The Donald Danforth Plant Science Center is a not-for-profit scientific facility located in Creve Coeur, Missouri, United States. The Center's mission is to "improve the human condition through plant science".Founded in 1998 by William Henry Danforth, a cardiologist, the Center was established through a $60 million gift from the Danforth Foundation, a $50 million gift from the Monsanto Fund, the donation of 40 acres of land from Monsanto, and $25 million in tax credits from the State of Missouri. Wikipedia.
Donald Danforth Plant Science Center | Date: 2016-09-04
The present disclosure relates generally to the field of molecular biology, specifically relating to small RNA-directed regulation of gene expression. In particular, it relates to methods for down-regulating the expression of one or more target sequences in vivo. The disclosure also provides polynucleotide constructs and compositions useful in such methods, as well as cells, plants and seeds comprising the polynucleotides.
Donald Danforth Plant Science Center | Date: 2017-03-22
Compositions and methods for increasing plant yield are disclosed. Compositions comprise transcription factors that find use in modulating the expression of a gene or nucleotide sequence of interest in a plant. Additionally, promoters and cis-regulatory elements are disclosed that may be used to drive the expression of a nucleotide sequence of interest in a plant. Methods for the use of such compositions as well as transformed plants are disclosed.
Umen J.G.,Donald Danforth Plant Science Center
Current Opinion in Microbiology | Year: 2011
Sexual reproduction in Volvocine algae coevolved with the acquisition of multicellularity. Unicellular genera such as Chlamydomonas and small colonial genera from this group have classical mating types with equal-sized gametes, while larger multicellular genera such as Volvox have differentiated males and females that produce sperm and eggs respectively. Newly available sequence from the Volvox and Chlamydomonas genomes and mating loci open up the potential to investigate how sex-determining regions co-evolve with major changes in development and sexual reproduction. The expanded size and sequence divergence between the male and female haplotypes of the Volvox mating locus (MT) not only provide insights into how the colonial Volvocine algae might have evolved sexual dimorphism, but also raise questions about why the putative ancestral-like MT locus in Chlamydomonas shows less divergence between haplotypes than expected. © 2011 Elsevier Ltd.
Agency: NSF | Branch: Continuing grant | Program: | Phase: PLANT GENOME RESEARCH PROJECT | Award Amount: 1.44M | Year: 2016
Increasing the yield and sustainability of crop production in a changing climate is one of the foremost challenges of our time. Corn is the most important crop in the United States, but despite steady increases in corn production, projected yields fall short of demands. Furthermore, petroleum-based nitrogen fertilizers have been identified as a primary driver of pollution of major waterways in the U.S. and globally. This project focuses on root systems, the hidden-half of plants, that are responsible for all of the water, nitrogen, and other nutrient acquisition. It leverages advanced imaging techniques, some of which were developed in the medical and industrial research sectors, to analyze the structure of root systems. Root structures from corn varieties that are known to be superior in nitrogen acquisition will be compared those that are inferior, and the genes that control root-nitrogen interactions will be identified. This will directly benefit corn and other crop breeders, and thus a major sector of U.S. agriculture, through identification of genes that control root growth and efficient nitrogen acquisition. An additional objective is to train the next generation of scientists by establishing after-school and summer educational programs for middle-school to undergraduate students. These trainees will gain first-hand experience building, programming, and employing plant imaging systems using 3D printers and affordable microprocessors.
Realizing the enormous potential of root systems to boost and stabilize crop yields under stress and to reduce unsustainable levels of fertilizer use will require a thorough understanding of their genetics and physiology. Image-based phenotyping has enabled high-throughput and accurate measurements of roots, but despite many new and promising methods, each has inherent tradeoffs that limit their individual power. This project employs an integrated root phenomic and physiological profiling approach to resolve the genetic basis and functional consequences of maize root architecture. It will profile the root architecture of two maize populations in four complementary ways: 3D/4D imaging of young plants in a gel based system, optical and X-ray based imaging of root crowns excavated from the field, and minirhizotron imaging of roots growing across the soil profile in the field. Quantitative genetic analyses from each of these methods will allow identification of the genes controlling these traits. Additionally, this integrated analysis of identical genotypes will generate the most comprehensive comparison of root phenotyping methods to date. One population will be selected from screening of the NAM parent lines in the first two years of the project, the other population will be the Illinois Protein Strain Recombinant Inbreds (IPSRIs). Over five years, this approach will address the following aims: 1. Identify genes driving phenotypic variation of root architecture, 2. Identify genes controlling phenotypic plasticity of root architecture to nitrogen supply, 3. Determine the functional impacts of root architecture on plant nitrogen status, elemental content and seed quality.
Agency: NSF | Branch: Continuing grant | Program: | Phase: EVOLUTION OF DEVELOP MECHANISM | Award Amount: 129.95K | Year: 2016
At the dawn of agriculture, our ancestors harvested wild grains and began replanting them year after year. This process rapidly led to selection for grains that stayed on the plant, instead of falling on the ground. Now, 10,000 years later, this capacity to stay on the plant until harvest has obvious economic importance. The change from wild grains that fall and cultivated ones that do not is caused by naturally occurring mutations in a normal (that is wild) process. However, the process of shedding seeds occurs differently in different grains. For example, the details of dropping seeds in wild rice are different from those in wild sorghum or wild millet. This project will discover what natural mutations led to the cultivated grains, and whether the natural process of shedding seeds in rice, sorghum, and millet is genetically similar. Because retaining seeds on the plant is the very basis of agriculture, it is an obvious aspect of plants that can engage students at all education levels. Master teachers and undergraduate education majors at Oklahoma State University, as well as undergraduate science majors and local high school students, will participate actively in the observations and data collection required for the project.
Shedding of seeds occurs via a characteristic zone of weakness, the abscission zone (AZ), in which the contents of cells and cell walls are modified to allow a fruit to fall off the parent plant. This project will test whether development is generally conservative, i.e., whether the AZ is produced by activating a conserved developmental program at different times or in different locations, or whether development produces novel structures (in this case, the AZ) by using novel gene combinations. Specifically, recombinant inbred lines and wild accessions will be used to identify genes that contribute to shattering in the model species green millet (Setaria viridis). These studies will be complemented by transcriptomic data on green millet in comparison to Brachypodium distachyon and rice. These investigations will test the hypothesis that some aspects of AZ development are shared among the three species but that many aspects differ because the AZ forms in a different position in each. The investigation will then be expanded to many other grasses, some of which are similar to millet, rice and Brachypodium, and some of which show distinct patterns of seed shedding. The results will define the extent of parallel and convergent evolution in an ecologically and economically critical pathway.
Agency: NSF | Branch: Continuing grant | Program: | Phase: SYMBIOSIS DEF & SELF RECOG | Award Amount: 422.71K | Year: 2016
The goal of this work is to investigate in plants the function and evolution of a novel class of regulatory small RNAs. Prior work demonstrated that plant genes like those known to confer resistance to pathogens are the targets of a set of microRNAs--suppressive regulatory RNAs just 22 nucleotides in length. These microRNAs are believed to function as master regulators of a very large family of protein coding disease-resistance genes, and part of their activity is to trigger the production of additional small RNAs (21 nucleotides in length) that have an unusual, regularly spaced pattern, or phasing of biogenesis. The regulation of this gene family, and several others targeted by microRNAs in the same way, is a new paradigm for microRNA function. The investigators have identified these small RNAs as conserved in many crop plants, including soybean, an alfalfa relative, tomato and potato. The aim of this project is to investigate this novel gene regulatory circuit to understand its function in plants, its role in plant defenses or beneficial microbial interactions, and whether it can ultimately be developed as a tool for improving plants or altering plant-microbe interactions to reduce disease or improve beneficial interactions. The project will utilize methods that include plant genomics, plant cell biology, plant-microbial interactions, and RNA analysis. The expected result is the dissection and understanding of a novel and complex gene regulatory mechanism. The broader impacts of the project range from a local impact on the training of students and a post-doc who will be directly involved in the project, to national and international impact to the scientific community in the databases and web tools that the project will release.
Agency: NSF | Branch: Continuing grant | Program: | Phase: Physiolg Mechansms&Biomechancs | Award Amount: 298.56K | Year: 2016
Due to their sessile nature, plants continuously adjust their growth, development and productivity in accordance with their surroundings. They respond to environmental stresses (e.g. drought, cold temperatures), various pathogens, low or high nutrient availability, and interactions with other organisms by precise modification of underlying signaling pathways. Several proteins, many of which are present in all organisms, have evolved plant-specific structural features and functions to effectively address these challenges. One such group of proteins is the heterotrimeric G-protein family, which although present in all eukaryotes, has certain plant-specific components and features. This research seeks to discover the unique signaling pathways regulated by a novel, plant-specific Gγ protein, AGG3, of Arabidopsis. Results obtained from this research will help us understand how plants maintain their yield against environmental stresses. These results will have potential practical applications in the breeding or engineering of more productive crops with limited resources. The work will also involve the training of a postdoctoral researcher in a multidisciplinary field and mentoring of undergraduate students. The research will help promote an understanding of plant science to the high school students and general public thorough a series of hands on experiments and interactive presentations.
Even though all eukaryotes possess heterotrimeric G-proteins and their overall signaling mechanisms are broadly conserved, plants have taken the core G-protein system and rewired it to meet their needs. One novel component of the plant G-protein system is the newly discovered, higher plant-specific, type III (or Class C) Gγ protein, represented by AGG3 in Arabidopsis. Type III Gγ proteins have a modular architecture, with an N-terminal domain similar to canonical Gγ , fused with a large C-terminal extension (up to 3 times the length of Gγ domain) that contains up to 35% cysteine (Cys). The type III Gγ proteins are currently a focus of intense research due to their involvement in regulation of many agronomically important processes in plants, including seed yield, organ size regulation, abscisic acid (ABA)-dependent signaling and stress responses, and nitrogen use efficiency. The mode of action of these proteins remains largely unknown, and some unique mechanisms that are independent of the classic G-protein cycle are also proposed. This research therefore aims to determine the G-protein-dependent and -independent roles of AGG3, and elucidate its underlying signaling mechanisms; especially those operative during abiotic stress signaling. Genetic complementation of single and higher order mutants will be performed using specific domains of AGG3, followed by identification of its protein interaction network. These analyses will help define the role of AGG3 and its network elements in abiotic stress signaling pathways and how it is related to its ability to control yield.
Agency: NSF | Branch: Continuing grant | Program: | Phase: PLANT GENOME RESEARCH RESOURCE | Award Amount: 274.65K | Year: 2016
The model plant Arabidopsis thaliana plays a unique and essential role as the reference organism for all seed plant species. This project will establish a Research Coordination Network that will lead to the development of informatics tools and resources for Arabidopsis in particular and for plant biology in general. It will be an open network that aims to draw in a broad cross-section of the US and international Arabidopsis communities. Arabidopsis research is at a critical junction; a broad range of new data types are becoming available, and the community?s ability to address important questions depends on the integration, visualization and analysis of these data. Diverse research groups are inventing new informatics approaches and thus the community needs a mechanism by which to identify, explore, promote, and enhance these resources. This project will catalyze a radical change in the way in which US and international researchers coordinate data generation, analysis and visualization. This project has the following goals: 1) The development of standards for Arabidopsis data deposition and display, 2) Development of a plan to develop Arabidopsis informatics tools and resources for the US and international communities, 3) Establishment of an International Arabidopsis Informatics Consortium that will build upon the activities and resources that will be generated in this project, 4) Establishment of a website as a resource for interested scientists and the general public.
Broader Impacts: Through the coordination of Arabidopsis informatics efforts, this project will advance plant biology, create novel opportunities for research and education, and lead to the establishment and growth of an International Arabidopsis Informatics Consortium. The problems that the Arabidopsis community is facing today will also challenge other communities, and this type of coordinated international approach to leveraging informatics resources across borders should provide an example (and resources) for such communities. Experiences learned from this application will have a broad impact across biology, particularly for crop plants for which a similar expansion in data is occurring and which often can build on efforts pioneered in Arabidopsis. The resources developed in this project will be widely and freely available and will be useful for students and researchers at educational institutions of all sizes, for industry, and for the public.
Agency: NSF | Branch: Continuing grant | Program: | Phase: PLANT GENOME RESEARCH PROJECT | Award Amount: 2.65M | Year: 2016
PI: Blake C. Meyers (University of Delaware)
CoPIs: Virginia Walbot (Stanford University) and Greg Abrams (Texas Advanced Computing Center/University of Texas - Austin)
Information generated from this project will provide new insights into the regulation of developmental events in the anther, the male reproductive organ, of maize and related grasses - crops that feed much of the world. New insights and resources of broad utility should ultimately contribute to controlling plant fertility in agriculture, particularly in the cereal crops. The project builds and improves on the varied and extensive outreach and education components of the PIs and their contributions via scientific leadership to continue a strong, positive impact on local and scientific communities, and on the next generation of scientists. Implementation of the Virtual Anther will make the project data widely accessible while helping students and the public understand how anthers develop. An undergraduate-focused project to sequence and annotate a basal grass genome will provide invaluable data for the project and to all those employing phylogenomics analysis in flowering plants, while training the next generation of plant biologists. All project outcomes will be accessible to the research community through a project website and long-term repositories such as GEO and MaizeGDB. All biological resources such as antibodies, clones and vectors will be available upon request. Seed will be deposited and distributed long-term through the Maize Genetics Cooperative. Software for the Virtual Anther will be made open-source and available via the Texas Advanced Computing Center website (https://www.tacc.utexas.edu/tacc-software/).
Male sterility is a common phenotype in natural species, functioning as one mechanism to promote outcrossing. Furthermore, control of pollen production by plant breeders is a fundamental technology that continues to underpin hybrid seed production in many crops. In the agricultural context, there is also a growing concern over climate disruption: both heat and cold cause male sterility in crop plants. This study seeks to more broadly understand the coordination of anther development and underlying cellular processes, including chromatin remodeling, as plant cells switch from mitosis to meiosis. The specific goals are to: (1) organize hierarchies of gene expression in individual anther cell types and (2) elucidate functions of small RNAs, particularly two unusual classes of phased secondary small RNAs (phasiRNAs) that are highly enriched in grass anthers. These phasiRNAs are processed from an extensive set of coordinately-expressed long non-coding RNA precursors into secondary small RNAs of 21 or 24 nucleotides. Using precisely staged maize anthers and laser microdissected cell types, the project will generate copious transcriptomic and proteomic data, organize transcriptional hierarchies of transcription factors, generate extensive data on small RNAs in a spatiotemporal context, and analyze the function and biogenesis of phasiRNAs. Genetic analysis using existing and engineered mutations will be used to test for essential roles of key transcription and phasiRNA biogenesis factors in anther development. Genetic and omics experiments will test new hypotheses about phasiRNA functions in anther cells and in meiosis. Most of the analysis will be conducted in maize because of its exquisite developmental regularity, the large size and ease of anther dissection, and existing molecular and genetic knowledge about maize anthers. Key insights will be evaluated in rice to distinguish general and species-specific points, with additional comparisons to other grasses. To generate new hypotheses, all data will be integrated into a Virtual Anther visualization system.
Agency: NSF | Branch: Standard Grant | Program: | Phase: BIOTECH, BIOCHEM & BIOMASS ENG | Award Amount: 745.00K | Year: 2016
Photosynthetic algae are a critical component of the earths carbon cycle. Carbon dioxide is taken up by algae and converted into macromolecules that are the building blocks for producing more cells; alternatively this carbon can be used to produce storage compounds such as starch and storage lipids (oil). Very little is known about the metabolic control mechanisms that direct carbon towards these different fates. This project uses the single celled green alga Chlamydomonas to investigate carbon partitioning under the control of a newly discovered signaling system involving a specialized class of molecules called inositol polyphosphates. The regulation of inositol polyphosphates by light, carbon and other environmental cues will be determined and their impact on carbon metabolism will be measured and modeled so that the mechanism by which they control intracellular carbon partitioning can be pinpointed. These studies will provide a deeper understanding of a key aspect of photosynthetic metabolism and enable the development of strategies for manipulating algae to improve yields of biotechnologically relevant compounds. Two postdoctoral fellows and multiple undergraduate will receive cross-disciplinary training and mentoring in algal cell biology and physiology, metabolic modeling and mass spectrometry in a facility whose mission is to perform transformative science and train the next generation of scientists.
A major challenge in biology is understanding how cells control the flux of carbon through metabolic networks to produce storage compounds versus growth to produce more cells. This project will decipher a new mode of intracellular signaling that uses inositol polyphosphates to control steady state metabolic flux into neutral lipids in a model photosynthetic eukaryote, Chlamydomonas. Inositol polyphosphates and their biosynthetic enzymes play diverse roles in intracellular signaling, but have not been previously linked to photosynthetic carbon partitioning. Because inositol polyphosphates are conserved, the outcomes of this research are likely to be broadly applicable for understanding algal and plant carbon partitioning. The PIs hypothesize that inositol polyphosphates produced by Chlamydomonas VIP1 control metabolic responses that specifically impact the production of storage lipids (triacylglycerol). This research will: i) characterize VIP1 protein activity in vitro and test whether its predicted catalytic activities are required for function; ii) test the hypothesis that inositol polyphosphate isomer levels reflect differences in growth metabolism under different trophic conditions; iii) characterize transcriptomes and metabolomes of wild type and vip1-1 under different trophic conditions to identify areas where the mutant shows altered metabolic regulation; iv) employ quantitative metabolic flux modeling (INST-MFA) to identify branch points in carbon metabolism impacted by inositol polyphosphates. This research will expose undergraduates from a primarily minority institution to cutting edge scientific instrumentation, analytical methods and modeling approaches and engage post-doctoral scientists in a highly collaborative project that requires integration across diverse disciplines and provides them with leadership and mentoring opportunities.