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Linkage disequilibrium (LD) mapping techniques, including candidate gene association analysis, provides new strategies to the identification and isolation of genes that underlie phenotypic variation in plant species. These LD mapping technologies require detailed information on the levels and patterns of single nucleotide polymorphisms (SNPs) in genomes, and the evolutionary forces that structure this SNP variation within species. The levels and patterns of SNP variation and genomic linkage disequilibrium remain unknown for most crop species, particularly selfing crops such as rice, barley, pearl millet, soybean and tomato. We will explore the evolutionary genomics of SNP variation and linkage disequilibrium in rice (Oryza sativa), setting the stage for LD mapping efforts in this model cereal crop species. Our broad research objectives are to examine patterns of nucleotide polymorphism in 12 reference rice genes, as well as 24 genes in the starch biosynthetic, flowering time, shoot development and seed pericarp pigmentation pathway and in 100 gene-based sequence-tagged sites. The extent of linkage disequilibrium in eight targeted 500-kb genomic regions will also be determined. Finally, we will test association mapping methods in rice and develop new analytical approaches in statistical genetics for use in linkage disequilibrium and candidate gene association mapping in selfing plant species. The study of the evolutionary genomics of SNP variation will provide the foundation for improved genome scanning and mapping techniques to isolate quantitative trait loci (QTLs), that can be used for crop improvement in rice, as well as in other selfing crop species. Moreover, 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, with the aid of NCSU Science House, 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. |
Research