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”的研究人员将在主要禾本科种子/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。由于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、小米和其他禾本科植物，因此禾本科植物家族介于人类和饥荒之间。人口增长和工业/住宅对耕地的侵占给农业带来了更大的压力，农业需要以更低的成本获得更高的产量。基因发现的现代能力为作物的内在遗传改良打开了新的大门，这种改良的方式与负责任的生物圈管理相一致。通过利用不同禾草基因组染色体上基因组织的相似性，高粱和水稻的小基因组将被用于加速对玉米和甘蔗等基因组大得多的作物的研究和改进。高粱小基因组（约760兆碱基）是水稻基因组（约440兆碱基）最合理的“草基因组模板”，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。这个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，它们彼此之间以及与其他大型基因组作物之间都是“交联”的。这将加速水稻序列物理图谱的完成，并将为推断高粱、玉米、甘蔗和其他禾草的基因组序列数据提供参考点。基因组的功能。将建立一个独特表达序列标签（ESTs）文库和相应的cDNA克隆，目标是获取高粱植株生长发育关键阶段表达的1万个不同基因的序列信息。这些资源将用于许多应用，包括研究植物生长发育关键阶段的基因表达。人口基因组学。研究在DNA水平上自然发生的等位基因多样性与高粱基因型之间形态/生态地理多样性之间关系的方法和知识结构，将作为遗传/物理方法的有价值的补充，用于鉴定在植物生长和发育的关键步骤中负责变异的基因。将开发和实施软件和基于网络的资源，使远程用户能够快速访问基因组数据。该项目连同与国家和国际努力的联系，将产生一套整合良好的共享资源，用于对作为农业基石的种子/谷物和生物质作物进行内在遗传改良。高粱是干旱半干旱农业的主要粮食；在世界粮食作物中排名第五。水稻虽然是美国的一种次要作物，但它为全世界人类提供的卡路里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，每年的产值约为1430亿美元。高粱属还包括世界上最具侵略性的杂草之一——强Johnsongrass (S. halepense)，它使玉米、大豆、棉花和其他主要作物的产量减少高达45%。高粱基因组学可能会导致对环境无害的植物生长调控的新策略，要么抑制杂草的蔓延，要么刺激理想的饲料和草坪草的密集生长。

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.