When marker and QTL are very close together, or when the marker is within the DNA sequence of the gene itself, a situation may arise in which there is an excess of some haplotypes and a deficiency of others across the population as a whole. This condition, termed linkage disequilibrium (LD), can be uncovered by an association test, which compares average trait value of the different genotypes at a marker across the population as a whole. Finding marker QTL LD indicates that the marker involved is very close to the QTL. Linkage disequilibrium can be generated by the random accumulation of small changes in frequency of the various marker QTL haplotypes over many generations. Identical by descent (IBD) mapping is based on the assumption that the mutation that produced a specific positive or negative QTL allele was a unique event that took place in a single ancestor chromosome, and will hence be in association with the specific marker alleles found in the haplotype of the ancestor chromosome within which the mutation arose. Thus, IBD mapping can lead to the very gene underlying the QTL.
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