Identification of a putative haplotype associated with recumbency in Holstein calves

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.

Early-onset muscle weakness syndrome (MW) in an Australian Holstein calf

Early-onset muscle weakness syndrome (MW) is a recessive genetic disorder known to affect Holstein cattle. This report describes the clinical findings in an Australian Holstein calf diagnosed with MW. The calf initially presented for examination at a dairy farm at 3 days of age, being recumbent since birth but able to stand with assistance. A presumptive diagnosis of traumatic injury was made at first. However, the calf was re-examined multiple times due to ongoing intermittent episodes of recumbency, prompting further diagnostic investigation. Given the non-specific nature of the clinical and laboratory findings, a presumptive diagnosis of MW was made after reviewing the calf's breeding pedigree. A definitive diagnosis, however, required genotype testing. To the authors knowledge, this case report represents the first peer-reviewed manuscript to describe the clinical presentation of MW in an Australian Holstein calf.

Invited review: Management of genetic defects in dairy cattle populations

When related animals are mated to one another, genetic defects may become apparent if recessive mutations are inherited from both sides of the pedigree. The widespread availability of high-density DNA genotypes for millions of animals has made it possible to identify and track known defects as well as to identify and track previously unknown defects that cause early embryonic losses. Although the number of known defects has increased over time, the availability of carrier information has been used to dramatically reduce the frequency of many disorders. The economic impact of known genetic defects in the US dairy cattle population has decreased by ∼2/3 since 2016, due largely to the avoidance of carrier-to-carrier matings. Effective population management requires robust systems for reporting new defects, identification of causal mechanisms, and development of commercially available tests. The United States and Canada depend on informal cooperation among many groups, including farmers, purebred cattle associations, genetics companies, and researchers, to identify emerging and causal defects. The structure of a collaborative system including all key sectors of the dairy cattle industry to support long-term population management is described. This review provides a comprehensive overview of the landscape surrounding genetic defects in dairy cattle. Topics covered include current defects of relevance to commercial dairy producers, trends in carrier frequencies over time, how best to manage these defects, strategies for detecting emerging diseases, and marketing and trade considerations.

A clinical case of CACNA1S-related muscle weakness in a Holstein calf with congenital astasia diagnosed by a genotyping test of stored blood

A homozygous calf with CACNA1S-related muscle weakness, a new autosomal recessive congenital disorder in Holstein cattle, was identified by genotyping 195 stored blood samples from Holstein calves aged less than 12 months. The patient was an 8-day-old male calf with congenital astasia which presented to a university hospital in 2019. The patient was unable to maintain an upright position with assistance to stand. Congenital abnormalities in the central nervous system were suspected, but necropsy revealed no specific lesion, with no clear diagnosis. CACNA1S-related muscle weakness should be considered a cause of congenital astasia or weakness in calves. Genotyping is required for a definitive diagnosis because clinical and laboratory findings are non-specific.

Sampling and Laboratory Logistics: How to Collect DNA Samples and Overview of Techniques for Laboratory Analysis

This article discusses different options and best practices for sample types and sample collection devices for downstream genotyping in today's sophisticated animal husbandry systems. Best practices for sample collection, shipping, and submission of samples are shown and an overview of techniques for laboratory analysis is provided. The ultimate goal is to facilitate the generation of useful and meaningful results for the client.

New mutation within a common haplotype is associated with calf muscle weakness in Holsteins

A recessive haplotype resulting in elevated calf mortality but with apparent incomplete penetrance was previously linked to the end of chromosome 16 (78.7-80.7 Mbp). Genotype analysis of 5.6 million Holsteins indicated that the haplotype was common and traced back to 1952, with a key ancestor born in 1984 (HOUSA1964484, Southwind) identified from chip genotypes as homozygous for the suspect haplotype. Sequence data from Southwind (an affected calf) and the sire of the affected calf were scanned for candidate mutations. A missense mutation with a deleterious projected impact at 79,613,592 bp was homozygous in the affected calf and heterozygous in the calf's sire and Southwind. Sequence data available from the Cooperative Dairy DNA Repository for 299 other Holsteins indicated a 97% concordance with the haplotype and an 89% call rate. The exon amino acid sequence appears to be broadly conserved in the CACNA1S gene, and mutations in humans and mice can cause phenotypes of temporary or permanent paralysis analogous to those in calves with the haplotype causing muscle weakness (HMW). Improved methods for using pedigree to track new mutations within existing haplotypes were developed and applied to the haplotypes for both muscle weakness and Holstein cholesterol deficiency (HCD). For HCD, concordance of the gene test with its haplotype status was greatly improved. For both defects, haplotype status was matched to heifer livability records for 558,000 calves. For HMW, only 46 heifers with livability records were homozygous and traced only to Southwind on both sides. Of those, 52% died before 18 mo at an average age of 1.7 ± 1.6 mo, but that death rate may be underestimated if only healthier calves were genotyped. The death rate was 2.4% for noncarriers. Different reporting methods or dominance effects may be needed to include HMW and other partially lethal effects in selection and mating. Direct tests are needed for new mutations within existing common haplotypes because tracking can be difficult even with accurate pedigrees when the original haplotype has a high frequency.