Evolutionary Genomics of Rice

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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.