CoPIs: Peter Bradbury (USDA-ARS), John Doebley (University of Wisconsin), Sherry Flint-Garcia (USDA-ARS/University of Missouri), Theresa Fulton, Sharon Mitchell and Qi Sun (Cornell University), James Holland (USDA-ARS/North Carolina State University), Jeffrey Ross-Ibarra (University of California-Davis) and Doreen Ware (USDA-ARS/Cold Spring Harbor Laboratory)
Senior Personnel: Jeff Glaubitz (Cornell University)
Key Collaborator: Jose de Jesus Sanchez Gonzalez (Universidad de Guadalajara, Mexico)
Genetic architecture is the constellation of gene effects and interactions that underlie variation in a quantitative trait, and can be thought of as the map that links phenotype and genotype. Understanding variation in genetic architecture is critical to understanding evolution, manipulating species for sustainable agriculture, and preserving variation as species adapt. This project has been very effective over the last several years at understanding the basic genetic architecture of traits, determining key genes, and identifying common variants. While these common variants play a central role in maize's adaptation to numerous large-scale environments, there is also a nearly infinite number of rare alleles that may play a significant role in phenomena such as inbreeding depression, genetic load, heterosis, hitchhiking, local adaptation, parallel evolution, gene flow, and the genetic architecture of quantitative traits such as yield. The ability to predict the combined effects of thousands of rare alleles is one of the important missing pieces in making the genotype-to-phenotype map. This project will establish the importance of rare alleles to fitness related traits across a diverse range of Zea germplasm. While the project will look at the full range of allelic variation, there will be special emphasis on testing hypotheses regarding rare alleles, as these comprise the most poorly understood yet potentially transformative class of variation. Extensive genomic profiling of nearly 90,000 diverse genotypes will be combined with a range of field trials to determine the phenotypic effects of individual polymorphisms. Using predictions generated from comparative genomics, molecular biology, and population genetics, this research will test hypotheses relating different classes of polymorphism to phenotypic variation. Statistical and computational models will be developed that incorporate the combined effects of rare alleles, and these models will be empirically tested in hybrid maize trials. The range of life histories of maize and its wild relatives, combined with the ability to phenotype at a massive scale, make maize a premier model for the study of the importance of rare alleles in the genotype-to-phenotype map.
Maize is the largest production crop in the world, and plays a central role in US agriculture and food production. Maize also has the greatest molecular and phenotypic diversity of any major crop species. This diversity enabled domestication and is key for future maize improvement. Understanding the role of rare alleles in maize genetic architecture will aid in the selection and development of future breeding lines, especially in predicting hybrid performance. In addition, this project will generate valuable germplasm and genomic annotation resources that will be used by many other groups to dissect numerous other traits and facilitate genomic breeding, allele mining, and genetic analysis. These resources will be made available through a project website (www.panzea.org), integration with community websites (MaizeGDB and Gramene), and stock centers [Maize Genetics Cooperation Stock Center and the North Central Regional Plant Introduction Station (NCRPIS)]. The outreach program, including the Maize: Mysteries of an Ancient Grain museum exhibit and related online teacher materials, Genotype-by-Sequencing (GBS) workshops, and the training of postdocs, graduate students and undergraduates, has reached a large number of people throughout the U.S. This successful program will be expanded to double the number of exhibit venues, increase the number of workshops/short courses, and supplement these with video courses.
