Method of QTL mapping in an F-2 population using phenotypic means of F-3 lines

Mapping of quantitative trait loci (QTLs) in plants was performed using the data of marker genotypes and phenotypic values of a quantitative trait in a segregating generation such as F-2 and BC1 derived from the crossing of t wo pure lines. A large sample must be examined to map QTLs with small effec ts. However genotyping of many markers for a large number of individuals is costly. For mapping QTLs using a F-2 population, useful information is inc luded in the derived F-3 lines. Phenotypic measurements of F-3 lines can be obtained at a relatively low cost. Therefore, by utilizing the phenotypic measurements of F-3 in addition to F-2 data, the detection of QTLs could be improved even when only a small number of F-2 individuals are genotyped. I n this paper a model for mapping QTLs is proposed, where the data of both F -2 individuals and F-3 lines are jointly analyzed. The effectiveness of thi s method is evaluated theoretically and numerically and it is shown that th e ability of detecting QTL can be remarkably enhanced, especially when the heritability of the trait is low.