Estimation of linkage disequilibrium in randomly mating populations

SummaryThe degree of linkage disequilibrium, D, between two loci can be estimated by maximum likelihood from the frequency of diploid genotypes in a sample from a random-mating population. Haploid genotypes can be identified directly in some species from a sample of chromosomes extracted from the population and made homozygous, or by test crossing. The maximum likelihood estimators of D are described, with examples, for both methods, including the cases where both loci are codominant and one or both are dominant.The efficiencies of the methods are compared when D = 0: If both loci are codominant the estimate of D has the same varianceV([Dcirc ]) = p(1 − p)q(1 − q)/N,from a sample of N identified diploids as from N identified haploid types, where p and q are the gene frequencies; therefore the diploid method is more efficient in practice since less labour is required. With dominance at either locus V([Dcirc ]) is lower for samples of the same size using the haploid method if the dominant alleles are at high frequency.