A Genome-Wide Association Study for Tolerance to Paratuberculosis Identifies Candidate Genes Involved in DNA Packaging, DNA Damage Repair, Innate Immunity, and Pathogen Persistence

Abstract

Although the genetic susceptibility to diseases has been extensively studied, the genetic loci and the primary molecular and cellular mechanisms that control disease tolerance are still largely unknown. Bovine paratuberculosis (PTB) is an enteritis caused by Mycobacterium avium subsp. paratuberculosis (MAP). PTB affects cattle worldwide and represents a major issue on animal health. In this study, the associations between host genetic and PTB tolerance were investigated using the genotypes from 277 Spanish Holstein cows with two distinct phenotypes: cases) infected animals with positive PCR and bacteriological culture results but without lesions in gut tissues (N= 24), and controls) animals with negative PCR and culture results but with PTB-associated lesions (N= 253). DNA from peripheral blood of the study population was genotyped with the Bovine EuroG MD Bead Chip, and the corresponding genotypes were imputed to whole-genome sequencing (WGS) data. A genome-wide association study was performed using the WGS data and the defined phenotypes in a case-control approach. A total of 142 single nucleotide polymorphisms (SNPs) were associated (false discovery rate ≤ 0.05, P values between 1.5 × 10-7 and 5.7 × 10-7) with tolerance (heritability= 0.55). The 40 SNPs with P-values < 5 × 10-7 defined 9 QTLs and 98 candidate genes located on BTA4, BTA9, BTA16, BTA25, and BTA26. Some of the QTLs identified in this study overlap with QTLs previously associated with PTB, bovine tuberculosis, mastitis, somatic cell score, bovine diarrhea virus persistent infection, tick resistance, and length of productive life. Two candidate genes with important roles in DNA damage response (ERCC4 and RMI2) were identified on BTA25. Functional analysis using the 98 candidate genes revealed a significant enrichment of the DNA packaging process (TNP2/PRMI1/PRM2/PRM3). In addition, the TNF-signaling (bta04668; TRAF5/CREB5/CASP7/CHUK) and the toxoplasmosis (bta05145; TGFβ2/CHUK/CIITA/SOCS1) pathways were significantly enriched. Interestingly, the nuclear Factor NF-κβ Inhibitor Kinase Alpha (CHUK), a key molecule in the regulation of the NF-κB pathway, was enriched in both pathways. Taken together, our results define a distinct immunogenetic profile in the PTB-tolerant animals designed to control bacterial growth, modulate inflammation, limit tissue damage and increase repair, thus reducing the severity of the disease.

Genome-wide association studies for the identification of cattle susceptible and resilient to paratuberculosis

“…In our study, PTB-tolerant cows are infected animals with positive PCR and bacteriological culture results but without lesions in gut tissues. Our results suggest that there is genetic variation associated with PTB tolerance ( h 2 = 0.55) and that this variation is indicative of an immunogenic profile in the PTB tolerant animals designed to control bacterial growth, modulate inflammation, and limit tissue damage ( Figure 2 ) ( 56 ). Some of the identified QTLs overlapped with QTLs previously associated with PTB, bovine tuberculosis, mastitis, somatic cell score, bovine diarrhea virus persistent infection, tick resistance, and length of productive life.…”

“…Recently, we have searched for genetic loci associated with tolerance to PTB by using WGS data from infected Spanish Holstein cows with MAP detected by tissue PCR and bacteriological culture but without lesions in gut tissues and regional lymph nodes. A PTB tolerant animal was PCR and culture-positive (infected) but no lesions could be observed in the histopathological analysis of gut tissues (no disease) ( 56 ). Although an earlier paper described a GWAS for PTB tolerance ( 57 ) with a subsequent refinement of genetic regions associated with MAP tissue infection and tolerance to PTB ( 58 ), our GWAS is the first to complete an analysis of the genetic markers associated with tolerance to PTB using WGS data and epidemiological data based on three diagnostic tests; histopathology, tissue PCR, and bacteriological culture.…”

Can Infectious Disease Control Be Achieved without Antibiotics by Exploiting Mechanisms of Disease Tolerance?

“…Despite harboring similar viral loads, some individuals produce an attenuated immune response, surviving viral infection and thus suggestive of a role of disease tolerance (7274). Finally, the loci involved in the development of clinical Mycobacterium avium subspecies paratuberculosis disease in cattle were identified by Zanella et al (75) in 2011, and, more recently, several candidate genes involved in the repair of damaged DNA and tissues and modulation of inflammation and innate immunity were discovered (76). These experiments provide supporting evidence for disease tolerance playing a critical role in controlling the outcome of infection for diseases impacting the animal agriculture industry (Table II).…”

The Upregulation of Cathepsin G Is Associated with Resistance to Bovine Paratuberculosis

“…Purified genomic DNA was quantified spectrophotometrically and subsequently genotyped with the EuroG10K MD BeadChip at the molecular genetic laboratory service of the Spanish Federation of Holstein Cattle (CONAFE) using the Infinium iScan software for allele assignation (Illumina, San Diego, CA, USA). Genotypes obtained from this case–control population have been used previously for several GWAS studies [ 16 , 17 , 31 ].…”