Stephen Moose - US grants

plant proteins; DNA binding protein; corn; protein sequence; DNA; intermolecular interaction; yeast two hybrid system; gel mobility shift assay; affinity chromatography; molecular cloning; genetic library; protein purification;

Adaptation of C4 Photosynthesis to Cold within the Miscanthus Genus

Not all plants are equal in the efficiency with which they convert sunlight energy into biomass and ultimately provide food for people. The most efficient plants known are C4 plants, which use carbon dioxide (CO2) and sunlight energy to make four carbon compounds as the initial product of photosynthesis. The majority of the world's plants are C3 plants, which when grown under ideal conditions are about 40% less efficient in their use of sunlight than C4 plants. C4 plants such as tropical grasses and the crop species corn, sorghum and sugarcane remain largely confined to warm temperate environments. These observations have led to the suggestion that the higher efficiency of C4 photosynthesis was inherently limited to warm conditions.
Recent work has shown that some Miscanthus species not only survive in cold climates, but that they achieve photosynthetic rates and efficiencies of conversion of light into biomass that exceed those of C3 species. Yet these species are exclusively C4 and are so closely related to tropical sugarcane that they can form fertile hybrids. From the center of diversity of sugarcane, forms classified as Miscanthus have radiated out into high-altitude cold grassland habitats in S.E. Asia; forming a likely progression of cold tolerance within the C4 mechanism. This very large range of cold tolerance within closely related taxa provides a unique opportunity to discover how cold tolerance has evolved within C4 photosynthesis. Taxa from this Miscanthus-Saccharum complex occurring in a range of habitats from tropical to cold temperate, will be characterized for their ability to develop photosynthetically competent leaves at low temperature and to photosynthesize at low temperature. This research will provide a basis for testing a range of competing, but not necessarily exclusive, theories on what normally limits C4 photosynthesis at low temperature. Theories include: that the catalytic capacity of the enzyme Rubisco at low temperature is too low, that the enzyme pyruvate orthophosphate dikinase (PPDK) is unstable at low temperature, and that there is inadequate capacity for protection against inhibition of photosynthesis by excess light. These will be assessed by in vivo and in vitro measurement of activity and quantities, using classical physiological and biochemistry techniques, and at the molecular level investigating gene sequence changes and protein stability, including association with chaperone proteins. Regression analysis will be used to assess which of these characters explains most variation in low temperature tolerance across the taxa of this complex.

This work will also have broader impacts to both educational activities and agriculture. An improved understanding of the physiological and molecular mechanisms associated with the adaptation of C4 photosynthesis to cold conditions may offer novel strategies to extending the growing season or cultivation environments of C4 crops such as corn, sorghum and sugarcane. This project will also emphasize research training for students from the high school, undergraduate and graduate levels, including internship opportunities for minority students that integrate plant biology and new approaches to crop production. Furthermore, research results will be communicated to the public at large through field tours and educational presentations that emphasize environmental change and its impacts to agriculture.

Large amounts of nitrogen fertilizer are used to increase yields of cereal crops worldwide, resulting in higher crop input costs, greater energy requirements for crop production, and negative impacts on water quality due to excess nitrogen. Despite the widespread use of nitrogen fertilizer, little is known about the genes that control nitrogen use efficiency in cereal crops. This project will identify and characterize genes regulating nitrogen use efficiency in maize, a model system for plant genomics research and an economically important cereal crop. Experiments that integrate physiological, genetic, and functional genomics approaches will identify genes whose expression changes in response to nitrogen, from its uptake by roots to its use by developing seeds. Emphasis will be placed on key regulatory genes that are associated with nitrogen use efficiency in environments and germplasm relevant to crop production, including ongoing breeding efforts for improving maize nitrogen use efficiency in west central Africa. To this end, the project includes a Developing Country Collaboration with the International Institute for Tropical Agriculture (IATA) in Nigeria to enhance ongoing breeding programs aimed at improving NUE for maize in Western and Central Africa. This project will provide training opportunities in the biology of the maize crop, plant genomics, and bioinformatics.

All project data and results will be made available through scientific publications, outreach to scientific and public audiences, and through the project website, http://www.nitrogenes.uiuc.edu.

The 51st Annual Maize Genetics Conference will be held March 12-15, 2009 at the Pheasant Run Resort and Spa in St. Charles, IL. The meeting offers members of the Maize Genetics community the opportunity to present and discuss their most recent research results. A wide range of topics investigating the structure and function of genes, pathways, and traits are included, spanning both basic studies of gene action and applications to crop improvement. The 51st Annual meeting will feature 45-minute talks by four invited plenary speakers: Joe Ecker, Salk Institute; Curt Hannah, University of Florida; Luca Comai, University of California-Davis; and Marja Timmermans, Cold Spring Harbor Laboratory. In addition the program will include approximately 30 15-minute talks given by speakers selected from submitted abstracts and two poster sessions.

Broader Impacts:

The Maize Genetics Conference program is designed specifically to allow students to participate and interact with their peers from other institutions and with scientists who are leaders in the field. The program provides multiple opportunities for graduate students and postdoctoral scientists to present their research ideas as invited platform talks or as poster presentations. For most of the students attending and presenting their data at this meeting, it is their first exposure to a research conference; the students begin to establish their scientific contact networks here, and as they continue to advance their scientific careers, this conference series remains valuable as a source of information and interactions in the area of maize genetics.

PI: Matthew Hudson, University of Illinois
Co-PI: Stephen Moose, University of Illinois

Heterosis or hybrid vigor is a scientific term to describe the more vigorous progeny from a genetic cross between parents that are not closely related. Hybrid vigor is one of the main foundations for greatly increased crop yields during the 20th century, especially in corn (maize). However, the reasons why the offspring of a cross between distantly related individuals tend to grow larger than their parents are still poorly understood. One popular and promising hypothesis is that hybrid vigor results from a combination of genes from both parents that control growth rate and stress tolerance. Noncoding, small RNAs are recently discovered regulatory molecules encoded by genes that may fit this hypothesis. Some small RNAs are known to control shoot development and others stress-responsive genes. Preliminary experiments have shown that several small RNAs are altered in their expression in hybrid corn plants when they are compared to the inbred parents. In addition, the machinery that produces these small RNAs may also be altered in its function in hybrids when compared to inbred corn. These results also hold true in the model plant Arabidopsis, indicating that small RNA may be involved in a common mechanism of hybrid vigor in all plants. This project will investigate further the effect of small RNA on hybrid vigor in both corn and Arabidopsis, focusing on the genes that control small RNA production and on whether small RNA levels can predict the performance of different hybrid combinations of corn plants. These populations represent current and historical genetic diversity in corn, and include inbred lines that are major contributors to commercially important maize varieties. A more complete understanding of the mechanisms of heterosis, and how these mechanisms relate to the increased crop yields that result from it, is anticipated from this research.

The greater vigor observed following hybridization is one of the most easily visualized genetic effects and is commonly observed in everyday life. The use of hybrids in plant and livestock breeding has greatly increased agricultural productivity with significant benefits to global society. However, the benefits of hybrids are currently unevenly spread, with corn benefiting more than any other crop. The research will provide insight into the mechanisms of heterosis, with potential improvements in crop yields, especially in crops where hybrids do not currently provide a major increase in yield. Increased yields of major crops have the potential to reduce pressure on the environment and decrease the need to convert more wild land into agricultural land. The maize germplasm used in this project is intentionally chosen to be free from intellectual property protections and the seed are freely available from the Germplasm Resource Information Network (GRIN, http://www.ars-grin.gov/). Experimental lines of maize and Arabidopsis produced as part of this project will be supplied to public repositories, the maize genetics co-op (http://maizecoop.cropsci.uiuc.edu/) and the Arabidopsis Biological Resource Center (http://www.arabidopsis.org/abrc/). Sequence data generated will be submitted to GenBank (http://www.ncbi.nlm.nih.gov/Genbank/index.html) and made available on the laboratory website (http://stan.cropsci.uiuc.edu). This project will also offer a number of educational opportunities. By using commercially relevant maize germplasm in this project, graduate-level education will be more relevant to the type of research conducted in commercial seed companies, enhancing the relevance of the research to modern agriculture. Young scientists, including a summer intern, will be offered excellent opportunities to learn and apply some of the most recent advances in plant genomics research. Because heterosis is a topic of high general interest, research results will be communicated broadly through publications, presentations, and public educational efforts that emphasize the positive impacts of plant genome research. Specific examples include distribution of an educational kit of seeds that exhibit strong seedling heterosis; living demonstrations of hybrids and their inbred parents to the public via field days; presentations at high schools and community colleges and an educational web page (hosted on http://stan.cropsci.uiuc.edu and also contributed to Wikipedia) on the importance of hybrid vigor

PI: Gloria Coruzzi (New York University)

CoPIs: Dennis Shasha (New York University), Stephen Moose (University of Illinois at Urbana-Champaign), Sandrine Ruffel and Gabriel Krouk (INRA, Montpellier, France)

Senior Personnel: Manpreet Katari (New York University) and W. Richard McCombie (Cold Spring Harbor Laboratory)

Improving nutrient use efficiency (NUE) in crop plants is critical to ameliorating the impacts of future climate change and to sustainably increasing global crop yields to meet projected food and energy demands. The NutriNet project seeks to identify and compare biologically connected gene networks whose collective expression patterns are predictive of phenotypic variation in NUE in Arabidopsis and maize. This cross-species network inspired approach may be readily applied to many other economically important traits, and adapted to other crops. The advantages of the NutriNet approach include: i) exploiting detailed datasets for gene and protein interactions in Arabidopsis, to inform analysis of data poor crop species, and ii) identification of robust network modules that can be applied in molecular breeding programs. Proof-of-principle studies will demonstrate both conserved and species-specific features of network modules (but not necessarily candidate genes) regulating nitrogen assimilation and remobilization. The new knowledge generated in this project will consist of gene discovery, elucidation of regulatory circuits, and a better understanding of the molecular basis for nutrient physiology that drives crop productivity. As a practical deliverable, network-inspired molecular breeding tools will be developed that are expected to perform better than candidate gene approaches in selecting genotypes with improved NUE. The NutriNet team links expertise in systems biology, plant physiology, and crop genomics, to increase the fundamental understanding of crop utilization of nutrients. The project offers multidisciplinary training to postdoctoral scientists, graduate and undergraduate students in New York and Illinois. High school students will be introduced to systems biology through co-mentorship by biologists and computer scientists at NYU. In addition, because of the broad public interest in nutrient-efficient crops, the project team will engage audiences through outreach activities at the Illinois Corn Breeders' school to leverage the pioneering efforts and long history of the University of Illinois in concert with breeders to understand crop responses to nutrients and breeding for nitrogen utilization.

Recent advances in genome sequencing, functional genomics, and computational tools enable a systems level understanding of key physiological and developmental processes including NUE in the model plant Arabidopsis thaliana. However, translating this "network knowledge" from Arabidopsis to crops to potentially enhance agriculturally important phenotypes in crop species remains challenging. The goal of this project is to develop network-connected gene modules that can be used to predict the outcome of NUE in crops, by exploiting Arabidopsis network knowledge. The project approaches this goal by developing novel data sets and analytical methods as follows: 1) integrating phenotypic variation for NUE with new and existing data for nutrient-responsive gene expression profiles which allows for the development of a training set that exploits the power of genetic diversity from both Arabidopsis and maize; 2) using a split-root experimental design to identify evolutionarily conserved gene mechanisms that function in root-shoot N-signaling that may control root foraging for nutrients in the soil; 3) defining network modules predictive of NUE traits using a bioinformatics pipeline to combine Arabidopsis "network knowledge" with maize transcriptome data to generate NutriNet modules that will be validated using and tested for their ability to predict NUE based on gene expression; and, 4), using information derived from NutriNet modules to select individual genotypes that possess optimal NutriNet configurations from diverse germplasm pools which will then be evaluated for improved NUE traits in the lab (Arabidopsis) and field (maize). A comparative analysis of lab-to-field results will directly assess the "translation" of network knowledge from Arabidopsis to maize to serve as a general proof-of-principle, which can be applied to other networks and species. All data and biological resources will be available upon request and accessible through long-term data and germplasm repositories.