Gene Ordering and Localization by Linkage Analysis

The essence of linkage analysis is a deviation from the Mendelian principle of independent, or random, assortment of gene pairs when transmitted from generation to generation. Two genes are said to be completely linked (see Section 4.1. for definitions of genetic terms) when there is no recombination between them; the same alleles or phenotypes are always transmitted together from generation to generation within a family. Two genes are completely unlinked if they are situated on different chromosomes; in this case, the transmission of alleles within a family will not deviate from the Mendelian principle of independent assortment. However, many gene pairs will be in an intermediate state of incomplete linkage, where there is a consistent and measurable deviation from independent assortment, but also a consistent recombination fraction between them. This recombination fraction is very roughly proportional to the physical distance between the two genes, and it is this principle that forms the basis of genetic linkage mapping.