Imagine that you could compare the complete genomic DNA sequence of any two people you meet today. Although their sequences would be very similar on the whole, they would certainly not be identical at each of the 3 billion base pair positions you examined (unless, perhaps, your subjects were identical twins – but even they may have some somatic differences). In fact, the genomic sequences of almost any two unrelated people differ at millions of nucleotide positions. Some of these differences would be found in the regions of genes that code for proteins. Others might affect the amount of transcript that is made for a particular gene. A person’s health, appearance, behavior, and other characteristics depend in part on these polymorphisms.
Most difference, however, have no effect at all. They have no effect on gene sequences or expression, because they occur within regions of DNA that neither encode proteins, nor regulate the expression of genes. These polymorphisms are nevertheless very useful because they can be used as molecular markers in medicine, forensics, ecology, agriculture, and many other fields. In most situations, molecular markers obey the same rules of inheritance that we have already described for other types of loci, and so can be used to create genetic maps and to identify linked genes.