POOLED DNA FOR LINKAGE ANALYSIS - PRACTICAL AND STATISTICAL CONSIDERATIONS

In an F-2 population, the alleles at two loci with a recombination fra ction r < 0.5 are in linkage disequilibrium. If r is small, then a poo l of DNA from k diploid individuals that are fixed at one locus has a relatively high probability (P = (1 - p)(2k)) of containing only the c oupled allele at the second locus. Based on this principle, several me thods have been described to detect linkage (using one or two pools) o r to estimate r (using a group of n pools). This report compares maxim um likelihood and approximate estimators of r for use in pooled-DNA an alysis and illustrates the use of this analysis for dominant markers. Expected values and expected mean squares for estimators of r were com puted for varying levels of r, k, and n. Both estimators were biased, but the bias and variability were slightly smaller for the maximum-lik elihood estimator. Bias was not severe except when k was large relativ e to r and (or) n. Methods for optimizing k are discussed relative to several criteria: minimizing variance, minimizing bias, minimizing the probability that linkage cannot be detected, and minimizing the numbe r of samples that must be screened.