Seeing red: The origin of grain pigmentation in US weedy rice

Authors: GOSS, BRIANA - Washington University; REAGON, MICHAEL - University Of Massachusetts; HSU, SHIH-CHUNG - Washington University; CAICEDO, ANA - University Of Massachusetts; Jia, Yulin; OLSEN, KENNETH - Washington University

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2009
Publication Date: 6/24/2010
Citation: Goss, B.L., Reagon, M., Hsu, S., Caicedo, A.L., Jia, Y., Olsen, K.M. 2010. Seeing red: The origin of grain pigmentation in US weedy rice. Molecular Ecology. 19:3380-3393.

Interpretive Summary: Red rice (Oryza sativa L.) is the major weed that causes tens of millions of dollars in crop losses annually in the US. The Rc gene in rice encodes a bHLH regulatory protein in the proanthocyanidin synthesis pathway. The loss of function mutation has been previously identified in cultivated white rice. In the present study, DNA sequence variation at Rc and its surrounding 4 Mb genomic regions in 137 rice accessions composed of weedy, domesticated, and wild Oryzas, was analyzed. The loss of function mutation has not been identified in all red rice strains, however, substantial haplotype diversity was identified in all weed strains tested. Sequence information from genomic regions flanking Rc identified the close relationship of red rice to Asian Oryzas that have never been cultivated in the US. We suggest that US red rice is most likely descended from undomesticated Oryza species or incipiently domesticated pigmented landraces, rather than from feral ‘de-domesticated’ modern cultivars.

Technical Abstract: Red rice (Oryza sativa L.) is the major weed of cultivated rice fields in the US, where it causes tens of millions of dollars in crop losses annually. This weedy crop-relative is characterized by several traits that are typical of wild Oryza species, including the anthocyanin-pigmented pericarp that gives red rice its common name. Previous studies using neutral molecular markers have indicated a close relationship between US red rice and domesticated rice (specifically, indica and aus varieties grown outside the US), suggesting that the weed may have originated through reversion of domesticated rice to a feral form. In the present study we have tested this reversion hypothesis by examining molecular variation at the Rc locus, the regulatory gene responsible for pericarp pigmentation differences between domesticated and wild rice. Loss-of-function mutations at Rc account for the absence of anthocyanins in cultivated rice grains, and the major crop rc allele has been shown to be capable of reversion to a functional form through additional mutation at Rc. Using a diverse sample of 137 weedy, domesticated, and wild Oryzas, we analyzed DNA sequence variation at Rc and its surrounding 4 Mb genomic region. We found substantial haplotype diversity and no evidence of rc crop allele reversion in all weed strains tested. In addition, sequences from genomic regions flanking Rc confirm the close relationship of red rice to Asian Oryzas that have never been cultivated in the US. These findings indicate that US red rice is most likely descended from undomesticated Oryza species or incipiently domesticated pigmented landraces, rather than from feral ‘de-domesticated’ modern cultivars.