Genotypic variation at multiple loci for seed dormancy (SD) contributes to plant adaptation to diverse ecosystems. Weedy rice (Oryza sativa) was used as a model to address the similarity of SD genes between distinct ecotypes. A total of 12 quantitative trait loci for SD were identified in a primary and two advanced backcross populations derived from a temperate ecotype of weedy rice (34.3°N Lat.). Nine (75%) of the 12 loci were mapped to the same positions as those identified from a tropical ecotype of weedy rice (7.1°N Lat.). The high similarity suggested that a majority of SD genes were conserved during the ecotype differentiation. These common loci are largely those collocated/linked with the awn, hull color, pericarp color or plant height loci. Phenotypic correlations observed in the populations support that indirect selections for the wild-type morphological characters, together with direct selections for germination time, were major factors influencing allelic distributions of SD genes across ecotypes. Indirect selections for crop-mimic traits (e.g. plant height and flowering time) could also alter allelic frequencies for some SD genes in agroecosystems. In addition, three of the 12 loci were collocated with segregation distortion loci, indicating that some gametophyte development genes could also influence genetic equilibria of SD loci in hybrid populations. The SD genes with a major effect on germination across ecotypes could be used as silencing targets to develop transgene mitigation strategies to reduce the risk of gene flow from genetically modified crops into weed/wild relatives.
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