Biology of Rare Alleles in Maize and Its Wild Relatives

PI: Edward Buckler （USDA-ARS/康奈尔大学）合作伙伴：Peter Bradbury (USDA-ARS), John Doebley（威斯康星大学），Sherry Flint-Garcia （USDA-ARS/密苏里大学），Theresa Fulton， Sharon Mitchell和Qi Sun（康奈尔大学），James Holland （USDA-ARS/北卡罗莱纳州立大学），Jeffrey rose - ibarra（加州大学戴维斯分校）和Doreen Ware （USDA-ARS/冷泉港实验室）高级人员：Jeff Glaubitz（康奈尔大学）Jose de Jesus Sanchez Gonzalez（墨西哥瓜达拉哈拉大学）基因结构是基因效应和相互作用的集合，是数量性状变异的基础，可以被认为是连接表现型和基因型的图谱。了解遗传结构的变异对于理解进化、为可持续农业操纵物种以及在物种适应过程中保存变异至关重要。在过去的几年里，这个项目在理解性状的基本遗传结构、确定关键基因和识别常见变异方面非常有效。虽然这些常见变异在玉米适应大量大规模环境中发挥着核心作用，但也有几乎无限数量的罕见等位基因可能在近交抑制、遗传负荷、杂种优势、搭便车、局部适应、平行进化、基因流动和产量等数量性状的遗传结构等现象中发挥重要作用。预测数千个罕见等位基因的综合效应的能力是制作基因型-表型图谱的重要缺失部分之一。本项目将在不同的玉米种质中确定稀有等位基因对适合度相关性状的重要性。虽然该项目将着眼于等位基因变异的全范围，但将特别强调测试关于罕见等位基因的假设，因为这些等位基因包含了最不为人所知但具有潜在变革性的变异类别。近9万个不同基因型的广泛基因组图谱将与一系列野外试验相结合，以确定个体多态性的表型效应。利用来自比较基因组学、分子生物学和群体遗传学的预测，本研究将检验有关不同类别多态性与表型变异的假设。将开发包含稀有等位基因综合效应的统计和计算模型，这些模型将在杂交玉米试验中进行实证检验。玉米及其野生近缘种的生活史范围，加上大规模显型的能力，使玉米成为研究稀有等位基因在基因型-表型图谱中重要性的首要模型。玉米是世界上最大的生产作物，在美国农业和粮食生产中发挥着核心作用。玉米也是所有主要作物物种中分子和表型多样性最大的。这种多样性使驯化成为可能，也是未来玉米改良的关键。了解罕见等位基因在玉米遗传结构中的作用，将有助于未来育种品系的选择和发展，特别是对杂交性能的预测。此外，该项目将产生宝贵的种质资源和基因组注释资源，这些资源将被许多其他团体用于解剖许多其他性状，并促进基因组育种，等位基因挖掘和遗传分析。这些资源将通过项目网站（www.panzea.org）、与社区网站（MaizeGDB和Gramene）和库存中心（玉米遗传合作库存中心和中北部地区植物引种站）整合提供。包括玉米：古代谷物博物馆展览和相关在线教师材料、基因型测序（GBS）研讨会以及博士后、研究生和本科生培训在内的外展计划已经覆盖了美国各地的大量人员。这一成功的计划将扩大到展览场地数量增加一倍，增加研讨会/短期课程的数量，并辅以视频课程。

PI: Edward Buckler (USDA-ARS/Cornell University)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.