A correlation method for detecting and estimating linkage between a marker locus and a quantitative trait locus using inbred lines.

The advent of molecular genetic markers has stimulated interest in detecting linkage between a marker locus and a quantitative trait locus (QTL) because the marker locus, even without direct effect on the quantitative trait, could be useful in increasing the response to selection. A correlation method for detecting and estimating linkage between a marker locus and a QTL is described using selfing and sib-mating populations. Computer simulations were performed to estimate the power of the method, the sample size (N) needed to detect linkage, and the recombination value (r). The power of this method was a function of the expected recombination value E(r), the standardized difference (d) between the QTL genotypic means, and N. The power was highest at complete linkage, decreased with an increase in E(r), and then increased at E(r)=0.5. A larger d and N led to a higher power. The sample size needed to detect linkage was dependent upon E(r) and d. The sample size had a minimum value at E(r)=0, increased with an increase in E(r) and a decrease in d. In general, the r was overestimated. With an increase in d, the r was closer to its expectation. Detection of linkage by the proposed method under incomplete linkage was more efficient than estimation of recombination values. The correlation method and the method of comparison of marker-genotype means have a similar power when there is linkage, but the former has a slightly higher power than the latter when there is no linkage.