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.

Producing calves with higher economic value by utilising semen from beef breeds in dairy herds (Beefon-Dairy, BoD) has become more common in recent times. Such crossbreed calves promise better carcass conformation and higher consumer acceptance due to the better flavour, but the widespread adaptation of BoD requires careful consideration of the sire breed to maximise the benefits. In this regard, two major traits of interest are calving difficulty and gestation length due to associated costs. In this study, 3 966 BoD calves from crossing Holstein dams with beef sires of the breeds Angus (n = 811), Belgian Blue (n = 2841), Limousin (n = 169) and Wagyu (n = 145) from 122 farms were evaluated to determine differences in calving difficulty and gestation length using binary logit and linear regression models. Lowest calving difficulty was observed for Wagyu crossbreds while Limousin crossbreds had the highest calving difficulty incidences. Selected sires from Angus and Belgian Blue breeds were also compared using chisquare analysis for differences in calving difficulty. The risk of calving difficulty was 1.94 times higher for male calves. Heifers had a significantly higher risk for calving difficulty when compared with the multiparous cows in the study. Calves with higher birth weight and longer gestation length were more prone to calving problems. For gestation length, Angus crossbreds had the shortest gestation (280.2 d), while the longest gestation (287.6) was observed in Limousin crossbreds. To maximise the benefits of the BoD breeding strategy, selecting appropriate sire breeds and within-breed sire selection for economically important traits, such as birth weight, appropriate gestation length, and reduced calving difficulty, may provide a viable solution. (c) 2024 The Author(s). Published by Elsevier B.V. on behalf of The Animal Consortium. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Background: Beef on Dairy (BoD) calves are born from the crossing of dairy cows with beef breeds. The genetic architecture of these calves differs significantly from the parent breeds due to heterosis and other dominance effects. Identification of the genomic regions associated with traits in BoD calves and the inheritance pattern of these regions can assist in the selection process. We conducted a genome-wide association study (GWAS) for Belgian blue and Angus crossbreds born from a Holstein dam, incorporating additive and dominance effects to identify genomic regions associated with birth weight, calving difficulty, and gestation length. Additionally, a haplotype-based GWAS was performed to compare the effectiveness of these two different methodologies and to identify the parental origin of the haplotypes based on similar allelic patterns between crossbred and parental breeds.Results: The heritability estimates for birth weight, calving difficulty, and gestation length were 0.29 (±0.03), 0.36 (±0.04), and 0.09 (±0.03), respectively. Using SNP-based GWAS for birth weight, a genomic region containing the GABRG1 gene on BTA 6 was identified. In addition, the haplotype-based analysis identified three more genes (CSER1, FAM13A, and LCORL) associated with birth weight. Incorporating dominance effects into the GWAS model led to the identification of an additional gene, SPP1, related to birth weight. For calving difficulty, SNP-based GWAS in Angus crossbreds revealed a genomic region containing the KCNIP4 gene. Most of the haplotypes associated with these traits originated from the three parental breeds, but six unique haplotypes for Angus and Belgian blue were identified.Conclusion: Based on this study, Haplotype GWAS was found to have superior statistical power in the identification of associated genomic regions in BoD crossbreds. However, for traits such as calving difficulty, SNP-based GWAS proved to be more effective. Both approaches are essential for the identification of genomic regions associated with traits of interest in BoD calves.