The Evolutionary Genomics of Weedy Rice

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.


  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. Determine 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.


Recent Publications from this Project:


Reagon, M., C.S. Thurber, K.M. Olsen, Y. Jia, and A.L. Caicedo (2011). The long and the short of it: sd1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice.  Molecular Ecology 20: 3743–3756.

Lee, S., Y. Jia, D.R. Gealy, M. Jia, K.M. Olsen, and A.L. Caicedo (2011). Molecular Evolution of the Rice Blast Resistance Gene Pi-ta in Invasive Weedy Rice in the USA.  PLoS ONE 6: e26260.

Reagon, M., C.S. Thurber, K.M. Olsen, Y. Jia, and A.L. Caicedo (2010) Genomic patterns of nucleotide diversity in divergent populations of invasive U.S. weedy rice.  BMC Evolutionary Biology 10: 180.

Gross, B.L., S.C. Hsu, A.L. Caicedo, Y. Jia, and K.M. Olsen (2010). Seeing red: the origin of grain pigmentation in US weedy rice.  Molecular Ecology 19: 3380-3393.

Thurber, C., M. Reagon, B.L. Gross, K.M. Olsen, Y. Jia, and A.L. Caicedo (2010). Molecular evolution of shattering loci in US weedy rice. Molecular Ecology 19: 3271-3284.

Gross, B.L. K.J. Skare, and K.M. Olsen (2009). Novel Phr1 mutations and the evolution of phenol reaction variation in US weedy rice (Oryza sativa L.). New Phytologist 184: 842–850.