For many years, gene mapping was limited in most organisms by the availability of genetic markers: variable genes with easily observable phenotypes whose inheritance could be studied. Traditional genetic markers include genes that encode easily observable characteristics such as flower color, seed shape, blood type, or biochemical differences. The paucity of these types of characteristics in many organisms limited mapping efforts.

In the 1980s, new molecular techniques made it possible to examine variations in DNA itself, providing an almost unlimited number of genetic markers that can be used for creating genetic maps and studying linkage relations. The earliest of these markers consisted of restriction fragment length polymorphisms (RFLPs), which are variations in DNA sequence detected by cutting the DNA with restriction enzymes (see Chapter 14). Later, methods were developed for detecting variable numbers of short DNA sequences repeated in tandem, called microsatellites. Now DNA sequencing allows the direct detection of individual variations in single nucleotides. All of these methods have expanded the availability of genetic markers and greatly facilitated the creation of genetic maps.

Gene mapping with molecular markers is done in essentially the same manner as mapping performed with traditional phenotypic markers: the cosegregation of two or more markers is studied, and map distances are based on the rates of recombination between markers. These methods and their use in mapping are presented in more detail in Chapter 14.