GPF-PG: Genome Structure and Diversity of Wheat and Its Wild Relatives

Kansas State University, Manhattan KS

Investigators

Abstract

Wheat (Triticum aestivum L.) is one of the world's most important food crops and a staple for billions throughout the world. Hidden within loaves of bread is one of largest and most complex genomes of important plant species. The size and complexity of the bread wheat genome, which is more than five times larger than the human genome, have hindered development of a reference framework that can serve as a resource for genetic studies and breeding applications. A better understanding of the wheat genome will also give insight into the structure, function and evolution of complex, polyploid plant genomes. Advancement of population-based sequencing methods for assembling plant genomes will have broad implications throughout the plant genomics community, particularly for species with limited genomic resources and large, intractable genomes. User-friendly tools for population sequencing developed through this project will enable applications of this approach in the broader plant genome community. Through integrated education and outreach activities, this project will recruit and train new generations of computational biologists to address complex and challenging genomics questions. In partnership with the Kansas Foundation for Ag in the Classroom (KFAC), multi-tiered educational materials on plant genomes and domestication will be developed and implemented in middle and high school classrooms across the state. Through KFAC, students will be given access to advanced material targeting Next Generation Science Standards, including resource materials on careers in plant science. At the undergraduate level, internships will be developed to attract non-biology students from computationally-intensive fields. Interns with diverse social and academic backgrounds will be challenged with cutting-edge bioinformatics through coursework and research in U.S. labs followed by summer internships working with European project collaborators. At the postdoctoral level, scholars working on this project will gain skills in cutting-edge genomics along with mentoring and international research experience. To disseminate bioinformatics approaches developed through this project, annual workshops for bioinformatics training in population sequencing and genotyping-by-sequencing will be held for graduate and postdoctoral training. As an approach for developing sequence resources for crop plants with large genomes, next-generation sequencing (NGS) can be applied to rapidly generate a whole genome sequence that is readily assembled into short contigs. These contigs primarily contain the gene-rich, non-repetitive portions of complex genomes. However, WGS assemblies have limited utility because these gene-rich contigs remain unanchored and unordered on the chromosomes. Novel, cost-effective approaches are needed for anchoring and ordering large, complex genomes. Through this project, new methods for assembling and ordering complex plant genomes will be developed and applied to understanding the genomes of wheat and its wild relatives. NGS will be applied to segregating populations of diploid, tetraploid and hexaploid wheat species, leveraging linkage information to develop an ordered whole-genome assembly for each species. This approach (POPSEQ) uses millions of genetic markers to order the assembled gene space onto a physical framework. The project will target 1x whole-genome sequence coverage across multiple diploid (AA and DD genomes), tetraploid (AABB) and hexaploid (AABBDD) populations to develop high-density genetic maps. These high-density genetic maps can then be used to anchor sequence contigs and scaffolds, giving physical context to genome assemblies. Ordered assemblies will be iteratively improved and made available to the wheat community through MIPS (http://mips.helmholtz-muenchen.de/plant/genomes.jsp), T3 (http://triticeaetoolbox.org/) and GrainGenes (http://wheat.pw.usda.gov/) databases. Genetic stocks will be made available through the KSU Wheat Genetics Resource Center and the USDA-ARS National Small Grains Collection.