Evolutionary Genomics of Maize

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The complete DNA sequence of crop genomes will dramatically change the landscape in which plant breeders, biotechnologists, and biologists in general operate. Among the wealth of new opportunities will be one to exploit genomic sequence data to better utilize naturally occurring variation for agronomically important traits in crops. As new genes of biological and agronomic importance are determined, we need to identify the amount, distribution and nature of functional variation in these genes that exist in the germplasm pools of crop species. The proposed research will create the necessary infrastructure to do this in maize. These investigators will define where in the maize germplasm pool and where in the maize genome useful variation is most apt to be found. They will examine nucleotide diversity in a set of candidate genes for agronomic traits and test whether specific DNA sequence polymorphisms can be associated with variation in the phenotype for these traits. The overall goals of this project are to better understand the distribution of genetic diversity within the maize genome and to facilitate the identification of polymorphisms at the nucleic acid level in candidate genes that control variation at the phenotypic level in agronomically and biologically important traits.The project has four components: (1) To examine how diversity is distributed among breeding lines, landraces and wild relatives of maize. Genetic diversity in the maize germplasm pool will be assayed using microsatellites (simple sequence repeats; SSRs). Agronomic trait data for maize germplasm will be organized and published. This portion of the project will help to define the degree of genetic similarity among maize lines, to estimate the level of genetic diversity in different segments of the germplasm pool, and to identify a core set of accessions that amply represent diversity in maize. (2) To examine how genetic diversity is distributed across the maize genome. Forces such as recombination rates, chromosomal position, linkage relationships, past selective sweeps, and nucleotide composition can all influence the level of nucleotide polymorphism in particular genes such that genes in different contexts in the same genome can exhibit vastly different levels of polymorphism. These investigators will measure how the above forces have shaped diversity across the maize genome. (3) To develop and test methods to associate phenotypic variation for specific agronomic traits with sequence variation in candidate genes. Association analyses of this type are now being widely used in the study of the inheritance of complex diseases in humans. Association analyses have yet to see significant use in agronomic research, despite their potential to provide more rapid and more specific results than quantitative trait locus mapping. (4) Because each of the first three sections involves extensive statistical analyses of multilocus genotypic data, the project includes a Biostatistics/Informatics Group that will devise new or refine existing statistical procedures for the analysis of the data collected. This group will also oversee World Wide Web publication of the information produced.