Two-Locus Models: The Controlled Crosses
Ben Hui Liu · 2017
Data analysis for genomic map construction involves the following five steps: single-locus analysis, two-locus analysis, linkage grouping, gene ordering, and multi-point analysis. This chapter focuses on linkage detection using goodness of fit statistics, likelihood ratio test statistics and recombination fraction estimation using likelihood approaches. It covers hypothesis tests among populations, dominant markers in F2 progeny, statistical properties of estimated recombination fraction and violations of assumptions in linkage analysis. The chapter empirically describes the way to obtain statistical properties. It reviews the disadvantages of dominant markers used in F2 progeny and discusses a strategy using trans dominant linked markers (TDLM). The chapter explains biases for recombination fraction estimation using different marker configurations. It explains linkage analysis using data with marker determination error, segregation distortion and lethal genes. Systematic marker or genotype classification error could be one of the reasons that segregation ratio distortion occurs.