ARS | Publication request: Evolutionary Genomics Of Invasive Weedy Rice

Submitted to: Plant and Animal Genome
Publication Type: Proceedings
Publication Acceptance Date: December 1, 2006
Publication Date: January 13, 2007
Citation: Olsen, K., Caicedo, A.L., Jia, Y. 2007. Evolutionary Genomics Of Invasive Weedy Rice . Plant and Animal Genome.

Technical Abstract: Red rice is an interfertile, weedy form of cultivated rice (Oryza sativa) that competes aggressively with the crop in the southern U.S., reducing yields and contaminating harvests. Weed strains range from ‘crop mimics,’ which share many domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have indicated that some weed strains are closely related to Asian taxa (including indica rice varieties, which have never been cultivated in the U.S., and the Asian crop progenitor, O. rufipogon), while others show genetic similarity to the tropical japonica varieties cultivated in the southern U.S. This project, recently funded by the NSF Plant Genome Research Program, seeks to examine the population genomic structure of red rice and the roles of foreign weed introduction, genomic introgression and selection in shaping the weed genome. Goals include: 1) using SNP diversity from STS loci across the weed genome to determine the population genomic structure of the weed and the proportion of the genome contributed by Asian wild Oryza species, Asian cultivated rice, and U.S. rice varieties; 2) determining the evolutionary origins of haplotypes at candidate genes underlying weed-associated traits; and 3) using patterns of linkage disequilibrium in genomic regions flanking weed-associated candidate genes to assess how selection and introgression have interacted to shape the evolution of red rice. The project will provide a comprehensive view of genome evolution in this weed and will contribute to public databases on Oryza SNP diversity, molecular markers, and linkage disequilibrium.