Unexpected recombination at the polled locus in a horned Holstein calf from the mating of a homozygous polled sire and a heterozygous polled cow

Abstract

In this study, I report an unexpected case of a Holstein calf that developed horns even though the sire was homozygous and the dam was heterozygous for polledness. After verifying and confirming the correct parentage, the parents and offspring were genotyped with the Illumina EuroG_MD BeadChip and the SNPs in the polled region on chromosome 1 were evaluated. In addition, the father was sequenced with next generation sequencing to identify possible, previously unknown variants. The deletion of two base pairs within the causative 80-kb duplication described for the Friesian polled variant was verified by melting curve analysis and the 80-kb duplication by droplet digital PCR. Analysis of all data showed that, as expected, the calf was heterozygous for all SNP positions flanking the 80-kb duplication but was homozygous wild type in the 80-kb duplication region and therefore carried horns. This is certainly a very rare case of a recombination within the highly conserved polled region, which on the one hand confirms that only the 80-kb duplication is responsible for the expression of the Friesian polled variant, but on the other hand also shows that caution is required when interpreting the usual routine genotyping of the horn status based on linked single nucleotide polymorphisms in the polled region on chromosome 1. Based on the present case, it is recommended that, in addition to the evaluation of the SNP data of the BeadChip, an extended diagnosis with direct detection of the 2-bp deletion (1:g.2629156_2629158delGT) should be carried out in any case when detecting the Friesian polled variant.