Correspondence analysis approach for finding allele associations in population genetic study

In population genetic study, one of the first analyses is to explore the relationships among the frequencies of alleles within or between loci. Hardy–Weinberg equilibrium is tested for two alleles of a single locus, and the linkage disequilibrium is tested for an allele from each of two loci. Although the equilibrium plays an important role and often serves as a basis for genetic inference, research on the graphical representation of this information is rare. In this study, we consider correspondence analysis and biplot approaches as tools for finding associations between alleles. We also propose the supplementary data method to compare allele frequencies of several populations from different studies. These approaches provide the graphical representation which makes it easy to interpret the patterns of disequilibrium and to compare the allele frequencies between populations. These proposed methods are illustrated with numerical examples.