Figure 1. Markers used in genome mapping. This hypothetical composite map shows several types of marker located on the genome (unbroken horizontal line). STS: sequence-tagged site, a region of known sequence that can be amplified and detected by the polymerase chain reaction (PCR) using flanking sequence-specific primers (arrows); if the STS lies within a gene, it is an ‘expressed sequence tag’ (EST). Sat.: microsatellite, an STS that encompasses a simple, tandemly repeated sequence; the number of tandem repeats can vary from one individual to the next, making the marker polymorphic. The length of the PCR product produced using the flanking primers (arrows) will reflect the number of repeats. RFLP: a polymorphic restriction site, present in some individuals but absent in others. If genomic DNA is digested with the appropriate restriction enzyme, the sizes of the fragments will reflect the presence or absence of the site. Contig: a series of cloned DNA fragments that overlap with one another in a contiguous series. The absolute position of the contig in the genome is known only if one or more of the clones contains a marker mapped by independent means. Probe: a labeled, cloned DNA fragment whose position in the genome can be observed directly by hybridizing it to metaphase chromosomes and observing it under a microscope. Locus: a gene or other sequence known only by its phenotypic effect. Its location in the genome can be inferred from the pattern of inheritance of the phenotype.

Figure 2. Principle of genetic linkage mapping (only one chromosome is shown). Diploid parental cells (top row) carry polymorphic marker alleles A, B and Z on one chromosome and alleles a, b and z on the other. Meiotic recombination can occur at any point (indicated by the hourglass shape) along the chromosomes, causing an exchange of markers on either side of the site of crossover (second row). The recombined chromosomes are then segregated to gametes (bottom). Recombination is unlikely to occur in the small interval between closely linked markers such as A and B – in this example, only one of the four parental cells (two of eight gametes) show recombined genotypes Ab or aB. Recombination between widely spaced markers B and Z is more common, producing many gametes with bZ or Bz genotypes. By genotyping the members of a pedigree, the pattern of recombination can be deduced, allowing the distances between markers to be estimated.

Figure 3. Dual-color fluorescence in situ hybridization. The image shows a spread of male canine metaphase chromosomes, probed with two plasmid clones that hybridize to the X chromosome (arrows). One clone has been visualized using a red fluorophore (Texas red), the other with a green fluorophore (fluorescein isothiocyanate). Each probe produces two adjacent spots, corresponding to the two sister chromatids. The distance between the probes is approximately 20 Mb. Picture courtesy of Dr H. F. Spriggs.