Evolutionary Genomics of Rice

水稻（Oryza sativa）是世界上最古老的驯化作物之一，在整个人类历史上，它比任何其他粮食植物都养活了更多的人。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）和单核苷酸多态性（SNPs）的水平和模式的研究，为改进基因组扫描和定位技术提供了基础，从而分离出可用于水稻和其他自交作物品种改良的数量性状位点。了解SNP相关性和多样性模式也是构建水稻全基因组单倍型图谱的必要条件。本项目可交付成果如下：在水稻亚种籼稻和粳稻及其祖先野生种紫花苜蓿中，确定10个500-kb目标基因组区域的LD程度。2. 将在高、中、低重组率的6个基因组区域之间比较LD的模式。3. 在驯化条件下，将围绕淀粉生物合成基因Waxy、候选茎部结构基因OsTb1、开花时间基因Hd1和花青素色素沉积基因Rc进行LD分析。在125个随机选择的基因片段中分析单核苷酸多态性的水平和模式，以确定水稻群体遗传参数的分布。5. 该项目预计总共需要153,000个测序读数。该项目的序列数据和进化分析结果将通过网络接口和公共数据库Gramene和Genbank向社区提供。我们还提出了一个综合的推广计划，以开发针对初高中学生的植物基因组学网络和实验室练习。该计划将传播给北卡罗莱纳州的学生和教师，努力将21世纪基因组学研究纳入学校课程，为更广泛的公众基因组学研究教育提供手段。

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.