This chapter reviews the sexually dimorphic nature of meiosis in mammalian species, since many aspects of recombination depend on whether the gamete is proceeding through spermatogenesis or oogenesis. Since meiotic recombination occurs at prophase during fetal development in mammalian females, few investigations of human recombination have focused on this stage. Linkage disequilibrium (LD) analysis provides a powerful tool for the generation of high resolution genetic maps. LD mapping does not require analysis of multiple generations in a family. Rather it is a simple assessment of haplotype blocks among different individuals. Fortunately, with improvements in immunostaining techniques and the increasing availability of antibodies capable of detecting meiosis-acting proteins, it has now become possible to analyze the processes of pairing, synapsis, and recombination in human fetal oocytes. Advances in mapping methodology have led to the generation of high-resolution male and female genetic maps.

This chapter describes the basic principles behind the most widely used human genetic strategies to identify inherited disease susceptibility factors. There are many extensions and modifications to the basis linkage and linkage disequilibrium (LD) mapping approaches. The chapter describes the intuitions and basic strategies behind a few of the more widely used extensions. There are also a number of issues that plague linkage and LD mapping strategies for identifying genetic variants that influence disease susceptibility. The chapter discusses a few of these issues and notes that all of them are well-recognized by the genetics community and that concerted efforts to deal with them in various ways have been made. Advances in DNA sequencing technologies have facilitated studies of rare variants, as these technologies can be used to exhaustively identify all forms of variation, common and rare, in a genomic region for a group of individuals.