Evolutionary Genomics of Rice

Overview

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, yet despite its position as the world's predominant cereal food crop and as a model for grass genomics research, relatively little is known about the evolutionary forces that shape genomic diversity in rice.

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 (HapMap).

The extent of linkage disequilibrium 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. Patterns of LD will be compared between regions of different recombination rates and between neutral loci and genes subjected to selection under domestication. The levels and patterns of single nucleotide polymorphisms will also be analyzed in a set of randomly chosen gene fragments to determine the distribution of population genetic parameters in rice. Sequence data and results of evolutionary analyses from this project will be made available to the community through web-based interfaces and public databases such as 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.

Upcoming
  • Developing Country Collaborations on the study of Isolated Rice Populations: In the coming year, we will genotype 30 microsatellites on these materials to examine population structuring and will sequence 3 genes to investigate LD. This is part of a new partnership with the International Rice Research Institute in Los Banos, Philippines.
  • Hitchhiking map for rice chromosome III. This is a collaboration with Dr. Ryuji Ishikawa at Hirosaki University in Japan. Dr. Ishikawa has genotypes rice lines for >120 chromosome III markers and we are coordinating with him to examine whether regions of low SSR diversity also correspond to regions of low SNP diversity. Moreover, a member of the Purugganan laboratory also joined Dr. Ishikawa and other Japanese scientists in Vietnam and Laos to collect O. rufipogon samples for an expanded study of the origins of domesticated rice.

    • Supported by the National Science Foundation.

    NSF

     

     

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