ARS | Publication request: Fine mapping and discovery of recessive mutations that cause abortions in dairy cattle

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: June 13, 2012
Publication Date: June 28, 2012
Citation: Van Raden, P.M., Null, D.J., Sonstegard, T.S., Adams, H.A., Van Tassell, C.P., Olson, K.M. 2012. Fine mapping and discovery of recessive mutations that cause abortions in dairy cattle. Journal of Dairy Science. 95(Suppl. 2):ii–iii(abstr. LB6). 2012.

Technical Abstract: Methods to trace the inheritance of 5 haplotypes affecting fertility (HH1, HH2, HH3, JH1, and BH1) were improved and implemented in December 2011. Programs that detect these haplotypes were modified to narrow the suspect region and detect additional crossover haplotypes believed to carry the lethal segment. To be consistent with haplotyping edits, only crossovers between BovineSNP50 (50k) genotyped animals and a 50K parent are used in narrowing the suspect region. An edit was added to allow crossovers of crossovers to be utilized in both designation of carrier status and used for fine mapping of the region. A further edit now allows for crossovers that carry at least 50% of the main carrier haplotype and the entire fine mapped region that is believed to be the lethal segment to be called as a carrier haplotype. These crossovers were not typically included in earlier versions because they came from a nongenotyped parent, and are not used for further narrowing down of the region, but are used in determining the animal’s carrier status. Only a few animals genotyped at 50K changed carrier status due to these modifications, and nearly all were changes from noncarrier to carrier status. To check the accuracy of carrier detection from using the BovineLD (LD) chip, a study was conducted by taking 1,000 (500 carriers and 500 non-carrier) 50K animals, reducing their genotypes to LD, and then imputing back up to 50K. Concordance was 100% between carrier status determined from LD or 50K for these animals with imputed genotypes. Concordance can be poorer for animals with incomplete pedigrees or if haplotyping is not done first. To improve accuracy for these animals and allow laboratories to determine haplotype status without imputing haplotypes, nearby markers were selected that had lowest frequency in the breed for alleles that were present in each of the five defective haplotypes. When added to the LD chip, selection of the best 40 markers per haplotype provided high concordance without requiring pedigrees or imputing haplotypes. Causative mutations can be added when they are found so that the nearby markers are no longer needed.