Malaysian Weedy Rice Shows Its True Stripes

Most weedy rice (Oryza sativa) found in rice production areas worldwide morphologically resembles domesticated rice and is thought to be derived from the domesticate. However, in Malaysia, the weed has also been proposed to be derived directly from its wild progenitor, Oryza rufipogon. We collected a total of 247 samples of weedy, cultivated and wild rice from across three different regions of Peninsular Malaysia. Based on preliminary morphological observations, we hypothesized that some weedy rice strains are genetically very close to domesticated rice, and some strains may be closer to O. rufipogon. Twenty-four microsatellite markers were used for testing these hypotheses. Weedy rice with grain morphologies resembling the crop — i.e., straw hulled and awnless weeds (SH) and straw hull awned weeds (SHA) — were found closely related to Malaysian elite cultivars. Many brown-striped and awnless strains (BR), brown-striped awned strains (BRA) and black hull and awnless (BH) strains possess their own unique genetic makeup, which is predominantly an admixture of SH, SHA and local crops. On the other hand, black hull awned (BHA) accessions do not fit within these two major groups and form a distinct class. Surprisingly, none of the BHA individuals is closely related to any wild or cultivated rice samples included in the analysis. Weak genetic isolation by distance was detected among the sampled populations (r = 0.4252, P < 0.0034). Results from STRUCTURE and principal component analysis suggest that Malaysian weedy rice is a dynamic genetic system influenced by introgression from both domesticated and wild rice.