ABSTRACT
Many of the methodologies for genomic analysis have been derived under some assumptions in the single-locus model. This chapter describes methods for detecting segregation distortion and determining sample size for marker screening in genomic analysis using controlled crosses. It introduces partition of chi-square and likelihood ratio test statistics, which are key concepts for heterogeneity testing among several populations. The chapter also describes statistics for characterizing a single marker in natural populations and the ways to screen markers. It explains the methods for determining the number of alleles and their frequencies, estimating the probability of heterozygosity, the concept of single locus Hardy-Weinberg equilibrium and estimation of a disequilibrium coefficient. The chapter defines disequilibrium coefficient and also explains methods for estimating disequilibrium. It discusses strategies for screening for highly polymorphic markers and explores approaches for estimating statistical power for detecting heterozygosity.
