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Scientific Objectives and Approaches Genetic architecture is the constellation of gene effects and interactions that underlie variation in a quantitative trait. Essentially, genetic architecture is the map between phenotype and genotype. Understanding variation in genetic architecture is key to understanding evolution, manipulating species for a sustainable agriculture, and preserving variation as species adapt. This project will improve our understanding of the genetic architecture of complex traits in maize and its wild relative, teosinte. Maize has a combination of life history, economic and societal value, and genetic tools that make it uniquely suited to studying genetic architecture. The project will identify genes that control domestication traits and three key agronomic traits: flowering time, plant height, and kernel quality. Genetic linkage, association, and fine mapping analyses will be performed on the largest and most diverse set of mapping families publicly available for any species. A large series of isogenic lines will be used to characterize allelic series and epistatic interactions. The genetic architecture of each of the four trait groups will be compared and contrasted, and the influence of recombination and past domestication bottlenecks on the genomic distribution of functional diversity will be examined. Finally, the ability of genetic architecture-based models to predict phenotype will be evaluated in a broad range of germplasm, including elite US hybrids. This project will take a step toward the ultimate goal of predicting phenotype from genotype. Broader Impacts Maize has the highest production of any crop in the world, and plays a central role in all of US agriculture and food production. Maize also has the greatest molecular and phenotypic diversity among crop species. This genetic diversity enabled domestication and is key for future maize improvement. Understanding maize genetic architecture will accelerate the breeding of future crops. In addition, this project will generate valuable germplasm resources and develop genomic tools to access and utilize maize and teosinte diversity. These resources will be used by many other research groups to dissect numerous other traits and facilitate marker assisted breeding, allele mining, and genetic analysis. Project resources will be made available to the public through a project website (www.panzea.org), integration with community websites (Gramene, www.gramene.org; MaizeGDB, www.maizegdb.org), and stock centers (Maize Genetics Cooperation Stock Center, maizecoop.cropsci.uiuc.edu; CIMMYT, www.cimmyt.org; North Central Regional Plant Introduction Station). Maize is also an excellent system for teaching about evolution, genetics, and agriculture. Outreach activities will target four audiences: (1) the general public and students through a traveling museum exhibit on maize domestication, diversity and improvement, (2) high school teachers through an enrichment course with North Carolina Agriculture & Technical State University, (3) collaborative science through an African Scientist Fellowship at Cornell's Institute of Genomic Diversity (www.igd.cornell.edu), and (4) undergraduate students through mentoring and research opportunities. Relevance and Justification Living organisms display tremendous natural genetic variation for development, chemical composition, and adaptations to specific environments. Understanding the nature of this genetic variation is key to understanding evolution, manipulating species for a sustainable agriculture, and preserving inter- and intra-specific variation through our current period of rapid environmental change. Although most detailed molecular genetic analyses have focused on genes of major effect, almost all standing genetic variation within natural and breeding populations is controlled by numerous genes that individually control less than 10% of the variation in species. This project will strive to improve our understanding of the genetic basis of complex traits. Maize (Zea mays ssp. mays) and the teosintes (seven other named taxa in the genus Zea, including Z. mays ssp. parviglumis, the closest wild relative of maize) have a combination of life history, economic and societal value, and genetic tools that together make Z. mays uniquely suited to studying genetic architecture. Genetic architecture is the constellation of gene effects and interactions that underlie variation in a quantitative trait. Essentially, it is the map between phenotype and genotype. Using the powerful set of genetic tools developed over the past decade by the members of this project along with others in the maize community, the goal of this new project is a comprehensive "phenomic" analysis of four complex traits: domestication syndrome, flowering, plant height, and kernel quality. Specifically, we will identify genes that control these traits, determine the effects of the series of polymorphisms at these loci, examine epistatic interactions between these genes, and evaluate the interaction of the genetic architecture with environment. With an enhanced understanding of the genetic architecture for these four diverse traits in maize, we will compare and contrast the architectures of maize and teosinte and relate their functional variation to basic genome structure and to the population-genetic consequences of the domestication bottleneck. We will address the extent to which modern functional variation is a product of standing variation that evolved over a several million year time scale versus mutations arising during domestication over the last few thousand years. Finally, we will use this understanding of genetic architecture to evaluate our ability to predict phenotype from genotype, the fundamental goal of modern genetics. Maize and the teosintes are an ideal system for understanding these aspects of genetic architecture. In coding regions, the average nucleotide diversity between any two maize lines (π = 1-1.4%) is similar to the divergence between humans and chimps, and even greater diversity (40% more) is harbored within ssp. parviglumis. It is not uncommon to find maize haplotypes that are 5% diverged from one another, indicating that the maize gene pool reaches back 2-4 million years or generations. In longer generation species (e.g., poplar), this would be the equivalent of tens of millions of years of evolution. Essentially, population genetics in maize is equivalent in terms of diversity to deep evolution in many other clades of plants and vertebrates. The advantage of maize and teosinte is that the entire range of diverse germplasm is interfertile, and seed stocks can be created, stored, and shared efficiently. Maize and teosinte are also predominantly outcrossing species, constantly producing new allelic combinations. The constant creation of new epistatic combinations, exposure to diverse environments, and relatively high migration rates between maize and some teosinte populations strongly influenced the genetic architecture of Z. mays. This type of genetic architecture is likely to be shared with most plants (80% are outcrossing) and animals, but it could be quite different from the genetic architecture of inbreeding species exemplified by Arabidopsis and rice. The phenotypic variation of maize mirrors the molecular variation. Maize and its progenitor, teosinte, represent the greatest morphological divergence between any crop-ancestor pair, making them the most interesting and powerful system for the investigation of morphological change during domestication. Even within the domesticated subspecies, abundant phenotypic variation is observed for many traits. Through heritable changes in flowering time, responses to photoperiod and temperature, and plant architecture, maize has adapted to extremely diverse environments ranging from Northern Europe and Canada to the lowland tropics and to the high Andes. Maize varies in height from less than 1m to over 6m and ranges tremendously in biomass and carbon allocation. Similarly, maize kernels vary ~10 fold in their composition for oil and protein content. This heritable variation is the basis of worldwide maize breeding efforts to improve the maize grown on 144 million ha worldwide. In the US, maize is grown on 34 million ha, and is a base commodity crop supporting the $1-2 trillion US food industry by providing protein, oil, and starch for food, animal feed, ethanol, and other biobased products. The only way to sustainably increase yield without increasing inputs or area under cultivation is to continually improve the genetic adaptation of maize to modern farm agroecology and changing climate conditions. Understanding genetic architectures sufficiently to predict phenotypes will be key to increasing maize yield and sustainability. Importantly, maize now has the some of the best genetic tools to conduct this research. Through our prior research efforts and recent contributions (e.g., a vast set of introgression lines donated by Syngenta to our project), we have nearly 15,000 genetic stocks that permit manipulation and isolation of the genetic variation throughout the entire species. With completion of the maize genome sequence in 2008 and the availability of next generation sequencing of maize diversity, it is now possible to use the full range of genomic tools to examine the genetic architecture of maize. Project Goals The proposed project has two parts: First, research on genetic architecture (Sections 1-4); Second, development of germplasm, genetic, and bioinformatic resources so that any trait can be dissected (Section 5). Obviously, these resources are needed to accomplish our scientific aims, but they will also be of tremendous value to maize community for other projects. Our specific aims are:
Plan to Integrate Research and Education Maize is an excellent system for teaching about evolution, genetics, and agriculture. Outreach activities will target four audiences:
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