In dairy cattle production, it is important to understand how inbreeding affects production, fertility, and health traits. However, there is still limited use of genomic information to estimate inbreeding, despite advancements in genotyping technologies. To address this gap, we investigated the effect of inbreeding on German Holstein dairy cattle using both pedigree-based and genomic-based inbreeding estimators. We employed one method based on pedigree information (F_ped) together with 6 genomic-based methods, including 3 genome-wide complex trait analysis software estimators (F_hat1, F_hat2, F_hat3), VanRaden's first method (F_VR1, with observed allele frequencies, and F_VR0.5, when allele frequencies are set to 0.5), and one based on runs of homozygosity (F_roh). Data from 24,489 cows with both phenotypes and genotypes were used, with a pedigree including 232,780 animals born between 1970 and 2018. We analyzed the effects of inbreeding depression on production, fertility, and health traits separately, using single-trait linear animal models as well as threshold models to account for the binary nature of the health traits. For the health traits, we transformed solutions from the liability scale to a probability scale for easier interpretation. Our results showed that the mean inbreeding coefficients from all estimators ranged from -0.003 to 0.243, with negative values observed for most genomic-based methods. We found out that a 1% increase in inbreeding caused a depression ranging from 25.94 kg (F_hat1) to 40.62 kg (F_hat3), 1.18 kg (F_hat2) to 1.70 kg (F_hat3), 0.90 kg (F_hat2) to 1.45 kg (F_roh and F_hat3), 0.19 (F_ped) to 0.34 d (F_hat3) for 305-d milk yield, fat, protein, and calving interval, respectively. The health traits showed very slight gradual changes when inbreeding was increased steadily from 0% to 50%, with digital dermatitis showing a rather contrasting trend to that of mastitis, which increased the more an animal was inbred. Overall, our study highlights the importance of considering both pedigree-based and genomic-based inbreeding estimators when assessing the impact on inbreeding, emphasizing that not all inbreeding is harmful.

The decline in farm revenue due to volatile milk prices has led to an increase in the use of beef semen in dairy herds. While this strategy (“Beef-on-dairy” (BoD)) can have economic benefits, it can also lead to unintended consequences affecting animal welfare. Semen sale trends from breeding organizations depict increasing sales of beef semen across the globe. Calves born from such breeding strategies can perform better when compared to purebred dairy calves, especially in terms of meat quality and growth traits. The Beef-on-dairy strategy can lead to unintentional negative impacts including an increase in gestation length, and increased dystocia and stillbirth rates. Studies in this regard have found the highest gestation length for Limousin crossbred calves followed by calves from the Angus breed. This increase in gestation length can lead to economic losses ranging from 3 to 5 US$ per animal for each additional day. In terms of the growth performance of crossbred animals, literature studies are inconclusive due to the vast differences in farming structure across the regions. But almost all the studies agree regarding improvement in the meat quality in terms of color, fiber type, and intra-muscular fat content for crossbred animals. Utilization of genomic selection, and development of specialized Beef-on-dairy indexes for the sires, can be a viable strategy to make selection easier for the farmers.

In recent years, Beef‐on‐Dairy (BoD) crossbreeding programs have gained momentum to enhance dairy cattle's economic and genetic merits while meeting the demand for high‐quality beef. However, bulls with superior growth potential can lead to calving problems; thus, Holstein dairy farmers must decide which semen to use to avoid calving problems while producing heavier BoD calves. In this study, our objective was to genetically evaluate beef sires using a BoD crossbred reference population for three major economic traits, i.e., gestation length (GL), birth weight (BW), and calving ease (CE). A population comprising 4420 BoD calves sired by bulls from Angus (ANG), Limousin (LIM), Wagyu (WAG), and White‐Belgian Blue (WBB) was used to perform a joint genetic evaluation of the sire for traits. Univariate and bivariate (linear‐linear or threshold‐linear) models were applied to estimate variance components and genomic breeding values using single‐step methods. Estimates from CE models were transformed from the liability to the observable scale for more straightforward interpretation. Direct heritabilities for GL, BW, and CE (after transformations) ranged from 0.33 to 0.35, 0.33 to 0.37, and 0.02 to 0.14, respectively, while maternal heritabilities ranged from 0.11 to 0.17 for all traits. Generally, male BoD calves had higher probabilities for calving difficulty, with calvings being more difficult if sired by LIM (13%) as compared to ANG (7%) and WBB (9%) when considering male calves. The bivariate models outperformed the univariate models. For CE, the accuracy of predictions was up by 95% with a reduction in bias and dispersion. WBB sires were preferred when crossing with higher parity cows compared to ANG sires. These findings demonstrate that a well‐structured BoD reference population enables accurate genomic evaluation of beef sires, facilitating the selection of sires that produce economically viable calves with reduced calving difficulties.