The Evolutionary Genomics of Weedy Rice

Plant Genome Research Program, DBI-103023

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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 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. 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.

Goals:

1. Use 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. Determinine the evolutionary origins of haplotypes at candidate genes underlying weed-associated traits.
3. Use 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 the red rice genome.

This is a field of cultivated rice in Arkansas. It is infested with weedy rice, which overtops the cultivar and is lighter in color.