Linkage Analysis Principles linkage the rate of cosegregation of two syntenic alleles (alleles appearing on the same chromosome) is inversely proportional to the distance between the alleles i.e. genes that are physically close on a chromosome will be inherited together more often genes that are physically far apart will be inherited together less often linkage group set of genes at different loci on the same chromosome that tend to act as a single set of genes in meiosis rather than undergoing independent assortment an exception is if crossing over occurs linkage analysis using a pedigree to determine the location of an allele based on the rate of cosegregation with other alleles of known location (genetic markers) can be used to track disease-causing mutation linkage analysis can localize a gene responsible for a trait when the sequence is unknown centi-Morgan (cM): a unit used to measure genetic linkage a length of DNA over which the frequency of homologous recombination is 1% 1% chance that a marker on a chromosome will become separated from a second marker on the same chromosome due to crossing over two loci that are 1 centimorgan apart will experience recombination between these two loci in 1% of meiosis. parental gamete the portion of chromosome looks the same as that of one of the parents no recombination nonparental gamete homologous recombination has occurred in the region of interest linkage disequilibrium when alleles occur together more often than can be accounted for by chance indication that 2 alleles are physically close together