The wild progenitor (Oryza rufipogon) of Asian rice (Oryza sativa) shows a wide range of variations in lifehistory traits, forming an annual-perennial continuum. A conspicuous feature of an annual type of wild rice is represented by its adaptability to disturbed habitats, and its short stature with many tillers and a prostrate growth habit. The present study was carried out to examine the genetic differentiation between wild annual and cultivated (Japonica type) rice strains by quantitative trait locus (QTL) analysis. In total, 20 adaptive and/ or domestication-related traits were evaluated in recombinant inbred lines (RILs). A total of 28 putative QTLs were detected across the genome. Six QTLs responsible for plant architecture were located on the short arm of chromosome 7. The near-isogenic line with the region containing the QTL cluster confirmed that the QTLs exerted a significant effect on the plant architecture in the genetic background of cultivated rice. A similar QTL cluster was also found in another annual strain of a different origin, suggesting that the QTL cluster might be predominant in annual wild rice. Furthermore, a QTL for tolerance to disturbance (simulated trampling) was detected within the region of the cluster on chromosome 7. These results are discussed in relation to their ecological significance in wild annuals of rice.

Phenotypic plasticity is an adaptive mechanism adopted by plants in response to environmental heterogeneity. Cultivated and wild species adapt in contrasting environments; however, it is not well understood how genetic changes responsible for phenotypic plasticity were involved in crop evolution. We investigated the genetic control of phenotypic plasticity in Asian cultivated (Oryza sativa) and wild rice (O. rufipogon) under 5 environmental conditions (2 nutrient and 3 density levels). Quantitative trait locus (QTL) analysis was conducted for traits affecting plant architecture and biomass production. By analysing the phenotypic means, QTLs of large effects were detected as a cluster on chromosome 7 under all the environmental conditions investigated; this might have contributed to transitions of plant architecture during domestication, as reported previously. Multiple QTLs of plasticity were also found within this QTL cluster, demonstrating that allele-specific environmental sensitivity might control plasticity. Furthermore, QTLs controlling plasticity without affecting phenotypic means were also identified. The mode of action and direction of allele effects of plasticity QTLs varied depending on the traits and environmental signals. These findings confirmed that cultivated and wild rice show distinctive genetic differentiation for phenotypic plasticity, which might have contributed to adaptation under contrasting environmental heterogeneity during the domestication of rice.