• Technology to screen for higher-yielding crop traits is now more accessible to scientists

    CHAMPAIGN (March 17, 2020)-- Like many industries, big data is driving innovations in agriculture. Scientists seek to analyze thousands of plants to pinpoint genetic tweaks that can boost crop production—historically, a Herculean task. To drive progress toward higher-yielding crops, a team from the University of Illinois is revolutionizing the ability to screen plants for key traits across an entire field. In two recent studies—published in the Journal of Experimental Botany (JExBot) and Plant, Cell & Environment (PC&E)—they are making this technology more accessible. “For plant scientists, this is a major step forward,” said co-first author Katherine Meacham-Hensold, a postdoctoral researcher at Illinois who led the physiological work on both studies. “Now we can quickly screen thousands of plants to identify the most promising plants to investigate further using another method that provides more in-depth information but requires more time. Sometimes knowing where to look is the biggest challenge, and this research helps address that." This work is supported by Realizing Increased Photosynthetic Efficiency (RIPE), an international research project that is creating more productive food crops by improving photosynthesis, the natural process all plants use to convert sunlight into energy and yields. RIPE is sponsored by the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research (FFAR), and the U.K. Government’s Department for International Development (DFID). The team analyzed data collected with specialized hyperspectral cameras that capture part of the light spectrum (much of which is invisible to the human eye) that is reflected off the surface of plants. Using hyperspectral analysis, scientists can tease out meaningful information from these bands of reflected light to estimate traits related to photosynthesis. “Hyperspectral cameras are expensive and their data is not accessible to scientists who lack a deep understanding of computational analysis,” said Carl Bernacchi, a research plant physiologist with the U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS) at the Carl R. Woese Institute for Genomic Biology. “Through these studies, our team has taken a technology that was out of reach and made it more available to our research community so that we can unearth traits needed to provide farmers all over the world with higher-yielding crops.” The RIPE project analyzes hundreds of plants each field season. The traditional method used to measure photosynthesis requires as much as 30 minutes per leaf. While newer technologies have increased efficiency to as little as 15 seconds per plant, the study published in JExBot has increased efficiency by an order of magnitude, allowing researchers to capture the photosynthetic capacity of hundreds to thousands of plants in a research plot. In the JExBot study, the team reviewed data from two hyperspectral cameras; one that captures spectra from 400-900 nanometers and another that captures 900-1800 nanometers. “Our previous work suggested that we should use both cameras to estimate photosynthetic capacity; however, this study suggests that only one camera that captures 400-900 is required,” said co-first author Peng Fu, a RIPE postdoctoral researcher who led the computational work on both studies. In the PC&E study, the team resolved to make hyperspectral information even more meaningful and accessible to plant scientists. Using just 240 bands of reflectance spectra and a radiative transfer model, the team teased out how to identify seven important leaf traits from the hyperspectral data that are related to photosynthesis and of interest to many plant scientists. “Our results suggest we do not always need ‘high-resolution’ reflectance data to estimate photosynthetic capacity,” Fu said. “We only need around 10 hyperspectral bands—as opposed to several hundred or even a thousand hyperspectral bands—if the data are carefully selected. This conclusion can help pave the way to make meaningful measurements with less expensive cameras.” These studies will help us map photosynthesis across different scales from the leaf level to the field level to identify plants with promising traits for further study. The RIPE project and its sponsors are committed to ensuring Global Access and making the project’s technologies available to the farmers who need them the most. ABOUT RIPE Realizing Increased Photosynthetic Efficiency (RIPE) aims to improve photosynthesis to equip farmers worldwide with higher-yielding crops to ensure everyone has enough food to lead a healthy, productive life. This international research project is sponsored by the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research, and the U.K. Government’s Department for International Development. RIPE is led by the University of Illinois in partnership with The Australian National University, Chinese Academy of Sciences, Commonwealth Scientific and Industrial Research Organisation, Lancaster University, Louisiana State University, University of California, Berkeley, University of Cambridge, University of Essex, and U.S. Department of Agriculture, Agricultural Research Service.


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  • Photosynthesis varies greatly across rice cultivars— natural diversity could boost yields

    Photosynthesis varies greatly across rice cultivars— natural diversity could boost yield CHAMPAIGN (MARCH 9, 2020)-- Rice is a direct source of calories for more people than any other crop and serves as the main staple for 560 million chronically hungry people in Asia. With over 120,000 varieties of cultivated rice (Oryza sativa) across the globe, there is a wealth of natural diversity to be mined by plant scientists to increase yields. A team from the University of Illinois and the International Rice Research Institute (IRRI) examined how 14 diverse varieties photosynthesize—the process by which all crops convert sunlight energy into sugars that ultimately become our food. Looking at a little-studied attribute of photosynthesis, they found small differences in photosynthetic efficiency under constant conditions, but a 117 percent difference in fluctuating light, suggesting a new trait for breeder selection. “Photosynthesis has traditionally been assessed under ‘constant conditions’ where plants are exposed to constant, high levels of light, but field conditions are never constant—especially considering the light that drives photosynthesis,” said RIPE Director Stephen Long, Ikenberry Endowed University Chair of Plant Biology and Crop Sciences at Illinois’ Carl R. Woese Institute for Genomic Biology. “We looked at 14 cultivars of rice that represent much of the crop’s diversity and asked the question: could there be variability in photosynthesis in fluctuating light that we might be able to capitalize on?” Published in New Phytologist, this work is part of Realizing Increased Photosynthetic Efficiency (RIPE), an international research project that enables crops to turn the sun’s energy into food more efficiently to increase global production sustainably with support from the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research (FFAR), and the U.K. Government’s Department for International Development (DFID). “If you look within the canopy of leaves of any crop, you will see that the light is fluctuating by one or two orders of magnitude,” Long said. “A plant’s access to light is not only impacted by clouds intermittently obscuring the sun but much more commonly by its own leaves, or those of a neighboring plant, as the sun’s angle changes throughout the day. Calculations show that the photosynthetic inefficiency imposed by these leaves slowly adjusting to each fluctuation in light may cost crops 20 to 40 percent of their potential productivity.” The researchers compared results from constant and fluctuating light conditions and found no correlation, which supports findings from a 2019 study on cassava. In other words, varieties that do well in fluctuating light might not do well in constant light and vice-versa, suggesting that selection for these traits should be conducted independently. “This lack of correlation, which seems to be consistent across species, calls for us to flip how we think about studying photosynthesis,” said first-author Liana Acevedo-Siaca, a graduate student in the College of Agriculture, Consumer, and Environmental Sciences (ACES). “Moving forward, we need to incorporate more dynamic measurements into the way that we understand photosynthesis, especially in an agricultural setting, because realistically those plants are never in a steady-state.” The team also evaluated how these plants cope with fluctuations in light intensity across the five major rice groups, sometimes considered to be subspecies. While no group appeared better than the other overall, the team believes that variation could be found in future research. In this study, three photosynthetic parameters were of particular interest: the speed of induction (how quickly photosynthesis activates, or starts), speed of assimilation (how quickly the plant physically fixes carbon into sugar), and how efficiently these rice plants use water. After switching from low light to high light, one variety activated (or began photosynthesizing) 117 percent faster than the slowest. In fluctuating light conditions, another variety from the Indica group assimilated more than double that of the “worst” variety (also an Indica), which was found to be the most water-use efficient variety. “Surprisingly, after making a more detailed analysis of these accessions, along with a well-studied control called IR64 from the Philippines, we found that biochemistry is the biggest limitation to efficiency as leaves transition from shade to sun,” Long said. “Biochemistry is a different limitation altogether than that found in a parallel study of cassava, illustrating the need to fine-tune photosynthesis separately in different crop species—despite the fact that the photosynthetic process is generally well-conserved and consistent across most food crops.” According to Acevedo-Siaca, the next step is to identify how to breed for (or engineer) rice with faster induction responses. “At the end of the day, the goal would be to have plants that can respond more quickly to light fluctuations to enable them to be more productive,” said Acevedo-Siaca, a 2016 recipient of the U.S. Borlaug Fellowship in Global Food Security that supported her to conduct much of this research at IRRI. “I am interested in ways that we can improve this process while preserving some of the germplasm we have out there—there’s so much diversity with which we could work. I think it would be a shame if we didn’t examine all of our options more deeply.” Long also published a landmark study in Science that showed crops are not fully adapted to deal with the dynamic light conditions in fields—and helping them can increase crop productivity by as much as 20 percent. The RIPE project and its sponsors are committed to ensuring Global Access and making the project’s technologies available to the farmers who need them the most. ABOUT RIPE Realizing Increased Photosynthetic Efficiency (RIPE) aims to improve photosynthesis to equip farmers worldwide with higher-yielding crops to ensure everyone has enough food to lead a healthy, productive life. This international research project is sponsored by the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research (FFAR), and the U.K. Government’s Department for International Development (DFID). RIPE is led by the University of Illinois in partnership with The Australian National University, Chinese Academy of Sciences, Commonwealth Scientific and Industrial Research Organisation, Lancaster University, Louisiana State University, University of California, Berkeley, University of Cambridge, University of Essex, and the U.S. Department of Agriculture, Agricultural Research Service.


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  • Boost Soybean Yields by Adapting Photosynthesis to Fleeting Shadows, According to Model

    WASHINGTON (February 24, 2020) -- Komorebi is a Japanese word that describes how light filters through leaves—creating shifting, dappled “sunflecks” that illustrate plants’ ever-changing light environment. Crops harness light energy to fix carbon dioxide into food via photosynthesis. In a special issue of Plant Journal, a team from the University of Illinois reports a new mathematical computer model that is used to understand how much yield is lost as soybean crops grapple with minute-by-minute light fluctuations on cloudy and sunny days. “Soybean is the fourth most important crop in terms of overall production, but it is the top source of vegetable protein globally,” said Yu Wang, a postdoctoral researcher at Illinois, who led this work for Realizing Increased Photosynthetic Efficiency (RIPE). “We found that soybean plants may lose as much as 13 percent of their productivity because they cannot adjust quickly enough to the changes in light intensity that are standard in any crop field. It may not sound like much, but in terms of the global yield—this is massive.” RIPE is an international research project that aims to improve photosynthesis to equip farmers worldwide with higher-yielding crops needed to ensure everyone has enough food to lead a healthy, productive life. RIPE is sponsored by the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research (FFAR), and the U.K. Government’s Department for International Development (DFID). Past models have only examined hour-by-hour changes in light intensity. For this study, the team created a dynamic computational ray-tracing model that was able to predict light levels to the millimeter across every leaf for every minute of the day in a flowering soybean crop. The model also takes into account two critical factors: photoprotection and Rubisco activase. Photoprotection protects plants from sun damage. Triggered by high light levels, this process dissipates excess light energy safely as heat. But, when light levels drop, it can take minutes to hours for photoprotection to relax, or stop—costing the plant potential yield. The team evaluated 41 varieties of soybean to find out the fastest, slowest, and average rate from induction to the relaxation of photoprotection. Less than 30 minutes is considered “short-term,” and anything longer is “long-term” photoprotection. Using this new model, the team simulated a sunny and cloudy day in Champaign, Illinois. On the sunny day, long-term photoprotection was the most significant limitation of photosynthesis. On the cloudy day, photosynthesis was the most limited by short-term photoprotection and Rubisco activase, which is a helper enzyme—triggered by light—that turns on Rubisco to fix carbon into sugar. The RIPE project has already begun to address photoprotection limitations in soybean and other crops, including cassava, cowpea, and rice. In 2016, the team published a study in Science where they increased the levels of three proteins involved in photoprotection to boost the productivity of a model crop by 14-20 percent. In addition, the RIPE team from the Lancaster Environment Centre at Lancaster University is seeking better forms of Rubisco activase in soybean and cowpea. The RIPE project and its sponsors are committed to ensuring Global Access and making these technologies available to the farmers who need them the most. “Models like these are critical to uncovering barriers—and solutions—to attain this crop’s full potential,” said RIPE Director Stephen Long, Ikenberry Endowed University Chair of Plant Biology and Crop Sciences at Illinois’ Carl R. Woese Institute for Genomic Biology. “We’ve already begun to address these bottlenecks and seen significant gains, but this study shows us that there is still room for improvement.” ### About RIPE Realizing Increased Photosynthetic Efficiency (RIPE) aims to improve photosynthesis to equip farmers worldwide with higher-yielding crops to ensure everyone has enough food to lead a healthy, productive life. This international research project is sponsored by the Bill & Melinda Gates Foundation, the U.S. Foundation for Food and Agriculture Research, and the U.K. Government’s Department for International Development. RIPE is led by the University of Illinois in partnership with The Australian National University, Chinese Academy of Sciences, Commonwealth Scientific and Industrial Research Organisation, Lancaster University, Louisiana State University, University of California, Berkeley, University of Cambridge, University of Essex, and U.S. Department of Agriculture, Agricultural Research Service.


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