typically remains high at mid-day for soybean, suggesting either a mid-day increase in Kleaf or that photosynthesis may be maintained at the cost of leaf water status, indicative of an anisohydric water management strategy in soybean. This study examined diurnal fluctuations in Kleaf and Ψleaf, showing a mid-day depression in Kleaf in a pattern closely reflecting that of Ψleaf, indicating that Kleaf depression is the result of cavitation in leaf xylem. The diurnal depression of Kleaf was not prevented by growth at elevated [CO2], which lowered stomatal conductance. Diurnal transcription patterns of aquaporin genes showed that a total of 34 genes belonging to 4 aquaporin families were expressed in soybean leaves, of which 22 were differentially expressed between at least two time points. These data suggest that mid-day Kleaf depression was driven primarily by cavitation at increasing xylem water tensions, but that aquaporins are also likely involved in diurnal regulation of soybean leaf water status. It is further concluded that because soybean photosynthesis is typically sustained at mid-day, Kleaf even at the depressed level was in excess of that needed to sustain a stomatal conductance sufficient to prevent depression of photosynthesis in soybean.}, journal={Environmental and Experimental Botany}, publisher={Elsevier BV}, author={Locke, Anna M. and Ort, Donald R.}, year={2015}, month={Aug}, pages={39–46} }
 @article{siebers_yendrek_drag_locke_rios acosta_leakey_ainsworth_bernacchi_ort_2015, title={Heat waves imposed during early pod development in soybean (<i><scp>G</scp>lycine max</i>) cause significant yield loss despite a rapid recovery from oxidative stress}, volume={21}, ISSN={1354-1013 1365-2486}, url={http://dx.doi.org/10.1111/gcb.12935}, DOI={10.1111/gcb.12935}, abstractNote={AbstractHeat waves already have a large impact on crops and are predicted to become more intense and more frequent in the future. In this study, heat waves were imposed on soybean using infrared heating technology in a fully open‐air field experiment. Five separate heat waves were applied to field‐grown soybean (Glycine max) in central Illinois, three in 2010 and two in 2011. Thirty years of historical weather data from Illinois were analyzed to determine the length and intensity of a regionally realistic heat wave resulting in experimental heat wave treatments during which day and night canopy temperatures were elevated 6 °C above ambient for 3 days. Heat waves were applied during early or late reproductive stages to determine whether and when heat waves had an impact on carbon metabolism and seed yield. By the third day of each heat wave, net photosynthesis (A), specific leaf weight (SLW), and leaf total nonstructural carbohydrate concentration (TNC) were decreased, while leaf oxidative stress was increased. However, A, SLW, TNC, and measures of oxidative stress were no different than the control ca. 12 h after the heat waves ended, indicating rapid physiological recovery from the high‐temperature stress. That end of season seed yield was reduced (~10%) only when heat waves were applied during early pod developmental stages indicates the yield loss had more to do with direct impacts of the heat waves on reproductive process than on photosynthesis. Soybean was unable to mitigate yield loss after heat waves given during late reproductive stages. This study shows that short high‐temperature stress events that reduce photosynthesis and increase oxidative stress resulted in significant losses to soybean production in the Midwest, U.S. The study also suggests that to mitigate heat wave‐induced yield loss, soybean needs improved reproductive and photosynthetic tolerance to high but increasingly common temperatures.}, number={8}, journal={Global Change Biology}, publisher={Wiley}, author={Siebers, Matthew H. and Yendrek, Craig R. and Drag, David and Locke, Anna M. and Rios Acosta, Lorena and Leakey, Andrew D. B. and Ainsworth, Elizabeth A. and Bernacchi, Carl J. and Ort, Donald R.}, year={2015}, month={May}, pages={3114–3125} }
 @article{heat waves imposed during early pod development in soybean (glycine max) cause significant yield loss despite a rapid recovery from oxidative stress, url={https://doi.org/10.1111/gcb.12935}, DOI={10.1111/gcb.12935}, abstractNote={AbstractHeat waves already have a large impact on crops and are predicted to become more intense and more frequent in the future. In this study, heat waves were imposed on soybean using infrared heating technology in a fully open‐air field experiment. Five separate heat waves were applied to field‐grown soybean (Glycine max) in central Illinois, three in 2010 and two in 2011. Thirty years of historical weather data from Illinois were analyzed to determine the length and intensity of a regionally realistic heat wave resulting in experimental heat wave treatments during which day and night canopy temperatures were elevated 6 °C above ambient for 3 days. Heat waves were applied during early or late reproductive stages to determine whether and when heat waves had an impact on carbon metabolism and seed yield. By the third day of each heat wave, net photosynthesis (A), specific leaf weight (SLW), and leaf total nonstructural carbohydrate concentration (TNC) were decreased, while leaf oxidative stress was increased. However, A, SLW, TNC, and measures of oxidative stress were no different than the control ca. 12 h after the heat waves ended, indicating rapid physiological recovery from the high‐temperature stress. That end of season seed yield was reduced (~10%) only when heat waves were applied during early pod developmental stages indicates the yield loss had more to do with direct impacts of the heat waves on reproductive process than on photosynthesis. Soybean was unable to mitigate yield loss after heat waves given during late reproductive stages. This study shows that short high‐temperature stress events that reduce photosynthesis and increase oxidative stress resulted in significant losses to soybean production in the Midwest, U.S. The study also suggests that to mitigate heat wave‐induced yield loss, soybean needs improved reproductive and photosynthetic tolerance to high but increasingly common temperatures.} }
 @article{locke_ort_2014, title={Leaf hydraulic conductance declines in coordination with photosynthesis, transpiration and leaf water status as soybean leaves age regardless of soil moisture}, volume={65}, ISSN={1460-2431 0022-0957}, url={http://dx.doi.org/10.1093/jxb/eru380}, DOI={10.1093/jxb/eru380}, abstractNote={Summary Short statement: Field and chamber studies show a decline in leaf hydraulic conductance as soybean leaves age that is independent of decreases in soil moisture.}, number={22}, journal={Journal of Experimental Botany}, publisher={Oxford University Press (OUP)}, author={Locke, Anna M. and Ort, Donald R.}, year={2014}, month={Oct}, pages={6617–6627} }
 @article{leaf hydraulic conductance declines in coordination with photosynthesis, transpiration and leaf water status as soybean leaves age regardless of soil moisture, url={https://doi.org/10.1093/jxb/eru380}, DOI={10.1093/jxb/eru380}, abstractNote={Summary Short statement: Field and chamber studies show a decline in leaf hydraulic conductance as soybean leaves age that is independent of decreases in soil moisture.} }
 @article{soybean leaf hydraulic conductance does not acclimate to growth at elevated [co2] or temperature in growth chambers and or the field, url={https://doi.org/10.1093/aob/mct143}, DOI={10.1093/aob/mct143}, abstractNote={BACKGROUND AND AIMS
Leaf hydraulic properties are strongly linked with transpiration and photosynthesis in many species. However, it is not known if gas exchange and hydraulics will have co-ordinated responses to climate change. The objective of this study was to investigate the responses of leaf hydraulic conductance (Kleaf) in Glycine max (soybean) to growth at elevated [CO2] and increased temperature compared with the responses of leaf gas exchange and leaf water status.


METHODS
Two controlled-environment growth chamber experiments were conducted with soybean to measure Kleaf, stomatal conductance (gs) and photosynthesis (A) during growth at elevated [CO2] and temperature relative to ambient levels. These results were validated with field experiments on soybean grown under free-air elevated [CO2] (FACE) and canopy warming.


KEY RESULTS
In chamber studies, Kleaf did not acclimate to growth at elevated [CO2], even though stomatal conductance decreased and photosynthesis increased. Growth at elevated temperature also did not affect Kleaf, although gs and A showed significant but inconsistent decreases. The lack of response of Kleaf to growth at increased [CO2] and temperature in chamber-grown plants was confirmed with field-grown soybean at a FACE facility.


CONCLUSIONS
Leaf hydraulic and leaf gas exchange responses to these two climate change factors were not strongly linked in soybean, although gs responded to [CO2] and increased temperature as previously reported. This differential behaviour could lead to an imbalance between hydraulic supply and transpiration demand under extreme environmental conditions likely to become more common as global climate continues to change.} }
 @article{locke_sack_bernacchi_ort_2013, title={Soybean leaf hydraulic conductance does not acclimate to growth at elevated [CO2] or temperature in growth chambers or in the field}, volume={112}, ISSN={1095-8290 0305-7364}, url={http://dx.doi.org/10.1093/aob/mct143}, DOI={10.1093/aob/mct143}, abstractNote={BACKGROUND AND AIMS
Leaf hydraulic properties are strongly linked with transpiration and photosynthesis in many species. However, it is not known if gas exchange and hydraulics will have co-ordinated responses to climate change. The objective of this study was to investigate the responses of leaf hydraulic conductance (Kleaf) in Glycine max (soybean) to growth at elevated [CO2] and increased temperature compared with the responses of leaf gas exchange and leaf water status.


METHODS
Two controlled-environment growth chamber experiments were conducted with soybean to measure Kleaf, stomatal conductance (gs) and photosynthesis (A) during growth at elevated [CO2] and temperature relative to ambient levels. These results were validated with field experiments on soybean grown under free-air elevated [CO2] (FACE) and canopy warming.


KEY RESULTS
In chamber studies, Kleaf did not acclimate to growth at elevated [CO2], even though stomatal conductance decreased and photosynthesis increased. Growth at elevated temperature also did not affect Kleaf, although gs and A showed significant but inconsistent decreases. The lack of response of Kleaf to growth at increased [CO2] and temperature in chamber-grown plants was confirmed with field-grown soybean at a FACE facility.


CONCLUSIONS
Leaf hydraulic and leaf gas exchange responses to these two climate change factors were not strongly linked in soybean, although gs responded to [CO2] and increased temperature as previously reported. This differential behaviour could lead to an imbalance between hydraulic supply and transpiration demand under extreme environmental conditions likely to become more common as global climate continues to change.}, number={5}, journal={Annals of Botany}, publisher={Oxford University Press (OUP)}, author={Locke, Anna M. and Sack, Lawren and Bernacchi, Carl J. and Ort, Donald R.}, year={2013}, month={Jul}, pages={911–918} }
 @article{over-expressing the c3 photosynthesis cycle enzyme sedoheptulose-1-7 bisphosphatase improves photosynthetic carbon gain and yield under fully open air co2 fumigation (face), url={https://doi.org/10.1186/1471-2229-11-123}, DOI={10.1186/1471-2229-11-123}, abstractNote={AbstractBackgroundBiochemical models predict that photosynthesis in C3plants is most frequently limited by the slower of two processes, the maximum capacity of the enzyme Rubisco to carboxylate RuBP (Vc,max), or the regeneration of RuBP via electron transport (J). At current atmospheric [CO2] levels Rubisco is not saturated; consequently, elevating [CO2] increases the velocity of carboxylation and inhibits the competing oxygenation reaction which is also catalyzed by Rubisco. In the future, leaf photosynthesis (A) should be increasingly limited by RuBP regeneration, as [CO2] is predicted to exceed 550 ppm by 2050. The C3cycle enzyme sedoheptulose-1,7 bisphosphatase (SBPase, EC 3.1.3.17) has been shown to exert strong metabolic control over RuBP regeneration at light saturation.ResultsWe tested the hypothesis that tobacco transformed to overexpressing SBPase will exhibit greater stimulation ofAthan wild type (WT) tobacco when grown under field conditions at elevated [CO2] (585 ppm) under fully open air fumigation. Growth under elevated [CO2] stimulated instantaneousAand the diurnal photosynthetic integral (A') more in transformants than WT. There was evidence of photosynthetic acclimation to elevated [CO2] via downregulation of Vc,maxin both WT and transformants. Nevertheless, greater carbon assimilation and electron transport rates (J and Jmax) for transformants led to greater yield increases than WT at elevated [CO2] compared to ambient grown plants.ConclusionThese results provide proof of concept that increasing content and activity of a single photosynthesis enzyme can enhance carbon assimilation and yield of C3crops grown at [CO2] expected by the middle of the 21st century.} }
 @article{rosenthal_locke_khozaei_raines_long_ort_2011, title={Over-expressing the C3 photosynthesis cycle enzyme Sedoheptulose-1-7 Bisphosphatase improves photosynthetic carbon gain and yield under fully open air CO2fumigation (FACE)}, volume={11}, ISSN={1471-2229}, url={http://dx.doi.org/10.1186/1471-2229-11-123}, DOI={10.1186/1471-2229-11-123}, abstractNote={AbstractBackgroundBiochemical models predict that photosynthesis in C3plants is most frequently limited by the slower of two processes, the maximum capacity of the enzyme Rubisco to carboxylate RuBP (Vc,max), or the regeneration of RuBP via electron transport (J). At current atmospheric [CO2] levels Rubisco is not saturated; consequently, elevating [CO2] increases the velocity of carboxylation and inhibits the competing oxygenation reaction which is also catalyzed by Rubisco. In the future, leaf photosynthesis (A) should be increasingly limited by RuBP regeneration, as [CO2] is predicted to exceed 550 ppm by 2050. The C3cycle enzyme sedoheptulose-1,7 bisphosphatase (SBPase, EC 3.1.3.17) has been shown to exert strong metabolic control over RuBP regeneration at light saturation.ResultsWe tested the hypothesis that tobacco transformed to overexpressing SBPase will exhibit greater stimulation ofAthan wild type (WT) tobacco when grown under field conditions at elevated [CO2] (585 ppm) under fully open air fumigation. Growth under elevated [CO2] stimulated instantaneousAand the diurnal photosynthetic integral (A') more in transformants than WT. There was evidence of photosynthetic acclimation to elevated [CO2] via downregulation of Vc,maxin both WT and transformants. Nevertheless, greater carbon assimilation and electron transport rates (J and Jmax) for transformants led to greater yield increases than WT at elevated [CO2] compared to ambient grown plants.ConclusionThese results provide proof of concept that increasing content and activity of a single photosynthesis enzyme can enhance carbon assimilation and yield of C3crops grown at [CO2] expected by the middle of the 21st century.}, number={1}, journal={BMC Plant Biology}, publisher={Springer Science and Business Media LLC}, author={Rosenthal, David M and Locke, Anna M and Khozaei, Mahdi and Raines, Christine A and Long, Stephen P and Ort, Donald R}, year={2011}, month={Aug} }