Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data.

Maria Canive,Joseba M Garrido,Marta Alonso-Hearn,José Luis Lavín,Almudena Fernández,Patricia Vázquez,Oscar González-Recio,Ramón A Juste,Gerard Badia-Bringué,Rebecca Lee Smith

doi:10.1371/journal.pone.0256091

Abstract

Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms underlying susceptibility to PTB infection in cattle and might be used to develop national genetic evaluations for PTB in Spain.

Highlights

Paratuberculosis (PTB) or Johnes disease is a chronic enteritis of domestic and wild ruminants caused by Mycobacterium avium susbp. paratuberculosis (MAP)
A previous study combined the data from two Genome-wide association studies (GWAS) to identify loci associated with MAP tissue infection and humoral immune response [20], our study provides the first comparison of the genetic effects associated with different phenotypic measurements or diagnostic definitions in a common set of samples using whole-genome sequence (WGS) data
Combining phenotypes and WGS into a joint GWAS improved the power for detecting genetic associations in Spanish Holstein cattle

Summary

Introduction

Paratuberculosis (PTB) or Johnes disease is a chronic enteritis of domestic and wild ruminants caused by Mycobacterium avium susbp. paratuberculosis (MAP). In Europe and North America, PTB is considered endemic in dairy cattle, with herd prevalence estimates higher than 50% [1]. This can result in great economic losses to the dairy industry due to decreased milk production, weight loss, replacement cost, reduced slaughter value, a greater risk to other health problems, premature culling or death from the clinical disease, and the costs of veterinary expenses and control measures [2,3]. MAP bacilli have been detected in the intestines of patients with CD, ulcerative colitis, and IBD-associated colorectal cancer [7,8]

Objectives

Methods

Results

Discussion

Conclusion