Introducing 305-AA: The new national standardized yield measurement enabling fair comparisons across individual cows and environments.

Multiplicative adjustment factors to standardize milk, fat, and protein lactation yields for age, parity, season of calving, geographical region, milking frequency, and previous days open were last updated in 1994. Since then, the national animal model has updated age-parity adjustments within each 5-year period, but those were not publicized or summarized until now. New multiplicative adjustment factors were estimated using 101.

Improving dairy calf health through inclusion of diarrhea and respiratory health data into a US national genetic evaluation.

Calf diarrhea (DIAR) and respiratory illnesses (RESP) are leading causes of calf mortality. This study aimed to develop a comprehensive US national genomic evaluation for these important calf health traits using producer-recorded data from the National Cooperator Database. Analyses included 207,602 calf records for DIAR (age 3 to 60 d) and 681,741 records for RESP (age 3 to 365 d) from all breeds (97.

Quantifying the use of and the genetic progress from advanced mating strategies in US dairy herds.

The use of mating technologies, including genomic testing and sexed semen, has recently increased in the breeding programs of commercial dairy herds, along with the use of beef semen. We aimed to quantify the use of advanced mating strategies in US dairy herds and the influence of these strategies on genetic merit. Breeding records (n = 35,124,479) that resulted in successful pregnancies of cows and heifers by semen type (conventional dairy, sexed dairy, and beef) and records of genomic testing of female dairy cattle were extracted from the National Cooperator Database for the years 2008 to 2023.

Correcting overestimation of approximate traditional reliabilities with herd-sire interactions when young genomic bulls are used in few herds.

Background: Differential treatment of daughters of the same sire within a herd is modelled as the herd-sire effect. Recent changes in management practices may have led to the extensive use of certain bulls in a limited number of herds. In that case, although the effect can be well accounted for in genetic evaluation models, some approximation methods for reliabilities do not consider it correctly, leading to an overestimation of some sires' approximated reliabilities.

Variance reduction and measurement errors in estimating lactation milk yields using best prediction: An analytical review.

Best prediction (BP) has been used in the United States to estimate unobserved daily and lactation yields from known test-day yields since 1999. This method has proven more accurate than its predecessors. However, it has 2 remarkable challenges in practice.

Improved computation of genomic and pedigree inbreeding and relationships accounting for the X chromosome.

Breeders for many decades used pedigrees to limit increases in inbreeding, but genomic measures of relationship and inbreeding provide more precise control. Previous calculations of pedigree inbreeding (F), genomic inbreeding (F), pedigree expected future inbreeding (EFI), and genomic expected future inbreeding (EFI) included the X chromosome but ignored its influence when estimating relationships. The X chromosome contributes to inbreeding in female progeny, for example, if parents with the same X chromosome are mated.

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.

Validating genomic predictions for economic traits in purebred US dairy heifers.

Most genotypes in the National Cooperator Database now originate from cows, but most previous studies validating genomic predictions have primarily focused on bulls. This study paired official within-breed genomic PTA (GPTA) and parent average (PA) for genotyped heifer calves born between 2019 and 2021 using the August 2021 database with their corresponding performance deviations (PDEV) for 17 different traits. The PDEV data became available when the heifers completed their first lactation and were extracted from the August 2023 database in which at least one PDEV value for those 17 traits existed for each genotyped heifer record.

Effects of germplasm exchange strategies on genetic gain, homozygosity, and genetic diversity in dairy stud populations: A simulation study.

Although genomic selection has led to considerable improvements in genetic gain, it has also seemingly led to increased rates of inbreeding and homozygosity, which can negatively affect genetic diversity and the long-term sustainability of dairy populations. Using genotypes from US Holstein animals from 3 distinct stud populations, we performed a simulation study consisting of 10 rounds of selection, with each breeding population composed of 200 males and 2,000 females. The investigated selection strategies consisted of selection using true breeding values, EBV, EBV penalized for the average future genomic inbreeding of progeny (PEN-EBV), or random selection (RAND).

Large-Sample Genome-Wide Association Study of Resistance to Retained Placenta in U.S. Holstein Cows.

A genome-wide association study of resistance to retained placenta (RETP) using 632,212 Holstein cows and 74,747 SNPs identified 200 additive effects with -values < 10 on thirteen chromosomes but no dominance effect was statistically significant. The regions of 87.61-88.

Dry matter intake in US Holstein cows: Exploring the genomic and phenotypic impact of milk components and body weight composite.

Large datasets allow estimation of feed required for individual milk components or body maintenance. Phenotypic regressions are useful for nutrition management, but genetic regressions are more useful in breeding programs. Dry matter intake records from 8,513 lactations of 6,621 Holstein cows were predicted from phenotypes or genomic evaluations for milk components and body size traits.

Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle.

This study leveraged a growing dataset of producer-recorded phenotypes for mastitis, reproductive diseases (metritis and retained placenta), and metabolic diseases (ketosis, milk fever, and displaced abomasum) to investigate the potential presence of inbreeding depression for these disease traits. Phenotypic, pedigree, and genomic information were obtained for 354,043 and 68,292 US Holstein and Jersey cows, respectively. Total inbreeding coefficients were calculated using both pedigree and genomic information; the latter included inbreeding estimates obtained using a genomic relationship matrix and runs of homozygosity.

Imputation accuracy from low- to medium-density SNP chips for US crossbred dairy cattle.

This study aimed at evaluating the quality of imputation accuracy (IA) by marker (IA) and by individual (IA) in US crossbred dairy cattle. Holstein × Jersey crossbreds were used to evaluate IA from a low- (7K) to a medium-density (50K) SNP chip. Crossbred animals, as well as their sires (53), dams (77), and maternal grandsires (63), were all genotyped with a 78K SNP chip.

A Million-Cow Genome-Wide Association Study of Three Fertility Traits in U.S. Holstein Cows.

A genome-wide association study (GWAS) of the daughter pregnancy rate (DPR), cow conception rate (CCR), and heifer conception rate (HCR) using 1,001,374-1,194,736 first-lactation Holstein cows and 75,140-75,295 SNPs identified 7567, 3798, and 726 additive effects, as well as 22, 27, and 25 dominance effects for DPR, CCR, and HCR, respectively, with log(1/p) > 8. Most of these effects were new effects, and some new effects were in or near genes known to affect reproduction including , , and , and a gene cluster of pregnancy-associated glycoproteins. The confirmed effects included those in or near the and regions of Chr06 and the region of Chr01.

Improving national fertility evaluations by accounting for the rapid rise of embryo transfer in US dairy cattle.

Dairy producers have improved fertility of their herds by selecting bulls with higher conception rate evaluations. This research was motivated by the rapid increase in embryo transfer (ET) use to 11% of recent births and >1 million total births, with >5 times as many ET calves born in the United States in 2021 compared with just 5 yr earlier. Historical data used in genetic evaluations are stored in the National Cooperator Database.

SLEMM: million-scale genomic predictions with window-based SNP weighting.

Motivation: The amount of genomic data is increasing exponentially. Using many genotyped and phenotyped individuals for genomic prediction is appealing yet challenging.

Results: We present SLEMM (short for Stochastic-Lanczos-Expedited Mixed Models), a new software tool, to address the computational challenge.

Invited review: Reliability computation from the animal model era to the single-step genomic model era.

The calculation of exact reliabilities involving the inversion of mixed model equations poses a heavy computational challenge when the system of equations is large. This has prompted the development of different approximation methods. We give an overview of the various methods and computational approaches in calculating reliability from the era before the animal model to the era of single-step genomic models.

Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle.

Maintaining a genetically diverse dairy cattle population is critical to preserving adaptability to future breeding goals and avoiding declines in fitness. This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in 5 breeds of US dairy cattle. We analyzed a sizable genomic data set containing 4,173,679 pedigreed and genotyped animals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds.

Invited review: Unknown-parent groups and metafounders in single-step genomic BLUP.

Single-step genomic BLUP (ssGBLUP) is a method for genomic prediction that integrates matrices of pedigree (A) and genomic (G) relationships into a single unified additive relationship matrix whose inverse is incorporated into a set of mixed model equations (MME) to compute genomic predictions. Pedigree information in dairy cattle is often incomplete. Missing pedigree potentially causes biases and inflation in genomic estimated breeding values (GEBV) obtained with ssGBLUP.

Gamevar.f90: a software package for calculating individual gametic diversity.

Background: Traditional selection in livestock and crops focuses on additive genetic values or breeding values of the individuals. While traditional selection utilizes variation between individuals, differences between gametes within individuals have been less frequently exploited in selection programs. With the successful implementation of genomic selection in livestock and crops, estimation and selection for gametic variation is becoming possible.