Selected Funding
Dissecting Natural Mechanisms for Genome Content Variation and the Impact on Phenotypic Variation
NSF ECA-PGR Award Number 1546727 (PI: Candice Hirsch, University of Minnesota; Co-PIs: Marna Yandeau-Nelson, Suzanne McGaugh (UMN))
Abstract. The nature of a plant or animal is defined in part by the DNA content in its genome. One might expect that this important role of imparting information is preserved in genomes over generations. In fact, genomes are known to be unstable and the constituent gene and non-gene content can change over time; genes can be copied, lost, or altered slightly, and such variation has significant impact on the appearance and function of an individual. As an example, the change in gene content in a corn plant can affect its growth or important agronomic traits, such as drought resistance, seed size or yield. The variation in gene content in individuals is puzzling to scientists and clearly beneficial to breeders: How and when does gene content change? What impact does it have on the traits, or phenotype, of the plant? And can the process be harnessed to identify new traits for agricultural improvement? This research project uses corn, or maize, as a model crop to answer these questions. The research is possible because the maize genome is remarkably variable in closely related lines, and there are extensive genetic resources that can be used to test how, when and why genome content changes. The project will identify signatures of genome change and will associate these changes to new traits. In the process, new participants will be trained from many educational levels. Specific efforts will focus on attracting young girls and women to scientific careers. Students and teachers will engage in a type of authentic research in plant genomics that has clear connections to outcomes in agriculture. Mentoring and training opportunities for female scientists will also be collated and disseminated through databases and public web portals.
Using maize as a model system, this project will systematically characterize the extent of genome content variation among a panel of diverse genotypes, identify the genetic mechanisms responsible for this variation in genome content through genomic signatures, and measure the impact on phenotypic variation. The research plan integrates genomics, metabolomics, quantitative genetics, and statistical genetics to further our understanding of genome content variation and the role mechanistic origin plays in phenotypic outcomes. Specifically, this project will 1) identify genome content variation between maize inbred lines using a combination of de novo genome assemblies and exome capture using a combination of short- and long-read sequencing technologies, 2) identify mechanistic signatures that elucidate the origin of genome content variation on a genome-wide scale, 3) implement Genome Wide Association Studies to identify genome content variation associated with quantitative, qualitative, essential, and dispensable phenotypic and chemotypic (surface lipid profiles and kernel content) classes of traits in a diverse panel of maize inbred lines, and 4) use statistical genetic approaches to determine if there is a relationship between the mechanisms that create genome content variation and phenotypic outcomes. The project also provides mentoring and training opportunities in new tools and technologies in metabolomics, genomics, and statistical genetics for high school, undergraduate and graduate students, postdoctoral associates, and faculty at primarily undergraduate institutions.
NSF-IOS Award Number 1354799 (PI: Marna Yandeau-Nelson; Co-PIs: Nick Lauter (USDA), Basil Nikolau (Iowa State University), Craig Abel (USDA)
Abstract. The aerial surfaces of land plants are protected by unique lipids, which provide a primary line of defense against numerous biological and environmental stresses. The surface lipids on the stigmatic silks of maize are biologically unique because they are rich in hydrocarbons, which are the inert end-point metabolites of the surface lipid network. This project will utilize maize silks as the model biological system to provide a fundamental understanding of this unique, discrete metabolic process by comprehensively dissecting within a single organism the metabolic and genetic networks that produce important surface lipids. Moreover, this project will elucidate the specific surface lipid constituents of maize silks that provide critical protection against environmental stresses (water stress and insect feeding) that commonly impact crops like maize during the often-stressful period of pollination. All metabolite and transcriptome data will be deposited in the Plant Metabolomics Resource database and the latter will also be deposited in the NCBI-SRA and NCBI-GEO databases. Quantitative trait locus (QTL) data will be searchable at MaizeGDB and made available at the integrated web portal for QTL dissection, GeneNetwork. Seed stocks for quantitative genetic mapping populations will be deposited at the Maize Genetics Cooperative Stock Center.
A significant societal impact of this project will be enhancement of the sustainability of US crop production via increased crop yields and/or decreased inputs. The identification of the protective surface lipids and the genes that produce them will provide the technological know how for applied breeding of customized lipid compositions that protect against many stresses, both in corn as well as in other crops. Further, the chemical similarity between silk surface lipids and petroleum components will be leveraged for applications in network bioengineering to produce advanced biofuels in other biological systems. During the project, >400 high school and college students from diverse socioeconomic, geographic and ethnic backgrounds will be exposed to hypothesis-driven research via three synergistic programs: A) a collaboration with Iowa State University's SCIENCE BOUND program will engage diverse secondary school students in scientific education via hands-on research modules; B) two SCIENCE BOUND students will conduct summer-research projects together with a high school teacher from a rural or high needs district and with a student from Chowan University, a 4-year undergrad institution with significant minority enrollment. These research experiences will help the teachers better engage an even larger number of students in scientific inquiry; and C) a discussion-based undergraduate course will be developed to serve as a bridge between fundamental knowledge learned through coursework and the application of that knowledge for conducting scientific research.
More details on NSF-IOS Award #1354799