Construction of High Resolution Physical Maps for Large Plant Genomes

PI：Shahryar F. Kianian（北达科他州州立大学-法戈）CoPIs：Anne M.丹顿（北达科他州州立大学-法戈）、Oscar Riera-Lizarazu（俄勒冈州州立大学）、Ming-Cheng Luo（加州大学-戴维斯）、Yong Qiang Gu和Gerry Lazo（加州大学-戴维斯/USDA-ARS）对许多作物（如小麦和其他谷物）的大型复杂基因组进行完全测序，给基因组学界带来了艰巨的挑战。为了开发3.2Gb人类基因组的完整图谱和完成的序列，使用90个全基因组辐射杂交体（RH）构建了由40，322个独特序列标记位点组成的独立的高分辨率标记支架。然后，这个基于RH的物理图谱被用于对超过15，000个重叠群的序列信息进行排序，以创建完整的人类基因组图谱。RH作图在人类中的成功激发了其在完成测序之前用于构建大多数动物基因组的完整物理图谱的用途。该项目将使用一种简单而优雅的方法来开发高分辨率RH物理图谱，该图谱将用于锚定六倍体小麦4.2 Gb D基因组的现有细菌人工染色体（BAC）重叠群和克隆。这种锚定和比对将补充国际小麦基因组学界为开发该基因组的全球物理图谱和全基因组序列所做的更大努力。该项目中开发的工具、方法和知识可以应用于其他作物品种，并将有助于以当前方法的一小部分成本构建物理地图。所生成的图谱将提供获取具有生物学和农业重要性的基因的便捷途径，并将有助于制定新的策略来操纵小麦，以更好地满足不断增长的世界人口的需求。此外，该项目中开发的信息将允许对小麦与水稻、玉米和其他草的基因组进行比较分析，以解决有关基因组织和染色体进化的重要生物学问题。 可通过项目网站（http：//wheat.tag.usda.gov/RHmapping）获取本项目开发的工具、方法和知识。 所有品系的种子都可以通过联系项目人员或通过美国农业部国家小颗粒收集中心（阿伯丁，ID）获得。 除了培训项目学生和博士后研究员外，该项目还将与少数民族服务机构合作，包括密西西比谷州立大学和波多黎各大学-马亚圭斯，让少数民族本科生参加为期八周的分子遗传学和生物信息学夏季研究培训计划。

PI: Shahryar F. Kianian (North Dakota State University - Fargo)CoPIs: Anne M. Denton (North Dakota State University - Fargo), Oscar Riera-Lizarazu (Oregon State University), Ming-Cheng Luo (University of California - Davis), and Yong Qiang Gu and Gerry Lazo (University of California - Davis/USDA-ARS)Complete sequencing of large and complex genomes of many crop plants such as wheat and other cereals provide a daunting challenge to the genomics community. In order to develop a complete map and finished sequence of the 3.2 Gb human genome, an independent high-resolution marker scaffold composed of 40,322 unique sequence tagged sites was constructed using ninety whole-genome radiation hybrids (RHs). This RH-based physical map was then used to order sequence information for more than 15,000 contigs to create the complete human genome map. The success of RH mapping in humans has inspired its use in the construction of complete physical maps for the majority of animal genomes prior to complete sequencing. This project will use a simple yet elegant method of developing high-resolution RH physical maps that will be used to anchor existing bacterial artificial chromosome (BAC) contigs and clones for the 4.2 Gb D-genome of hexaploid wheat. This anchoring and alignment will complement a larger effort by the international wheat genomics community to develop a global physical map and whole-genome sequence of this genome. The tools, methods, and knowledge developed in this project can be applied to other crop species and will facilitate the construction of physical maps at a fraction of the cost of current methods. The maps generated will provide easy access to genes of biological and agricultural importance and will enable the development of new strategies to manipulate wheat to better serve the needs of a growing world population. In addition, the information developed in this project will allow for comparative analysis of wheat with rice, maize and other grass genomes to address important biological questions regarding gene organization and chromosome evolution. Access to the tools, methods, and knowledge developed in this project will be available through the project website (http://wheat.pw.usda.gov/RHmapping). Seed for all lines will be available by contacting project personnel or through the USDA National Small Grains Collection (Aberdeen, ID). In addition to the training of project students and postdoctoral associates, the project will partner with minority serving institutions including Mississippi Valley State University and the University of Puerto Rico - Mayaguez to engage minority undergraduate students with an eight-week summer research training program in molecular genetics and bioinformatics.