This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2019. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Grace A. Mason is "Leveraging Quantitative Genetic Mapping Data for Discovery of Novel Regulatory DNA in Solanum lycopersicum". The host institutions for the fellowship are the University of California, Davis/University of Minnesota, Twin Cities and the sponsoring scientists are Drs. Siobhan Brady and Chad Myers.
Traditionally, crop improvement relies solely on selective breeding for desired traits. While successful, this laborious methodology reduces breeders' ability to quickly predict traits based on genetic variation as well as improve available breeding resources. To allow for faster and more systematic breeding, this project aims to systematically test genetic variation within the tomato genome for their effects on gene expression and on selected root architecture phenotypes. Potential regulatory variants will then be tested first for the ability to influence gene expression and then for its effect on plant root architecture phenotypes, traits that are generally understudied and could be of potential use to tomato breeders. The broader impacts of the project include providing hands-on training in basic research for local high school and undergraduate students from diverse backgrounds as well educating the general public about tomato breeding and how modern technologies can allow for non-transgenic crop improvement. Training objectives include acquiring skills in the use of quantitative genetics and computational science and tool development in an economically relevant crop plant.
Variation in regulatory DNA is thought to be a major factor for phenotypic variation in wild species as well as domestication of cultivated crop plants. Enhancers, a type of regulatory DNA, regulate target gene expression in a spatiotemporal manner and can be relatively distal to their target genes, thus making them difficult to characterize. In animal systems, hundreds of enhancers are well-characterized and have been linked to target genes. In plants, despite recent efforts to identify genome-wide regulatory elements, only thirteen enhancers in four plant species have been directly linked to target genes. Of these, only variation in the tb1 enhancer in Zea mays (corn) is demonstrably linked to domestication and crop improvement. To address this disparity, the overall goal of this project is to discover allele-specific plant enhancers and link them to their target genes. Specifically, regulatory enhancer elements will be identified in Solanum lycopersicum (tomato) using novel computational methods for genetic mapping data with a specific focus on root architecture traits. The research will take advantage of several diverse genetic resources, including an extensive catalog of domesticated tomato accessions, existing quantitative trait data sets, as well as a genetically divergent set of isogenic introgression lines. Large-scale enhancer assay techniques will be used to yield allele-specific regulatory regions linked to root architecture phenotypes. While there has been intense effort to characterize the regulatory landscape in several cultivated plants, these experiments will be the first to directly test plant-based association mapping variants using large-scale sequencing technologies. Sequencing data from this project will be archived and publicly available through the National Center for Biotechnology Information (NCBI) GEO and Probe databases. Additionally, all CRISPR-Cas9 constructs will be made available by request and through Addgene, the nonprofit global plasmid repository (www.addgene.org/). Software and analysis scripts will be made available through GitHub.
Keywords: tomato, gene expression, genetic variation, regulatory DNA, enhancer element, root architecture, quantitative genetics
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
