ARS | Publication request: Seeing Red: The origin of grain pigmentation in US Weedy rice

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 1, 2010
Publication Date: N/A

Technical Abstract: Red rice is a weedy relative of cultivated rice (Oryza sativa) that infests rice fields worldwide and is a leading cause of crop losses. The weed is characterized by a combination of traits found in wild Oryza species and domesticated rice. Studies using neutral genetic markers have consistently indicated a very close relationship between US red rice strains and Asian cultivated varieties, suggesting that the weed may have originated through reversion of domesticated rice to a feral form. We have tested this reversion hypothesis by examining molecular variation at Rc, the regulatory gene responsible for grain pigmentation differences between domesticated and wild rice. Loss-of-function mutations at Rc account for non-pigmented grain of cultivated rice; the major domestication allele, rc, can revert to a functional form, leading to restoration of the ancestral red-grain phenotype. Our data indicate that the pigmented grain of US red rice has not originated through crop allele reversions, but rather that the weeds carry ancestral functional gene copies. Sequences from genomic regions flanking Rc confirm the close relationship of red rice to Asian Oryzas that have never been cultivated in the US. Together these findings indicate that US red rice most likely originated from Asian undomesticated Oryzas or from rare red-pigmented crop landraces, rather than through a process of ‘de-domestication’ of modern cultivars.