All-breed single-step genomic best linear unbiased predictor evaluations for fertility traits in US dairy cattle.

The US dairy cattle genetic evaluation is currently a multistep process, including multibreed traditional BLUP estimations followed by single-breed SNP effects estimation. Single-step GBLUP (ssGBLUP) combines pedigree and genomic data for all breeds in one analysis. Unknown parent groups (UPG) or metafounders (MF) can be used to address missing pedigree information.

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.