Linkage disequilibrium (LD) is a property of SNPs on a contiguous stretch of genomic sequence that describes the degree to which an allele of one SNP is inherited or correlated with an allele of another SNP within a population. The term linkage disequilibrium was coined by population geneticists in an attempt to mathematically describe changes in genetic variation within a population over time. It is related to the concept of chromosomal linkage, where two markers on a chromosome remain physically joined on a chromosome through generations of a family. In figure 2, two founder chromosomes are shown (one in blue and one in orange). Recombination events within a family from generation to generation break apart chromosomal segments. This effect is amplified through generations, and in a population of fixed size undergoing random mating, repeated random recombination events will break apart segments of contiguous chromosome (containing linked alleles) until eventually all alleles in the population are in linkage equilibrium or are independent. Thus, linkage between markers on a population scale is referred to as linkage disequilibrium.
