December 2023 Evaluation Changes: What’s New?

Changes for the December 5, 2023, CDCB evaluations include updated imputation results for all breeds, new haplotype calls for early onset muscle weakness syndrome in Holsteins, and update to the haplotype calls for cholesterol deficiency in Holsteins.

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Full-population imputation update for all breeds

By Ezequiel Nicolazzi

The imputed genotypes for all animals will be updated in the CDCB evaluations on December 5, 2023, which is expected to result in higher variability of haplotype calls. This is a periodic process that last occurred in April 2021.

In the time between full-population updates, new animals or those who have added information – such as those genotyped with higher density chips, have genotyped progeny or parents now available – receive a new imputation during any given monthly evaluation utilizing the latest available haplotype library.

A full-population imputation, as we will see in December, is done periodically as CDCB updates quality control measures and ensures the complete population is able to benefit from the latest information available regarding which SNPs are usable on individual chips. This is not done monthly or annually due to the time required and to provide more stability to the evaluation system.

CDCB anticipates higher variability of haplotype calls in December due to the full imputation. Higher variability of genomic evaluations and Breed Base Representation (BBR) values can be expected, especially in specific subsets of the population. Animals most affected will be 1) non-genotyped dams (e.g., fully imputed); 2) animals genotyped at low density or with the newest chips; 3) animals with partial or incomplete pedigree; 4) animals with weak or no links to the U.S. reference population.

Animals with complete pedigrees and genotyped with a high-density test are expected to remain stable.

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Haplotype calls for Early Onset Muscle Weakness in Holstein

By Ahmed Al-Khudhair, Dan Null and Paul M. VanRaden

The December 5, 2023, dairy cattle genetic evaluations will contain a new haplotype call for Early Onset Muscle Weakness Syndrome in Holsteins. Abbreviated HMW, U.S. genetic evaluations will include the reporting of noncarrier (0), carrier (1), homozygous (2), probable carrier (3), or probable homozygous (4) status of an animal for Early Onset Muscle Weakness Syndrome (MW).

In a test run using November 2023 genotypes, 87.7% of the Holstein population was reported as noncarrier (0), 2.3% as carrier (1), 0.02% as homozygous (2), 9.6% as probable carrier (3) and 0.4% as probable homozygous (4).

Of the more than 7,000 direct MW gene tests received by Holstein Association USA (HAUSA) and confidentially shared with CDCB and USDA AGIL for HMW development, only 41 animals received haplotype calls that did not match their lab test. Among the 41, there were 39 animals identified as carriers through the gene test but could not be confirmed by pedigree during the HMW call process, and these 39 animals were given an HMW 0 code for noncarrier. The remaining two animals were identified homozygous through the gene test, but the haplotyping algorithm was unable to confirm the descendance of the mutated haplotype from one or both sides of the pedigree, which resulted in a HMW 0 and 1 result for the two respective animals.

In the coming months, further development using the lab tests to improve the accuracy of HMW carrier status for tested animals and their descendants will continue. Breeders are encouraged to continue submitting MW lab results to HAUSA as we work together to continue building a stronger understanding of this genetic condition that remains under investigation by HAUSA.

More information and further resources on this genetic condition and haplotype are provided in the November 15 joint statement from CDCB, Holstein Association USA and National Association of Animal Breeders.

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Including 1.3 million female lab tests for Cholesterol Deficiency in haplotype calls in Holstein­

By Dan Null and Paul M. VanRaden

The December 5, 2023, dairy cattle genetic evaluations will contain an update to the haplotype call for Cholesterol Deficiency (HCD) in Holsteins. Through collaboration with Holstein Association USA (HAUSA), CDCB and AGIL were granted access to more than 1.3 million female lab tests for Cholesterol Deficiency. Similar to the methodology applied to the Early Onset Muscle Weakness Syndrome haplotype (HMW), the pedigree tracing algorithm that determines carrier or probable carrier animals is now excluded from the imputation process and performed during the haplotype calling procedure.

In a test run using November 2023 genotypes, 96.6% of the Holstein population was reported as noncarrier (0), 1.5% as carrier (1), 0.01% as homozygous (2), 1.9% as probable carrier (3) and 0.02% as probable homozygous (4) for HCD. 

Of the more than 1.3 million lab tests received from HAUSA, only 0.09% received haplotype calls that did not match their lab test; in most cases, animals were identified as carriers by the haplotyping algorithm but were not confirmed by pedigree, so set to noncarrier (0). In two cases, animals tested as homozygotes received a carrier status. All other tests matched the test lab results. These CD lab test results will only be used for imputation and HCD calling improvements and will not be shared publicly.