Evolutionary Genomics of Maize

作物基因组的完整DNA序列将极大地改变植物育种家、生物技术专家和生物学家的工作环境。在丰富的新机会中，将有一个利用基因组序列数据，以更好地利用作物中重要农艺性状的自然变异。随着具有生物学和农艺学重要性的新基因的确定，我们需要确定存在于作物物种种质库中的这些基因的功能变异的数量、分布和性质。拟议中的研究将建立必要的基础设施，在玉米中做到这一点。这些研究人员将确定在玉米种质库和玉米基因组中哪里最容易发现有用的变异，他们将检查一组农艺性状候选基因的核苷酸多样性，并测试特定DNA序列多态性是否与这些性状的表型变异有关。本项目的总体目标是更好地了解玉米基因组内遗传多样性的分布，并促进在核酸水平上鉴定候选基因的多态性，这些基因控制着在农艺学和生物学上重要性状的表型水平上的变异。将使用微卫星（简单重复序列; SSR）分析玉米种质库中的遗传多样性。将组织和出版玉米种质的农艺性状数据。项目的这一部分将有助于确定玉米品系之间的遗传相似程度，估计种质库不同部分的遗传多样性水平，并确定一套充分代表玉米多样性的核心种质。(2)研究遗传多样性在玉米基因组中的分布。诸如重组率、染色体位置、连锁关系、过去的选择性扫描和核苷酸组成等力都可以影响特定基因中的核苷酸多态性水平，使得相同基因组中不同背景下的基因可以表现出极大不同的多态性水平。这些研究人员将测量上述力量如何塑造玉米基因组的多样性。(3)开发和测试将特定农艺性状的表型变异与候选基因的序列变异相关联的方法。这种类型的关联分析现在被广泛用于研究人类复杂疾病的遗传。关联分析在农艺学研究中还没有得到显著的应用，尽管它们有可能比数量性状基因座作图提供更快速和更具体的结果。(4)由于前三个部分都涉及对多位点基因型数据进行广泛的统计分析，因此该项目包括一个生物统计学/信息学小组，该小组将设计新的或改进现有的统计程序，用于分析所收集的数据。该小组还将监督万维网公布所产生的信息。

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.