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

Reference ID

54910

Title

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

Source

Mol Ecol, 2010, vol. 19, pp. 3380-3393

Authors (6)

Gross-B-L	Reagon-M
Hsu-S-C	Caicedo-A-L
Jia-Y	Olsen-K-M

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 analysed 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 they are compatible with a close relationship of red rice
to Asian Oryzas that have never been cultivated in the US.