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者、生物技术专家和生物学家的总体运作格局。在丰富的新机会中，将有一个利用基因组序列数据来更好地利用作物中重要的农艺性状的自然发生的变异。随着具有生物学和农学重要性的新基因的确定，我们需要确定这些基因中存在于作物物种种质库中的功能变异的数量、分布和性质。拟议中的研究将在玉米上建立必要的基础设施来实现这一点。这些研究人员将确定在玉米种质池中的哪里，以及在玉米基因组中最容易找到有用的变异的地方。他们将检查一组农艺性状候选基因的核苷酸多样性，并测试特定的DNA序列多态是否与这些性状的表型变异有关。该项目的总体目标是更好地了解玉米基因组中遗传多样性的分布，并促进在核酸水平上鉴定候选基因的多态，这些基因在农学和生物学上的重要试验中控制表型水平的变异。该项目包括四个部分：(1)研究多样性如何在玉米育种系、地方品种和野生近缘之间分布。玉米种质池中的遗传多样性将利用微卫星(简单序列重复；SSR)进行分析。将整理和公布玉米种质资源的农艺性状数据。该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，估计种质池不同部分的遗传多样性水平，并确定一组充分代表玉米多样性的核心材料。(2)研究遗传多样性如何在玉米基因组中分布。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因素都会影响特定基因的核苷酸多态水平，从而使同一基因组中不同环境中的基因表现出非常不同的多态水平。这些研究人员将测量上述因素如何影响整个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。关联分析在农学研究中尚未看到重大用途，尽管它有可能提供比数量性状基因座定位更快速和更具体的结果。(4)由于前三部分都涉及对多基因座基因类型数据的广泛统计分析，该项目包括一个生物统计/信息学小组，该小组将设计新的统计程序或改进现有的统计程序，以分析收集到的数据。该小组还将监督万维网发布所产生的信息。

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.