Improved tracking of recent mutations within common haplotypes causing cholesterol deficiency, muscle weakness, and BLIRD

Authors: Null, Daniel; Vanraden, Paul; Al-Khudhair, Ahmed; NICOLAZZI, EZEQUIEL - Council On Dairy Cattle Breeding

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/11/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Improved methods were applied to track new mutations within existing haplotypes for cholesterol deficiency (HCD), muscle weakness (HMW), and bovine lymphocyte intestinal retention defect (BLIRD). Gene tests were available for HCD and HMW but not yet for BLIRD. Concordances of gene tests with haplotype status were improved by processing pedigree from earliest to latest and including gene tests of ancestors to confirm true carriers and document connections to the carrier ancestors. Among 30,633 animals with gene tests for HCD, 779 bulls were carriers. Without including gene tests, the previous computer code correctly identified only 37.2% of the carriers (code 1), 7.6% as probable carriers (code 3), and 55.2% were labeled non-carriers, whereas the new code correctly identified 58.8% as HCD carriers (code 1), 32.0% as probable carriers, and only 9.1% were still labeled non-carriers. Directly imputing gene tests sometimes gave unstable results. Recessive effects of BLIRD homozygotes from U.S. data are consistent with the French research. Heifer livability was 97.6% for normal calves but averaged 88.8% for 178 homozygotes (code 2) and 94.1% for 2,029 probable homozygotes (code 4) with corresponding estimates of -8.6% and -3.3% from an animal model. Yield trait effects for 412 code 2 homozygotes were -1,799 kg milk, -63 kg fat, and -55 kg protein with a cost of -$1,206 using lifetime net merit values; other traits not yet studied may increase that cost. Mating a BLIRD carrier randomly to a population with 8.9% allele frequency would cause economic loss of $1,206 * 0.089 / 2 = $54 because half of progeny would inherit the carrier’s normal allele. Those losses should already be reflected in evaluations which average the merit across normal, carrier, and homozygous daughters. Genomic predictions do not fully track those losses because new mutations are poorly correlated with nearby markers. However, U.S. adjustments for future inbreeding automatically reduce evaluations of popular ancestors by more than the cost of these individual defects. Gene tests are needed for new mutations within common haplotypes because tracking can be difficult even with accurate pedigrees.