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

Abstract

Weedy forms of crop species infest agricultural fields worldwide and are a leading cause of crop losses, yet little is known about how these weeds evolve. Red rice (Oryza sativa), a major weed of cultivated rice fields in the US, is recognized by the dark-pigmented grain that gives it its common name. Studies using neutral molecular markers have indicated a close relationship between US red rice and domesticated rice, 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 the absence of proanthocyanidin pigments in cultivated rice grains, and the major rc domestication allele has been shown to be capable of spontaneous reversion to a functional form through additional mutations at the Rc locus. Using a diverse sample of 156 weedy, domesticated, and wild Oryzas, we analyzed DNA sequence variation at Rc and its surrounding 4 Mb genomic region. We find that reversion of domestication alleles does not account for the pigmented grains of weed accessions; moreover, we find that haplotypes characterizing the weed are either absent or very rare in cultivated rice. Sequences from genomic regions flanking Rc are consistent with a genomic footprint of the rc selective sweep in cultivated rice, and are compatible with a close relationship of red rice to Asian Oryzas that have never been cultivated in the US.

Association Between Seed Dormancy and Pericarp Color Is Controlled by a Pleiotropic Gene That Regulates Abscisic Acid and Flavonoid Synthesis in Weedy Red Rice

“…This similarity suggests that Rc alleles from tropical (e.g., SS18-2 and TKN12-2) and temperate (e.g., LD and C9541) weed ecotypes share some evolutionary mechanisms with those from indica and japonica subspecies, respectively, such as selection pressures from temperatures and cropping systems or common gene donors. Exceptions exist for Rc alleles from weedy genotypes in new rice-growing areas, such as US1 (group I) and other U.S. weedy rice lines discussed in detail by Gross et al (2010). However, our research suggests that the dormancy function of SD7-1 alleles in red rice may not vary with their phylogenetic distances but that detection of the dormancy effect can be influenced by the genetic backgrounds and/or experimental methods.…”

Archaeological and genetic insights into the origins of domesticated rice

“…However, in every case where the survey included an evolutionary component, the origin of the domestication allele was found to be the japonica subspecies (80,81). As a result, the phylogenies generated from domestication genes showed japonica and indica as a monophyletic group (69,84), consistent with a single origin for allele controlling a domestication trait. In contrast, neutral loci generally recovered a polyphyletic relationship (51,59), and analyses that included O. rufipogon showed that japonica and indica were more closely related to different populations of the wild species than to each other, consistent with multiple origins.…”

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

“…6). Along with seed shattering and seed dormancy, pericarp pigmentation is not favorably selected during the course of rice domestication (Sweeney and McCouch, 2007;Gross et al, 2010). It is possible that ancient rice farmers used the red pericarp color as a visual cue to discard red rice seeds due to perceived association with inferior grain quality.…”