Oryza rufipogon

Oryza rufipogon is a species of flowering plant in the family Poaceae. It is known as brownbeard rice, wild rice, and red rice. In 1965, Oryza nivara was separated off from O. rufipogon. The separation has been questioned, and some sources consider O. nivara to be a synonym of O. rufipogon. O. nivara may be treated as the annual form of O. rufipogon.

It is native to East-, Southeast- and South- Asia. It has a close evolutionary relation to Oryza sativa, the plant grown as a major rice food crop throughout the world. Both have an AA genome.

Invasive species
Oryza rufipogon is an invasive species and listed as a 'noxious weed' by the United States, and also listed as a noxious weed in Alabama, California, Florida, Massachusetts, Minnesota, North Carolina, Oregon, South Carolina, and Vermont. According to the NAPPO (North American Plant Protection Organization), O. rufipogon blends in with cultivated O. sativa so well that it cannot be detected. In this position it competes with the cultivated rice and uses valuable fertilizer and space. O. rufipogon sheds most of its seeds before the harvest, therefore contributing little to the overall yield. In addition, the rice grains produced by the plant are not eaten by consumers, who see it as a strange foreign particle in otherwise white rice.

Selection
As with a great many plants and animals, O. rufipogon has a positive correlation between effective population size and magnitude of selection pressure. O. r. having an EPS of ~140,000, it clusters with others of about the same EPS, and has 78% of its amino acid sites under selection.

Precious germplasm
In India, the Pallikaranai marshland contains the wild rice O. rufipogon, described by the Sálim Ali Centre for Ornithology and Natural History (SACON) as a "precious germplasm."

Domestication
Dai et al., 2012 discover LHD1, an allele of DTH8/Ghd8. Dai also finds LHD1 produces the late heading O. rufipogon phenotype. This is one of the traits bred out during O. sativa domestication.