P5005 Hitchhiking effects influence allele frequencies and exclusion probabilities of microsatellites used for parentage control in Holstein Friesian cattle

Methods for parentage control in cattle have changed since their initial implementation in the late 1950s from blood group typing to single nucleotide polymorphism determination nowadays. In the early 1990s, a panel of 12 microsatellites was selected as international standard for parentage control and has been used since then, accompanied by international comparison tests ensuring permanent validity for the most common cattle breeds. Although nearly every parentage can be resolved using these microsatellites, cases with very close relatives became an emerging resolution problem during recent years. Thus, it must be presumed that although microsatellites have been selected based on their polymorphism information content and exclusion probabilities, and no direct selection against their variability was applied, other effects have induced a trend to the fixation of alleles and monomorphism. To determine changes of allele frequencies and exclusion probabilities, we analyzed the development of these parameters for the 12 microsatellites from 2004 to 2014. 168,000 recorded Holstein Friesian cattle genotypes were evaluated. During this time certain alleles of nine microsatellites increased significantly (t-values > 5). When calculating the exclusion probabilities for 11 microsatellites, reduction was determined for the three situations, i.e., one parent is wrongly identified (p= 0.01), both parents are wrongly identified (p= 0.005), and the genotype of one parent is missing (p= 0.048). With the addition of BM1818 to the marker set in 2009, this development was corrected leading to significant increases in exclusion probabilities. Although, the exclusion probabilities for the three family situations using the 12 microsatellites are > 99%, the clarification of 142 relationships in 40,000 situations where one parent is missing will still be impossible. 25 sires were identified that are responsible for the most significant microsatellite allele increases in the population. The corresponding alleles are mainly associated with milk protein and fat yield, body weight at birth and weaning, as well as somatic cell score, milk fat percentage, and longissimus muscle area. Our data show that most of the microsatellites used for parentage control in cattle are not neutral DNA markers and are influenced by hitchhiking effects.