Inheritance of bovine lymphocyte intestinal retention defect disorder affects Holstein production performance and longevity

Improved methods previously developed for tracking new mutations within existing haplotypes for cholesterol deficiency (HCD) and muscle weakness (HMW) now also were applied to track the bovine lymphocyte intestinal retention defect (BLIRD) discovered in France. Gene tests were available in US data for HCD and HMW, but not yet for BLIRD. Haplotype statuses for 3 million genotyped animals that also had US phenotypes were used to compare recessive effects of BLIRD homozygotes with French estimates. Heifer livability was 97.6% for normal calves with no copies of the haplotype (code 0) but averaged 88.8% for 178 homozygotes (code 2) and 94.1% for 2,029 uncertain homozygotes (code 4), with corresponding estimates of -8.6% and -3.3% from an animal model. Haplotype carriers verified by pedigree (code 1) or uncertain carriers (code 3) were not affected. Yield trait effects for 412 code 2 homozygotes were -1,799 kg of milk, -63 kg of fat, and -55 kg of 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 an economic loss of $1,653 × 0.089/2 = $74 because half of the progeny would inherit the carrier's normal allele. Those losses should already be reflected in evaluations that 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, US 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.