ABSTRACT
This chapter introduces the concept of disequilibrium, the relationship between disequilibrium and linkage, the transmission/disequilibrium test (TDT) and other disequilibrium-based tests. The purpose of controlled crosses for mapping populations is to maximize linkage disequilibrium within the progeny of the crosses. Methods for two-locus disequilibrium analysis are needed to define disequilibrium in a multiple-locus context. Linkage equilibrium is commonly assumed in natural populations under a large number generations of random mating. The chapter briefly introduces methods of relative risk (RR), haplotype relative risk (HRR) and linkage analysis using population admixture. It discusses methods for partitioning the confounded factor in order to estimate recombination fraction. The chapter shows how population admixture affects the inference of linkage from association analysis. The key for analysis using population admixture is to pick the loci and to establish random mating after the admixture.
