YIA: Genomics of Rice, Sorghum and Maize

YIA：水稻、高粱和玉米的基因组学

• 批准号: 0333074
• 负责人: Doreen Ware
• 金额: $ 129.52万
• 依托单位: Cold Spring Harbor Laboratory
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-01 至 2009-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0333074&HistoricalAwards=false
• 关键词: YIA; Genomics; Rice; Sorghum; Maize

Cereals are a large and diverse set of agronomically important crops from the family Gramineae. They are the main source of dietary calories for most human populations whether they are consumed directly, as in rice, or indirectly as animal feed. The primary subject of this research is gene colinearity, the evolutionarily conserved order along the chromosome of genes among different species. The movement of blocks of genes of rice chromosome 1 relative to the corresponding regions of maize and sorghum will be analyzed. The research will enhance the understanding of genome organization of these agronomically important cereal crops. The structure of cereal genomes and their genes are key to understanding the evolutionary relationships within this important family. However, due to the size and complexity of these genomes it is unlikely in the next few years that complete sequences will be available from each of these genomes. Although there has been much work on cereal macro and micro-colinearity, gene dense islands, and links between gene amplification and gene movement among the cereal genomes, there has been no large-scale analysis of these phenomena to date. This project will take an unbiased large-scale approach to identify whether these are indeed true trends or represent selected events in cereal genomes. To do this, a rough map of shared segments between rice, sorghum and maize using existing public data will be generated. Gaps in the comparative maps will be closed by selecting candidate rice genes to use as additional anchor points and map them to conserved blocks in the sorghum and maize genetic and physical maps. The final product will be a high-resolution comparative map of rice 1 with the corresponding regions of sorghum and maize. The comparative physical maps will be a starting point for studies to understand the organization of the three cereal genomes and their evolutionary relationship. In the process, methods will be developed for building and finishing comparative maps, which can be applied to genome-scale projects in the future. It will also serve as a valuable resource for the identification of genes involved in agronomically important traits.Information generated:1.70 maize genetic markers anchored to the maize IBM map and maize physical map2.SSR database for maize and sorghum sequences3.STC database for BACs found in the maize and sorghum physical maps BAC end sequences for clones selected in the minimum tiling path 200 rice gene models anchored to maize 75 rice gene models directly sequenced from maize and sorghum 4.Integrated BAC map of maize and sorghum across colinear regions in rice chromosome 1 based upon sequence similarity and overgo hybridization.5.1 MB of cereal BAC sequences6.Develop a pilot curriculum for high school students on "Colinearity of Genes in Cereal Genomes"

谷物是来自禾本科的大量且多样的农艺学上重要的作物。 它们是大多数人膳食热量的主要来源，无论是直接食用，如大米，还是间接作为动物饲料。基因共线性是指不同物种间基因在染色体上沿着进化上的保守顺序。将分析水稻1号染色体基因块相对于玉米和高粱相应区域的移动。 这项研究将提高对这些重要农艺作物基因组结构的理解。谷物基因组及其基因的结构是理解这一重要家族内进化关系的关键。 然而，由于这些基因组的大小和复杂性，在未来几年内不太可能从每个基因组中获得完整的序列。 虽然已经有大量的工作谷物宏观和微观共线性，基因密集岛，基因扩增和基因运动之间的联系，谷物基因组中，至今还没有大规模的分析这些现象。 该项目将采取无偏见的大规模方法，以确定这些是否确实是真正的趋势或代表谷物基因组中的选定事件。为此，将利用现有的公共数据绘制水稻、高粱和玉米共有部分的粗略地图。 通过选择候选水稻基因作为额外的锚点，并将其定位到高粱和玉米遗传和物理图谱中的保守区块，将填补比较图谱中的空白。最后产品将是一份高分辨率的水稻1与相应的高粱和玉米地区的比较图。比较物理图谱将是研究三种谷物基因组的组织及其进化关系的起点。 在这一过程中，将制定建立和完成比较图谱的方法，这些图谱今后可应用于基因组规模的项目。它还将作为鉴定涉及重要农艺性状的基因的宝贵资源。1.70个锚定在玉米IBM图谱和玉米物理图谱上的玉米遗传标记2.玉米和高粱序列的SSR数据库3.玉米和高粱物理图谱中发现的BAC的STC数据库最小平铺路径中选择的克隆的BAC末端序列200个锚定在玉米上的水稻基因模型75个直接从玉米和高粱测序的水稻基因模型4.基于序列相似性和overgo杂交的玉米和高粱跨水稻1号染色体共线区域的整合BAC图谱5. 1 MB谷物BAC序列6.为高中生开设“谷物基因组中基因的共线性”试点课程