Overview of known and new genetic defects and their prevalence in Swiss Fleckvieh cattle

In the Swiss Fleckvieh (SF) cattle breed, derived from crosses between the Holstein (HO) and Simmental (SI) breeds, two inherited diseases, thrombocytopathy (TP) and bovine dilated cardiomyopathy (BDCMP), and four so-called fertility haplotypes, Fleckvieh haplotype 1,2,4,5 (FH1,2,4,5), have been described so far. In addition, the APOB-related hereditary disease cholesterol deficiency (CD) has been thoroughly described in the closely related HO breed after its discovery in 2015, but to date it has not been reported in the SF breed. The hereditary disease retinitis pigmentosa (RP), which leads to progressive retinal degeneration in homozygous carriers of a pathogenic variant of the RP1 gene, has been shown to occur in several European cattle breeds, but has not been described in the SF population. The aim of this study was to determine the prevalence of the known genetic defects and fertility haplotypes, as well as CD, in SF and the two closely related breeds, HO and SI. We also investigated the prevalence of RP in the SF population and characterised the genetic disease through a case series. To determine the prevalence, the SNP array genotyping data of over 65 000 cattle from the Swiss breeding association database were analyzed and based on those results, four RP1 homozygous animals were clinically evaluated. The allele frequency of the RP causing allele in SF was 13 % and the CD causing allele, previously described only in HO, was found in SF with an allele frequency of 1,17 %. The remaining six genetic defects occurred in SF either with a low allele frequency (TP 0,24 %, BDCMP 1,93 %, FH2 0,03 %, FH5 0,02 %) or not at all (FH1, FH4). The four RP1 homozygous animals with a mean age of 7,5 years old Showed varying degrees of visual impairment. Overall, the clinical and pathological findings were consistent with RP1-associated RP. In a suspected case, RP1 genotyping by genetic testing can confirm the diagnosis of RP. Due to the routine use of SNP genotyping to estimate breeding values, the genotypes of genetic defects are known, at least in the active breeding population, and can therefore be considered before matings. Avoiding risk mating will improve animal health and welfare and prevent animal losses, and therefore economic losses.