ABSTRACT
This chapter focuses on how linkage analysis can be done using naturally available populations. In controlled crosses, linkage phases are usually known when the crosses are made. In natural populations, the linkage phase is usually unknown unless extensive pedigree information is available. The chapter discusses the linkage phase problem and also discusses populations produced by both self and random mating. It describes methodologies for determining linkage phase when the phase is either one or the other. The chapter presents analyses using a mixture phase model for situations when the linkage phase is biologically mixed. For backcross progeny, linkage is detected by the linkage relationship of segregating gametes from a single parent. In other words, for a two-locus model, one of the parents has to be heterozygous at both loci to give linkage information. The chapter utilizes phase-unknown linkage analysis.
