April 2023 Evaluation Changes: What’s New?

Written by CDCB

March 07, 2023

<strong>April 2023 Evaluation Changes: What’s New?</strong>

The Council on Dairy Cattle Breeding and USDA Animal Genomics Improvement Laboratory are implementing a series of changes with the triannual U.S. evaluations on April 4, 2023.

Implementing Constructed ID’s

By George Wiggans, Lillian Bacheller, Jay Megonigal, Ezequiel Nicolazzi and José Carrillo

To fill in more pedigree gaps, the Council on Dairy Cattle Breeding (CDCB) is implementing a new solution. This new method – coined “Constructed IDs” – will build a more complete pedigree for genotyped animals that previously had no link to their maternal ancestors. This technology was developed by the Animal Genomics Improvement Laboratory (AGIL, USDA; Nani et al., 2019). As a result, the genetic evaluations for affected animals will be more accurate and reliable, so the U.S. genetic evaluations overall will improve in accuracy.

The implementation of the Constructed IDs will be gradual so the April evaluation will likely include only a low number of Constructed IDs. Gradually over the next several months, more than one million genotyped animals are expected to be linked to additional pedigree information. A test run including all the animals in a single solution showed only minimal impact on the evaluations, with the animals including more information receiving more accurate evaluations.

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Brown Swiss Fertility Haplotype BH14

By Paul VanRaden, Dan Null and Norm Magnussen

Switzerland in 2022 began reporting a new lethal haplotype in Brown Swiss (BH14) that causes early pregnancy loss. BH14 has been added to the list of genomic haplotypes reported in the U.S., following USDA AGIL analysis of records in the CDCB database. Routine publication of BH14 status will support breed fertility improvement by allowing appropriate selection and mating of males and females.

Brown Swiss Cattle Breeders of the U.S. received a list of 1,254 carrier bulls from Switzerland, which USDA AGIL compared to haplotype calls for BH14 from CDCB data for the same bulls. In both analyses, the haplotype traced primarily to BSUSA175545 VENTURES ESP BABARAY (W) born in 1978, and no homozygous animals were detected in the Swiss (CHE) or USA analyses. Of the carrier bulls from the CHE file, 94% were also carriers from CDCB data, and 6% of the carriers from CHE data were non-carriers here. Of those 73 non-matching bulls, only five were USA bulls and those had no daughters. Likely almost all 43,000 non-carrier bulls matched, and if so, the concordance is very high for BH14. For some bulls, the CHE analysis may have included a gene test for the MRPL55 mutation on chromosome 7 at ARS-UCD1 location 2,996,436. Carrier frequency was 6.1% reported by Häfliger et al. (2021).

In CDCB data, the number of genotyped carriers was 1,113 of 16,207 USA animals (6.9%) and across all countries was 2,960 animals of 59,127 genotyped (5.0%) as of April 2022. CDCB conception rate data included less than 100 matings of carrier sires to carrier maternal grandsires (the dam’s sire for the potential embryo being created). A conception loss of about 0.04 or 4% is expected if an extra 1 / 8 of embryos do not survive. The significant effect on fertility reported in CHE was not significant in USA because so few observed matings gave a standard error > 5%. Haplotype or gene tests from CHE may be reported initially, but routine publication of BH14 status in USA will allow selection and mating of males and females to further improve BS fertility.

Häfliger, Irene M., Franz R. Seefried, Mirjam Spengeler & Cord Drögemüller. 2021. Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success. Genetics Selection Evolution 53:95.

Holstein Cholesterol Deficiency (HCD) Inheritance Update

By Dan Null and Paul VanRaden

The haplotype for cholesterol deficiency (HCD) is difficult to trace because a normal and a mutated version of that same haplotype are both frequent in the Holstein breed. Gene tests continue to be recommended for the most accurate identification of HCD; however, new methods result in much more accurate haplotype tests for the millions of Holsteins that have been genotyped by not gene-tested.

The HCD mutation that causes death in homozygous calves occurred just before the earliest carrier bull Maughlin Storm HOCAN5457798 was born in 1991. Our previous computer methods to trace HCD were inefficient and detected too few carriers. When new methods were applied to December 2022 genotypes, the percentage of HCD carriers (code 1) decreased from 1.2% to 1.0%, whereas percentage of suspect carriers (code 3) increased from 1.7% to 2.2%.

Of the 772 carrier bulls identified by gene test results provided by Holstein Association USA, only 37% were correctly identified as HCD carriers by the previous haplotype test, 8% were probable carriers, and 55% were labelled noncarriers. Using the new methods, 59% were correctly identified as HCD carriers by the haplotype test, 32% were probable carriers, and only 9% were still labelled noncarriers. For the 29,854 gene tests that indicated non-carriers, the previous and new methods were both accurate and stable. Only four bulls with the previous methods and three bulls (0.02%) with the new methods were falsely labelled HCD carriers, while 12 bulls with previous methods and 19 (0.06%) with new methods were falsely labelled as probable carriers by the haplotype test. Thus, the new methods identify more of the true or suspect carriers. Only 74 of the 30,626 bulls disagreed, plus 19 suspect carriers that were not carriers, with overall 99.7% agreement of haplotype and gene tests.

Updated frequencies below show the percentage of carriers plus suspect carriers (3.1%) is now about half the percentage (6.0%) in 2015 when HCD was first identified, indicating good progress in reducing this harmful mutation.

The enhanced methodology will be first implemented in official evaluations in April 2023, whereas for weekly evaluations the procedure be used effective immediately.

Counts and percentages of currently genotyped Holsteins (December 2022) with HCD codes 0 to 4 as defined below

05,470,68596.9%Non-carrier: free of HCD
153,5260.9%Carrier: haplotype confirmed with pedigree information
23550.01%Homozygous: confirmed on both sides of pedigree
3122,8272.2%Suspect carrier:  haplotype origin could not be confirmed from pedigree
41,3410.02%Suspect homozygous: probable carrier and may be homozygous; origin of haplotypes could not be confirmed from pedigree

Counts and percentages of genotyped Holsteins from the initial release of HCD (August 2015)

0772,67594.0%Non-carrier: free of HCD
135,7934.4%Carrier: haplotype confirmed with pedigree information
22860.03%Homozygous: confirmed on both sides of pedigree
312,9961.6%Suspect carrier:  haplotype origin could not be confirmed from pedigree
41980.02%Suspect homozygous: probable carrier and may be homozygous; origin of haplotypes could not be confirmed from pedigree

Gestation Length edit for Unreported Embryo Transfer

By Jana Hutchison, Asha Miles and Paul VanRaden

A new edit for unreported embryo transfer (ET) was applied to gestation length (GL) following similar edits applied in 2022 to sire, heifer, and cow conception rates. Misreporting embryo implantation as AI could bias the gestation length downward by several days. Most implantations are still not reported instead of wrongly reported. The edit had small impact because previous edits had selected only reproductive events within 15 days above or 20 days below the expected conception date. The new edit removed about 100,000 of the 2.8 million previous GL records from herds with high rates of unreported ET. Some bulls decreased in reliability. For the last 10 years of proven Holstein bulls the PTA correlation was 0.998 and the PTA Standard Deviation (SD) and correlation of PTA with birth year (genetic trend) did not change.

New Edits for Heifer Livability

By Paul VanRaden, Mahesh Neupane and Ezequiel Nicolazzi

Heifer livability measures percentages of calves that die on the farm compared to those that live to at least 18 months. Edited data previously included calves with other termination codes that were sold before they were able to prove they could survive to 18 months. Those calves are now deleted. Such calves showed up as alive in our inspection of calves homozygous for the cholesterol deficiency haplotype (HCD) that were supposed to die, and now they are removed from the data as providing no information. Most calves removed from the data were sold for unspecified reasons before the 18-month required life. The new edit removed 97,350 records, or 1.5% of the observed phenotypes (5,728,980 vs 5,631,630). The better separation of live from dead calves increased the PTA SD but had very little effect on ranking because all dead calves remain dead. Correlations of PTA before and after the new edit were 0.998 and no bulls had large changes.

Inclusion of many more records in health evaluations

By Kristen Gaddis, Jay Megonigal and Ezequiel Nicolazzi

A large number of health records were submitted to the CDCB cooperator database after the December 2022 evaluation. The characteristics of the submission are expected to impact the April 2023 evaluation, especially in Mastitis Resistance results.

Most events to be added occurred from 2020 or later, although the submitted health events included events from 2014 to 2022. Approximately 35,000 new health events were added to the database across all evaluated breeds, with more than 75% of those being mastitis events. The largest impacts were seen for evaluations of mastitis resistance (MAST). 

The impact of the large inclusion of records was assessed in a test run using the December 2022 evaluation. The correlation of MAST PTAs among sires born since 2010 with reliability > 50% was 0.98 between the data available for the December evaluation and with the added data. Lower trends on MAST for younger animals were observed, as expected, especially in the Jersey population. Trends for older animals remained stable. PTA correlations for all other health traits were greater than 0.99. However, large single animal variation in a reduced set of bulls was observed.

SNP Usability Updates and Imputation Error Rate Increase

By Ezequiel Nicolazzi, Heather Enzenauer, Lillian Bacheller, Daniel Null and Paul VanRaden

The yearly SNP usability update was implemented in the March evaluation and will be in effect for the April 2023 evaluation. This regular update is performed to improve the performance of SNPs for newest chips and resulted in the change of usability for more than 5,000 SNPs across all chips analyzed. Also, imputation error rate was increased in an effort to better identify undesirable haplotypes. Neither of these two changes are expected to have any noticeable impact on evaluations. However, a change in carrier status for undesirable haplotypes is expected in a reduced subset of animals.

Yearly BBR Update

By Ezequiel Nicolazzi

The yearly Breed Base Representation (BBR) update will be implemented during the April 2023 evaluation for the first time. In previous years, the April evaluation information was used to update the reference population, and the BBR update was introduced in the following monthly evaluation, in May. This process was anticipated of one month to implement the change in the April evaluations. The objective is to reduce monthly evaluation variation in case of large changes in the reference population.

Excluding Interbull MS Type Evaluations

By Ezequiel Nicolazzi

Milking Shorthorn (MSH) evaluations are sent to the Interbull (International bull evaluation) in the Red Dairy Cattle (RDC) breed. This solution is used because MSH is not evaluated separately. While most of the trait groups analyzed (i.e., production, fertility) are effectively used across countries, the use of conformation traits is not desirable because of the different trait definition. The conformation evaluation in USA has always been actively removing these records, at a later stage, before the blending of national and foreign evaluations. However, in many cases, and due to various animal characteristics, some MS bulls were still receiving the undesired foreign evaluation for conformation. The procedure was therefore modified to exclude all animals with MSH breed code in the files received from Interbull before they are processed further.

Exclusion of NZL from pedigree and PTA of foreign dam exchange

By Ezequiel Nicolazzi and Jay Megonigal

CDCB regularly exchanges pedigrees and (traditional) PTA of females with many countries. This exchange program is mutually beneficial to all countries because it allows inclusion of direct Predicted Transmitting Abilities (PTA) instead of a less reliable domestic Parent Average (PA) or a generalized breed average value (when information is not available at all).

After the December 2022 evaluation, New Zealand communicated their unilateral decision to terminate such exchange with USA. Therefore, in the April 2023 evaluations, female animals previously receiving direct PTA from New Zealand will receive PAs, which will result in larger variation to their evaluations and their progeny’s evaluations.

International Evaluations for Clinical Mastitis in Brown Swiss

By Rodrigo Mota and Kristen Gaddis

The intended enhancement announced in December 2022 was not introduced. Therefore, effective with the April 2023 evaluation, Brown Swiss foreign evaluations will be included in the U.S. Clinical Mastitis evaluations. The impact of this inclusion is expected to be limited, as only two other foreign countries (France and Switzerland) contribute to the CDCB Mastitis evaluation.