Host Genetics Underlying Pathological Outcomes to Mycobacterium Avium Subsp. Paratuberculosis Infection is Governed by Distinct Genetic Variants

Abstract

Abstract Bovine paratuberculosis (PTB), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic granulomatous enteritis that affects cattle worldwide. According to their severity and extension, PTB-associated histological lesions have been classified into the following groups; focal, multifocal, and diffuse. It is unknown whether these lesions represent sequential stages or divergent outcomes. In the current study, the associations between host genetics and pathology were explored by genotyping 813 Spanish Holstein cows with no visible lesions (N= 373) and with focal (N=371), multifocal (N=33), and diffuse (N=33) lesions in gut tissues and regional lymph nodes. DNA from peripheral blood samples of these animals was genotyped with the Bovine EuroG MD Bead Chip, and the corresponding genotypes were imputed to whole-genome sequencing (WGS) data using the 1,000 Bull genomes reference population. A genome-wide association study (GWAS) was performed using the WGS data and the presence or absence of each type of histological lesion in a case-control approach. No overlap was seen in the SNPs controlling the three PTB-associated lesions. A total of 192 and 92 SNPs defining 13 and 9 distinct quantitative trait loci (QTLs) were highly-associated (P ≤ 5 x 10-7) with the multifocal (heritability= 0.075) and the diffuse (heritability= 0.189) lesions, respectively. Some of the identified QTLs overlapped with QTLs previously associated with PTB, bovine tuberculosis, mastitis, and IgG levels. Pathway analysis with candidate genes overlapping the identified QTLs revealed a significant enrichment of the keratinization pathway and cholesterol metabolism in the animals with multifocal and diffuse lesions, respectively. While keratin variants may predispose cows to the development of multifocal lesions, cholesterol variants associate with the more severe lesions. Taken together, these findings suggest that the variation in MAP-associated pathological outcomes might be genetically determined and indicative of distinct host responses in genetically predisposed individuals.