Genome‐wide association study for antibody response to Mycobacterium avium ssp. paratubeculosis in goats

Abstract

Mycobacterium avium ssp. paratuberculosis (MAP), causes Johne's disease (JD), or paratuberculosis, a chronic enteritis of ruminants, which in goats is characterized by ileal lesions. The work described here is a case–control association study using the Illumina Caprine SNP50 BeadChip to unravel the genes involved in susceptibility of goats to JD. Goats in herds with a high occurrence of Johne's disease were classified as healthy or infected based on the level of serum antibodies against MAP, and 331 animals were selected for the association study. Goats belonged to the Jonica (157) and Siriana breeds (174). Whole‐genome association analysis identified one region suggestive of significance associated with an antibody response to MAP on chromosome 7 (p‐value = 1.23 × 10−5). These results provide evidence for genetic loci involved in the antibody response to MAP in goats.

A high-density genome-wide approach reveals novel genetic markers linked to small ruminant lentivirus susceptibility in sheep

“…Based on the increased analytical power in reducing the number of false positive signals when multiple methodologies are adopted in parallel ( Mastrangelo et al, 2018 ), this study used three distinct approaches in conjunction with the use of high-density SNP data. Despite the moderate sample size of our study, like previous GWASs in small ruminants ( Mastrangelo et al, 2018 ; Cecchi et al, 2019 ; Lei et al, 2020 ; Letko et al, 2021 ; Minozzi et al, 2023 ), this combined approach can boost the detection accuracy and reduce unknown biases ( Schiavo et al, 2018 ). The identification of candidate genomic regions by more than one methodology may be seen as strong evidence of the activity on a particular phenotype.…”

The effects of case/control ratio and sample size on genome‐wide association studies: A simulation study

“…In the veterinary field, GWAS is commonly used for the detection of genetic variations related to a trait. In this respect, GWAS is used for the detection of SNPs related to resistance to diseases such as Mycobacterium Avium subspecies paratuberculosis (Alpay et al, 2014;Canive et al, 2021;Fisher et al, 2011;Kirkpatrick et al, 2022;Minozzi et al, 2022), bovine leukemia virus (Brym et al, 2016;Carignano et al, 2018), bovine spongiform encephalopathy (Murdoch et al, 2010), and ovine foot-root disease (Raadsma et al, 2018). In addition, cattle idiopathic male subfertility (Pausch et al, 2014) and coat colour-related genetic variations (Mastrangelo et al, 2019) are evaluated by GWAS.…”

“…In these studies, a different case–control ratio and a different sample size are preferred. Some researchers prefer a case/control ratio of 1:1 (Alpay et al., 2014; Canive et al., 2021; Minozzi et al., 2022), while others prefer a case/control ratio of 1:4 (Fisher et al., 2011; Kirkpatrick et al., 2022). Furthermore, association analysis is carried out using unbalanced case/control ratio in some studies (Pausch et al., 2014).…”

“…At this point, molecular genetic approaches offer opportunities. Genome‐wide association studies (GWAS) is a useful tool for the detection of genetic variations that may affect binary traits in ruminants (Alpay et al., 2014; Mastrangelo et al., 2019; Minozzi et al., 2022). To detect genetic variations related to a binary trait, case/control studies are designed in GWAS.…”