Cross-Linked Sorghum and Rice Physical Maps as a Foundation for Analyzing Genome Structure, Function, and Variation in C4 Grasses

来自垂直整合的“无墙中心”的研究人员将在领先的禾本科（禾本科）种子/谷物作物、生物质作物和主要杂草的结构、功能和种群基因组学方面进行密切协调的研究。草类植物是人类和饥荒之间的屏障，因为人类和牲畜消耗的大部分热量来自高粱、水稻、玉米、小麦、甘蔗、小米和其他草。人口增长和工业/住宅对可耕地的侵占给农业带来了更大的压力，要求农业以更低的成本获得更高的产量。基因发现的现代能力以符合负责任地管理生物圈的方式为作物的内在遗传改良打开了新的大门。通过利用不同禾本科植物基因组染色体上沿着排列的基因组织中已确立的相似性，高粱和水稻的小基因组将被用于加速研究和改进具有更大基因组的作物，如玉米和甘蔗。小高粱基因组（约760兆碱基）是对水稻基因组（约440兆碱基）的最合理的补充，作为“草基因组模板”，并且是与玉米（约2500兆碱基）和甘蔗（2500 - 4200兆碱基）等密切相关的大基因组作物的重要桥梁。该项目有四个主要组成部分：基因组组织。 高粱和水稻基因组的物理图谱将被开发出来，这些图谱彼此“交联”，也与其他大基因组作物“交联”。这将加速完成水稻的测序物理图谱，并将为将基因组序列数据外推到高粱、玉米、甘蔗和其他禾本科植物提供参考点。 将开发一个独特的表达序列标签（EST）和相应的cDNA克隆文库，目标是获得10，000个不同基因的序列信息，这些基因在高粱植物生长和发育的关键阶段表达。这些资源将用于许多应用，包括研究植物生长和发育关键阶段的基因表达。群体基因组学。 调查自然发生的等位基因多样性在DNA水平和形态/生态地理多样性之间的关系的方法和知识结构之间的高粱基因型将开发作为一个有价值的补充，遗传/物理方法，以确定基因负责变异的关键步骤植物生长和发育。 将开发和使用软件和网上资源，使远程用户能够迅速获取基因组数据，该项目加上与国家和国际努力的联系，将产生一套完整的共享资源，用于作为农业基础的种子/谷物和生物量作物的内在遗传改良。高粱是干旱和半干旱农业的主要谷物，在世界粮食作物中的重要性排名第五。大米虽然是美国的一种次要作物，但它为全世界的人类提供的热量比任何其他作物都多。甘蔗可以说是世界上最有价值的作物，每年约1430亿美元。高粱属还包括世界上最具侵略性的杂草之一-“约翰逊草”（S。Halepense）-使玉米、大豆、棉花和其他主要作物的产量减少45%。sorbicygenomics可能会导致新的策略，对环境友好的植物生长调节，无论是抑制杂草的蔓延或刺激密集的理想饲料和草坪草。

Researchers from a vertically integrated "center without walls" will conduct closely coordinated research in structural, functional, and population genomics across leading Poaceae (grass family) seed/grain crops, biomass crops, and major weeds. The grass family stands between humankind and famine, as most calories consumed by humans and livestock derive from sorghum, rice, maize, wheat, sugarcane, millet, and other grasses. Population growth and industrial/residential encroachment on arable land place greater pressure on agriculture to secure higher yields at less cost. Modern capabilities for gene discovery open new doors to intrinsic genetic improvement of crops in a manner that is consistent with responsible stewardship of the biosphere. By utilizing well-established parallels in the organization of genes along the chromosomes of different grass genomes, the small genomes of sorghum and rice will be used to accelerate study and improvement of crops with much larger genomes such as maize and sugarcane. The small Sorghum genome (approximately 760 megabases) is the most logical complement to that of rice (approximately 440 megabases) as a "grass genome template", and is an important bridge to closely related large genome crops such as maize (approximately 2500 megabases) and sugarcane (2500 - 4200 megabases). This project has four major components:Genome organization. Physical maps for the sorghum and rice genomes will be developed that are "cross-linked" to each other and also to other large genome crops. This will accelerate completion of a sequence-ready physical map for rice, and will provide reference points to extrapolate genomic sequence data to sorghum, maize, sugarcane, and other grasses.Genome function. A library of unique expressed sequence tags (ESTs) and corresponding cDNA clones will be developed, with a target of obtaining sequence information for 10,000 different genes, expressed at key stages in the growth and development of the sorghum plant. These resources will be used for many applications, including study of gene expression at key stages of plant growth and development.Population genomics. Both a methodological and intellectual structure for investigating relationships between naturally occurring allelic diversity at the DNA level and morphological/ecogeographic diversity among Sorghum genotypes will be developed as a valuable complement to genetic/physical approaches to the identification of genes responsible for variation in key steps of plant growth and development.Informatics. Software and web-based resources will be developed and implemented to make genomic data rapidly accessible by remote users.This project, together with links to national and international efforts, will yield a well-integrated set of shared resources for intrinsic genetic improvement of both seed/grain and biomass crops that are keystones of agriculture. Sorghum is a leading cereal grain in arid and semi-arid agriculture; ranking fifth in importance among the world' s grain crops. Rice, although a minor U.S. crop, provides more calories to humans worldwide than any other crop. Sugarcane is arguably the world's most valuable crop at approximately $143 billion per year. The sorghum genus also includes one of the world's most aggressive weeds - "Johnsongrass" (S. halepense) - that reduces yields of maize, soybean, cotton and other major crops by up to 45%. Sorghum genomics may lead to new strategies for environmentally benign plant growth regulation, either suppressing the spread of weeds or stimulating dense stands of desirable forage and turf grasses.