Recombination events restored the functional horned haplotypes in the offspring of polled parents

Breeding of genetically polled animals is a desirable approach in modern cattle husbandry for welfare and economic reasons. At least four different genetic variants associated with polledness in cattle have been identified, suggesting genetic heterogeneity. These dominant variants are located on chromosome 1 between approximately 2.42-2.73 Mb (reference: ARS-UCD1.3), also called the POLLED locus. Among these variants, Friesian (P_F, ~ 80 kbp duplication) and Celtic (P_C, 212 bp complex InDel) are the most common across breeds in the production systems globally, such as in Holstein-Friesian (HF) and Fleckvieh (FV). While studies have provided strong evidence supporting the association of the P_F allele with the polledness, it has not yet been functionally validated, unlike the P_C allele.

Here, we conduct whole-genome sequencing analyses of two trios exhibiting unexpected inheritance patterns related to the P_C and P_F variants. In both instances, horned offspring were produced from mating pairs where one parent was homozygous for the polled variant and the other was homozygous for the ancestral horned variant. By analyzing the WGS data generated using Nanopore technology, we show that the de novo generation of the ancestral horned phenotype in both offspring was the result of distinct recombination events. Specifically, in the HF trio, it was the result of non-allelic homologous recombination in the gametes of the sire (P_F/P_F), while in the FV trio, it was the result of allelic homologous recombination in the gametes of the dam (P_C/P_F). The findings from the HF trio support the hypothesis that ~ 80-kbp duplication is the genetic variant responsible for the polled phenotype of Friesian origin.

We show that different genomic arrangements in the POLLED locus can lead to the emergence of de novo ancestral horn phenotypes. Such arrangements can complicate phenotype prediction in offspring, even when sires or dams have been tested as genetically homozygous polled. Therefore, it is important, for a better understanding of the relationship between the POLLED locus and the POLLED phenotype, that any deviation from the expected result is critically analysed. Possibly, some of these cases can further narrow down the sequence motif that is essential for polledness in cattle.