Conservation & local programs

On the horns of a dilemma: impact of selecting for polledness on genetic diversity in the Danish Holstein population

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Abstract

Increasing the frequency of naturally hornless (polled) cattle offers a cost-effective alternative to dehorning and disbudding, two interventions causing acute pain in cattle. The polled phenotype is controlled by a dominant allele inherited at a locus on chromosome 1, with the Friesian variant being the primary allele segregating in Holstein. Historically, its frequency was very low in Danish Holstein (0.85 on 6 generations). Phenotypes (horned/polled) were deducted from genotypes at the polled locus for 321,505 heifers. Heifers were genotyped on low- and medium-density SNP panels. Their genotypes were imputed to 47,599 markers using files produced for routine genomic evaluations. Runs-of-homozygosity (ROH) were identified using the PLINK software. At each SNP, the proportion of animals carrying a ROH was compared between horned and double-carrier heifers using a chi-square test. Extended haplotype homozygosity (EHH) was computed for haplotypes carrying the Friesian allele after phasing of genomic data. Approximately 30% of genotyped heifers born in 2025 were polled, mostly single carriers (27.9%), compared to only 8% in 2020. This increase has been driven by the intensive use of a few high genetic merit bulls; for example, eight bulls sired 50% of polled heifers born in 2024 versus 14 for horned contemporaries. Most polled bulls descended from a few carrier ancestors tracing back to a single polled bull born in the early seventies. Over the last decade, the average pedigree-based inbreeding coefficient remained 0.6 to 1% points higher in double carriers compared to horned heifers. ROHs were detected in 94.8% of double carriers within the region encompassing the polled locus, versus 13.5% in horned animals, with a highly significant difference in ROH frequency between groups (-log10(P) >20) across a 11.8 Mb stretch at the proximal end of chromosome 1. This was corroborated by very high EHH values ( > 0.91) on a 2.5 Mb-long haplotype flanking the Friesian variant. Additional genomic regions with significantly increased ROH frequency in double carriers were detected on chromosome 1 and other chromosomes. Altogether, these results indicate limited genetic diversity for haplotypes harboring the Friesian allele in Danish Holstein and evidence of a strong selection sweep around the polled locus. Incorporating haplotype information into selection and mating strategies is recommended to limit the accumulation of inbreeding in this region.

Keywords: 2026

How to Cite:

Bouquet, A. & Cai, Z., (2026) “On the horns of a dilemma: impact of selecting for polledness on genetic diversity in the Danish Holstein population”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286305. doi: https://doi.org/10.31274/wcgalp.23916

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