Quantitative trait locus (QTL) analysis was conducted to study variation among annual and perennial ecotypes of Oryza rufipogon, the wild progenitor of rice. The 101 F2 offspring analyzed resulted from a cross between a single annual and a single perennial plant regenerated from seeds collected in Bangkok, Thailand. Each F2 genotype was split into two clones grown on adjacent short-day plots at Mishima, Japan, during the summer of 1994, and traits measured (see table). Several measurements were combined to capture the tendency toward annuality or perenniality, such as the ratio of panicles to tillers (high in annuals and low in perennials). Broad-sense heritability of each trait was calculated using an ANOVA model. Each genotype was cored for 40 molecular markers single and multiple regression was used to estimate the proportion of phenotypic variation. Genetic variation explained by markers was estimated by dividing the phenotypic R2 by the broad-sense heritability of each trait.