Genome-wide association study for tail alterations in German Holstein dairy cows

Abstract

Objectives
Tail injuries and pathological alterations have been reported in many species. In cattle, they were investigated
mainly in fattening bulls and feedlot cattle. In dairy cows high prevalences for different tail alterations were
found. However, aetiology and pathogenesis of this health trait are still unclear and need further investigation.
Out of 4443 phenotypes of different tail alterations we assorted seven groups common in dairy cows: 1. very
tip of the tail , 2. ring-like, 3. scurf, 4. swelling, 5. thinning, 6. axis anomaly, and 7. verruca-like mass. The
objective of this study was to identify genomic regions that may influence the occurrence of different tail
alterations in dairy cows, which could be useful for a potential implementation of a genomic selection tool for
more robust and healthy cows in the future.
Material and methods
Occurrence data of each tail alteration group were collected monthly from 167 German Holstein cows. The
cows originated from a German 1300 cows dairy herd. Data collection was performed from May to December
2021, since calving of all included cows was from April to May. The cows were in their first to seventh lactation.
The phenotype was encoded binary, where 0 means the absence and 1 the presence of a tail alteration group
within the whole timespan.
For 118 cows, Illumina EuroG10k genotypes were available and imputed up to 45k (FImpute). The remaining
cows were genotyped with the Illumina EuroG MD (V1, V1.1, V2) with 45613 SNPs. After quality check (only
segregating SNPs, at least two groups with a minimum of 10 observations, no duplicated markers, a minor
allele frequency of 1%, and within Hardy-Weinberg-Equilibrium P>0.01), 41062 SNPs remained.
A genome-wide association study was performed using the software GEMMA and the univariate linear mixed
model. Each tail alteration group was treated as a separate phenotype. A standardized relatedness matrix was
included in the model and calculated on SNP chip data to consider the population stratification, since many
half-sib groups were present. The lactation (1st, 2nd, ≥3rd) was included as covariate. The genotype matrix was
included in the model and the effect size per marker was estimated and tested for significance using a Wald
test.
For positional candidate gene analysis, genomic regions around top markers (P < 0.0001) of 325kbp wereconsidered,since the linkage disequilibrium decay analysis gave a mean r² of >0.61 within this distance. The
marker positions are given on the ARS-UCD 1.2 Bos taurus genome assembly.
Results
In total 51 top markers resulted for all seven tail alteration groups, whereof one marker reached Bonferronicorrected
genome-wide significance threshold for tail alteration group “thinning” (BTA1: rs42577957, −log10(P)
= 9.22). The markers were found on 18 different chromosomes. Close to these markers, 65 positional
candidate genes reside. Among them CCDC122 (rs42421906, −log10(P) = 5.46), which was associated with
the phenotype “scurf” in our analysis. CCDC122 is one of the top differentially expressed genes in liver
metabolism in pigs showing swine inflammation and necrosis syndrome (Ringseis et al., 2021). This syndrome
results in severe tail alterations in pigs as well.
Conclusions
This first genetic investigation of tail alterations in dairy cows showed the potential of finding genetic markers
for this novel health trait. Nonetheless, it is recommended to increase the sample size of cows and to further
investigate the cause of tail alterations, to substantiate the reported phenotypes.

Literature

Ringseis, R., Gessner, D. K., Loewenstein, F., Kuehling, J., Becker, S., Willems, H., et al. (2021). Swine inflammation and necrosis syndrome is associated with plasma metabolites and liver transcriptome in affected piglets. Animals 11, 1–14. doi:10.3390/ani11030772

Sargolzaei, M., Chesnais, J. P., and Schenkel, F. S. (2014). A new approach for efficient genotype imputation using information from relatives. BMC Genomics 15. doi:10.1186/1471-2164-15-478

Zhou, X., and Stephens, M. (2014). Efficient Algorithms for Multivariate Linear Mixed Models in Genome-wide Association Studies. Nat Methods 11, 407–409. doi:10.1038/nmeth.2848

Acknowledgement
We thank the MASTERRIND GmbH, Verden, Germany, for providing the genotypes from the investigated
cows.
Funding
Part of the data results from the project TINCa Dairy, which is funded by the Tönnies Forschung, Rheda,
Germany.

Mehr zum Titel

Titel Genome-wide association study for tail alterations in German Holstein dairy cows
Medien ---
Verlag ---
Heft ---
Band 2022
ISBN ---
Verfasser/Herausgeber Prof. Dr. med. vet. habil. Prisca Kremer-Rücker, Kim F. Schubert, Dr. Saskia Meier
Seiten ---
Veröffentlichungsdatum 04.09.2022
Projekttitel TINCa Dairy - Tail Inflammation and Necrosis in Dairy Cattle
Zitation Kremer-Rücker, P.; Schubert, K.; Meier, S. (2022): Genome-wide association study for tail alterations in German Holstein dairy cows . 2022, Abstract No. 1229.