ARS | Publication request: Origins and evolution of weedy rice in the US

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: December 1, 2008
Publication Date: January 10, 2009
Citation: Olsen, K.M., Reagon, M., Caicedo, A.L., Gross, B.L., Jia, Y., Lee, S. 2009. Origins and evolution of weedy rice in the US. In: Proceedings of Plant and Animal Genome Conference XVII, January 10-14, 2009, San Diego, CA. W506.

Technical Abstract: Red rice is a weedy form of cultivated rice (Oryza sativa) that infests crop fields and reduces US rice harvests by up to 80%. This agricultural weed has been proposed to arise either through de-domestication of feral US crop germplasm and/or introduction of foreign germplasm (potentially including wild, weedy, or cultivated Asian rice). We have examined DNA sequence variation in a genome-wide sample of 48 sequence-tagged site (STS) loci to characterize the population genomic diversity of the weed and its relationship to candidate progenitor germplasm. Bayesian analysis of population structure reveals genetic differentiation among weed strains that correlates with phenotypic variation. The two major phenotypic variants (blackhull awned, strawhull awnless) show closest genetic similarity to varieties of Asian cultivated rice that are not grown in the US (indica and aus varieties, respectively). There is little evidence that US crop varieties have played a major role in the evolution of the weed, although some evidence for crop-to-weed introgression is detected. Nucleotide diversity in the weed is low in comparison to cultivated rice and to wild Oryza samples, consistent with genetic bottlenecks during the establishment of the weed in the US.