Evolutionary Genomics of Rice

水稻的进化基因组学

• 批准号: 0319553
• 负责人: Gregory Gibson
• 金额: --
• 依托单位: North Carolina State University
• 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 2007-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0319553&HistoricalAwards=false
• 关键词: Evolutionary; Genomics; Rice

Rice (Oryza sativa) is one of the oldest domesticated crop species in the world, and has fed more people throughout human history than any other food plant. Rice is also widely recognized as a model system for the study of cereal crop genomes. The study of the evolutionary genomics of rice, specifically levels and patterns of linkage disequilibrium (LD) and single nucleotide polymorphisms (SNPs) provides the foundation for improved genome scanning and mapping techniques to isolate quantitative trait loci that can be used for crop improvement in rice, as well as in other selfing crop species. Understanding the patterns of SNP correlations and diversity is also necessary for the construction of a whole genome rice haplotype map. The deliverables for this project are as follows:1. The extent of LD in ten targeted 500-kb genomic regions will be determined in O. sativa subspecies indica and japonica, as well as the progenitor wild species O. rufipogon. 2. Patterns of LD will be compared between six genomic regions of high, moderate and low recombination rates. 3. LD will be analyzed around four genes subjected to selection under domestication - the starch biosynthetic gene Waxy, the candidate shoot architecture gene OsTb1, the flowering time gene Hd1 and the anthocyanin pigmentation gene Rc. 4. The levels and patterns of single nucleotide polymorphisms will be analyzed in a set of 125 randomly chosen gene fragments to determine the distribution of population genetic parameters in rice. 5. This project will require a projected total of 153,000 sequencing reads. Sequence data and results of evolutionary analyses from this project will be made available to the community through web-based interfaces and the public databases Gramene and Genbank. We also propose an integrated outreach program to develop web-based and laboratory exercises in plant genomics that are targeted to middle and high school students. This program will be disseminated to students and teachers of North Carolina in an effort to bring 21st century genomics research into school curricula, providing a means for wider education of the public in genomics research.

水稻是世界上最古老的驯化作物之一，在人类历史上养活了比其他任何粮食作物都多的人。水稻也被广泛认为是研究谷类作物基因组的模式系统。水稻进化基因组学的研究，特别是连锁不平衡(LD)和单核苷酸多态(SNPs)水平和模式的研究，为改进基因组扫描和作图技术以分离可用于水稻和其他自交作物物种改良的数量性状基因座奠定了基础。了解SNP相关性和多样性的模式对于构建全基因组水稻单倍型图谱也是必要的。本项目的成果如下：1.将在水稻亚种水稻和水稻以及野生野生稻野生稻中确定10个目标500kb基因组区域的LD范围。2.比较高、中、低重组率的6个基因组区域的LD图谱。3.对驯化选择的四个基因--淀粉生物合成基因waxy、候选地上部构型基因OsTb1、开花时间基因hd1和花青素着色基因Rc进行分析。4.对随机选择的125个基因片段的单核苷酸多态水平和模式进行分析，以确定水稻群体遗传参数的分布。5.该项目预计将需要153000个测序读数。该项目的序列数据和进化分析结果将通过基于网络的界面和公共数据库Gramene和Genbank向社区提供。我们还提出了一个综合推广计划，以开发针对初中生和高中生的植物基因组学网络和实验室练习。该计划将向北卡罗来纳州的学生和教师传播，努力将21世纪基因组研究纳入学校课程，为公众提供更广泛的基因组研究教育手段。