Evaluation of Single Nucleotide Polymorphisms (SNPs) Associated with Genetic Resistance to Bovine Paratuberculosis in Marchigiana Beef Cattle, an Italian Native Breed

SIMPLE SUMMARY: Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis (PTB), chronic enteritis of ruminants spread worldwide. PTB is, by now, considered a conditioned disease, depending on both environmental and genomic factors. PTB susceptibility seems to be related to some genes coding for immune regulators involved in the cell-mediated response during infection: genetic markers, particularly single nucleotide polymorphisms (SNPs), have been investigated in several studies, and different candidate genes have been highlighted as associated with PTB resistance/susceptibility. The aim of this preliminary study was to verify, for the first time in a local beef cattle breed, known as Marchigiana, an association between MAP infection status and SNPs in candidate immune-genes. Specifically, in a MAP-infected herd, IFN-γ tests, ELISA, qPCR, and cultures were performed, for a follow-up range of 3–6 years, on 112 bovines to evaluate the state of MAP infection. Animals with positive results for at least one test were considered infected. DNA samples of bovines with a known MAP status were analyzed to assess the presence and the genotypic frequency of SNPs in genes encoding for gamma-interferon (BoIFNG), interleukin receptor 10 (IL10RA), interleukin receptor 12 (IL12RB2), and toll-like receptors (TLR1, TLR2, TLR4). For the IL10RA and IL12RB2 genes, relevant differences in genotypic frequencies among the considered cattle groups were observed. For all the investigated candidate genes, SNP genotypes that have been associated with PTB resistance in the literature, were found more frequently, suggesting potential genetic resistance traits in the Marchigiana breed. ABSTRACT: Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis (PTB), a widespread chronic enteritis of ruminants. The progression of the infection depends on the containment action of innate and cell-mediated immunity (CMI), and it is related to environmental and genetic factors. In particular, PTB susceptibility seems to be associated with specific genes coding for immune regulators involved in the cell-mediated response during the infection. The aim of this preliminary study was to verify, in Italian beef cattle, an association between MAP infectious status and the presence of single nucleotide polymorphisms (SNPs) in candidate genes. To the best of our knowledge, this is the first investigation conducted on a native beef cattle breed, known as Marchigiana, reared in Central Italy. The present research, based on a longitudinal study, aimed to identify and correlate phenotypic and genetic profiles characteristic of the subjects potentially able to contrast or contain PTB. In a MAP-infected herd, ELISA, IFN-γ tests, qPCR, and cultures were performed at a follow-up, occurring within a period ranging from three to six years, to evaluate the individual state of infection. Animals testing positive for at least one test were considered infected. DNA samples of 112 bovines, with known MAP statuses, were analyzed to verify an association with SNPs in the genes encoding gamma-interferon (BoIFNG), interleukin receptor 10 (IL10RA), interleukin receptor 12 (IL12RB2), and toll-like receptors (TLR1, TLR2, TLR4). Regarding statistical analysis, the differences among target genes and pairs of alleles in the analyzed groups of animals, were evaluated at a significance level of p < 0.05. For IL10RA and for IL12RB2 genes, relevant differences in genotypic frequencies among the considered cattle groups were observed. For all candidate genes studied in this investigation, SNP genotypes already associated with PTB resistance were found more frequently in our population, suggesting potential resistance traits in the Marchigiana breed.