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Title: Reporting of haplotypes with recessive effects on fertility

item Vanraden, Paul
item Null, Daniel
item OLSON, K - National Association Of Animal Breeders
item Hutchison, Jana

Submitted to: Interbull Annual Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 8/26/2011
Publication Date: 9/7/2011
Citation: Van Raden, P.M., Null, D.J., Olson, K.M., Hutchison, J.L. 2011. Reporting of haplotypes with recessive effects on fertility. Interbull Annual Meeting Proceedings. Stavanger, Norway, Aug. 26–28, 4 pp.

Interpretive Summary: Five recently discovered lethal recessive defects in three dairy cattle breeds were examined to determine carrier status. Methods to discover, fine map, and aid breeders in identifying carriers were developed and compared. The first method detects carriers using both genotype and pedigree information. The second method detects carriers only if a particular haplotype could be part of the animal’s genotype but does not include information from the pedigree. A third method uses the causative mutation and would be preferable, but the causative mutations are not yet known for these defects. Accuracies of determining carrier status from less dense genotypes were compared by reducing 50,000 markers to 3,000 and then imputing back to 50,000. A slight decrease in accuracy was observed, however over 95% of test results were the same from the two chip densities. Crossover haplotypes contain part of the source haplotype and part of some other haplotype and were used to refine the location containing the causative mutation. Fine mapping was accomplished by checking if any genotyped animals had both the source haplotype and a crossover haplotype. Beginning with August 2011 genomic evaluations, carrier status is reported for all 127,588 genotyped animals in the North American database. Once animals have been identified, dairy producers can avoid mating carrier animals without further testing expense using these new carrier designations, thereby saving time, increasing profitability, and reducing these defects in the population.

Technical Abstract: Genomic discovery of five haplotypes with recessive effects on fertility requires new automated tracking methods for QTL causing embryo loss in breeding programs. Most of the losses are early in gestation. Approximate locations of the five QTL were refined using crossovers detected within the pedigree. Of the top 100 available proven bulls for net merit, 15 Holsteins, 21 Jerseys, and 14 Brown Swiss are carriers of these haplotypes. Beginning with August genomic evaluations, carrier status is reported for all 127,588 genotyped animals in the North American database but is slightly less accurate for those with 2,900 markers or for imputed dams. Breeders should continue to use mating programs and index selection instead of direct selection against these haplotypes because their additive economic effects are small and are included in evaluated fertility traits.