- The study used detailed phenotyping for DD stages in two housing systems: conventional cubicle barns (CON) and compost bedded pack barns (CBPB).
- 2,980 observations were made for the three traits DD-sick, DD-acute, and DD-chronic from 1,311 Holstein-Friesian and 399 Fleckvieh-Simmental cows.
- The study found an average disease prevalence of 20.47% for DD-sick, 13.88% for DD-acute, and 5.34% for DD-chronic, with a higher prevalence in CON than in CBPB.
- After quality control of 50K genotypes, 38,495 SNPs from 926 cows remained for genomic analyses.
- Genetic correlations between same DD traits from different housing systems and between DD-sick, DD-chronic, and DD-acute were estimated via bivariate animal models.
- Genetic correlations among DD-sick, DD-acute, and DD-chronic ranged from 0.58 to 0.81.
- SNP main effects and SNP x housing system interaction effects were estimated simultaneously via GWAS considering only the phenotypes from genotyped cows.
- GWAS for main effects indicated heterogeneous Manhattan plots for DD-acute and DD-chronic, indicating particularities in disease pathogenesis.
- Some shared annotated potential candidate genes were identified for DD-sick and DD-acute, with direct or indirect effects on disease resistance or immunology.
The current research aims to employ thorough phenotyping for the claw disease digital dermatitis (DD), taking into account distinct DD phases in two housing systems (conventional cubicle barns = CON and compost bedded pack barns = CBPB), to predict potential genotype x housing system correlations. The DD-stages contained 2,980 observations for the three features DD-sick, DD-acute, and DD-chronic in 1,311 Holstein-Friesian and 399 Fleckvieh-Simmental cows. The 5 CBPB and 5 CON herds were selected using a special process to produce a high degree of herd similarity in terms of climate, food, milking system, and location, but with significant housing system variances. Five additional farms used “a mixed system” with two sub-herds, one representing CBPB and the other representing CON. The CBPB system had 899 cows (1530 observations), whereas the CON system had 811 cows (1450 observations). The average illness prevalence was 20.47% for DD-sick, 13.88% for DD-acute, and 5.34% for DD-chronic, with CON showing a greater frequency than CBPB. Following quality screening of 50K genotypes, 38,495 SNPs from 926 cows remained for further genomic analysis. Genetic parameters for DD-sick, DD-acute, and DD-chronic were computed using single-step techniques for single-trait repeatable animal models, taking into account the whole data set, as well as the CON and CBPB subsets individually. Genetic connections between the same DD features in various housing systems, as well as between DD-sick, DD-chronic, and DD-acute, were assessed using bivariate animal models. Heritabilities based on the whole data set were 0.16 for DD-sick, 0.14 for DD-acute, and 0.11 for DD-chronic. A modest increase in heritabilities and genetic variations was seen in CON as compared to the “well-being” CBPB system, showing a greater genetic differentiation of illnesses in a more stressful environment. Genetic correlations between identical DD characteristics recorded in CON or CBPB were close to 0.80, excluding out clear genotype x housing system interactions. Genetic correlations between DD-sick, DD-acute, and DD-chronic varied from 0.58 to 0.81. SNP main effects and SNP x housing system interaction effects were calculated concurrently using GWAS using solely genotyped cow phenotypes. Ongoing annotations of putative candidate genes are centered on chromosomal regions 100 kb upstream and downstream of the substantially related candidate SNP. GWAS for main effects revealed varied Manhattan plots, particularly for DD-acute and DD-chronic, suggesting differences in disease pathophysiology. Nonetheless, a few shared annotated putative candidate genes, including METTL25, AFF3, PRKG1, and TENM4, for DD-sick and DD-acute, were discovered. These genes have a direct or indirect impact on disease resistance or immunology. For the SNP x housing system interaction, the annotated genes ASXL1 and NOL4L on BTA 13 were significant for DD-sickness and DD-acute. Overall, the extremely comparable genetic parameters for the same qualities in various habitats, as well as the insignificant genotype x housing system interactions, suggest that housing system differences have very small influence on genetic assessments for DD.
