The aim of the present study was to detect significant SNP (single-nucleotide polymorphism) effects and to annotate potential candidate genes for novel udder health traits in two different farming systems. We focused on specific mastitis pathogens and differential somatic cell fractions from 2198 udder quarters of 537 genotyped Holstein Friesian cows. The farming systems comprised compost-bedded pack and conventional cubicle barns. We developed a computer algorithm for genome-wide association studies allowing the estimation of main SNP effects plus consideration of SNPs by farming system interactions. With regard to the main effect, 35 significant SNPs were detected on 14 different chromosomes for the cell fractions and the pathogens. Six SNPs were significant for the interaction effect with the farming system for most of the udder health traits. We inferred two possible candidate genes based on significant SNP interactions. HEMK1 plays a role in the development of the immune system, depending on environmental stressors. CHL1 is regulated in relation to stress level and influences immune system mechanisms. The significant interactions indicate that gene activity can fluctuate depending on environmental stressors. Phenotypically, the prevalence of mastitis indicators differed between systems, with a notably lower prevalence of minor bacterial indicators in compost systems.

Compost-bedded pack barns (CBP) are of increasing interest in dairy farming due to their positive effect on animal welfare. The temperature and the moisture content of the bedding material characterising the composting process can promote the growth of thermophilic aerobic sporeformers (TAS). Therefore, the aim of this study was to determine CBP bedding material characteristics, such as moisture content and temperature, and to determine TAS species. The dilution, the heat inactivation of all non-TAS species and the incubation of 13 bedding samples from four CBP groups resulted in a mean TAS amount over all samples of 4.11 log10 cfu/g bedding material. Based on the subsequent sequencing of parts of the 16S rRNA-gene of 99 TAS colonies, the TAS species Aneurinibacillus thermoaerophilus, Bacillus licheniformis, Geobacillus thermodenitrificans, Laceyella sacchari, Thermoactinomyces vulgaris and Ureibacillus thermosphaericus were identified. The moisture content of the bedding material, the relative humidity above the bedding material and the sampling season significantly affected the amount of TAS. The moisture content or relative humidity above the bedding material significantly influenced the concentration of Ureibacillus thermophaericus or Laceyella sacchari. Consequently, an optimal CBP management including a dry lying surface and an optimal composting process will contribute to a moderate microbial, especially TAS amount, and TAS species distribution.

By-products like sawdust and straw are applied in compost bedded-pack barns (CBP) for cattle. These materials, which are gradually mixed with excreta and undergo a composting process, serve as a lying bed for the cattle. This study aims to assess the perception of consumers and farmers regarding the use of CBP during the grazing season of cattle for raising other animals or for growing food crops. This was examined by combining surveys with consumers from eight European countries and cattle farmers, focus groups with consumers, and in-depth interviews with individual farmers who implemented alternative uses of compost. The results showed that farmers preferred the compost bedded-pack system to the cubicle system in terms of sustainability and market aspects, although the cost of the bedding material required for CBP was seen as a significant negative aspect. Around half of all consumers indicated that the compost can be used for non-edible products and 26% indicated the compost can be used for raising other animals. Furthermore, 5% of consumers felt that compost should not be used for any other purpose. There were statistically significant differences between countries; therefore, regional specificities should be taken into account when marketing products from compost in CBP barns.

The aim of this study was to establish and evaluate a structural equation model to infer causal relationships among environmental and genetic factors on udder health. For this purpose, 537 Holstein Friesian cows were genotyped, and milk samples were analyzed for novel traits including differential somatic cell counts and specific mastitis pathogens. In the structural model, four latent variables (intramammary infection (IMI), production, time and genetics) were defined, which were explained using manifest measurable variables. The measurable variables included udder pathogens and somatic differential cell counts, milk composition, as well as significant SNP markers from previous genome-wide associations for major and minor pathogens. The housing system effect (i.e., compost-bedded pack barns versus cubicle barns) indicated a small influence on IMI with a path coefficient of −0.05. However, housing system significantly affected production (0.37), with ongoing causal effects on IMI (0.17). Thus, indirect associations between housing and udder health could be inferred via structural equation modeling. Furthermore, genotype by environment interactions on IMI can be represented, i.e., the detection of specific latent variables such as significant SNP markers only for specific housing systems. For the latent variable genetics, especially one SNP is of primary interest. This SNP is located in the EVA1A gene, which plays a fundamental role in the MAPK1 signaling pathway. Other identified genes (e.g., CTNNA3 and CHL1) support results from previous studies, and this gene also contributes to mechanisms of the MAPK1 signaling pathway.

Tail docking is still used in pigs to reduce the prevalence of tail biting, although it is purely symptomatic and contrary to animal welfare. Genetic selection for shorter tails might, however, help to avoid tail docking and has therefore been proposed. A genetic basis for tail length is known for many species. Variability in tail length, including moderate heritability, has also been demonstrated in pigs. The aim of the present study was to identify genetic markers for tail length and to define candidate genes. To this end, 140 piglets were phenotyped and genotyped at 3 days of age and a genome-wide association study was performed. Seven SNPs were mapped on chromosomes 1, 2, 6, 11, and 15. Two linked SNPs on chromosome 2 resulted in a functional amino acid exchange. The genotypes at the SNPs were only associated with small differences in relative tail length of up to 16.5% (short genotype versus long genotype at SSC15), but at the same time with the occurrence of malformations in the form of tail kinks. The small effect size and the association between tail length and tail kinks, together with the generally pure symptomatic effect on tail biting, argue against the applicability of selection for shorter tails in pigs.