Discovery of expression quantitative trait loci associated with Johne’s disease using both RNA-seq and DNA variants


Bissonnette, N., J.-S. Brouard, O. Ariel, N. Gévry, E. Ibeagha-Awemu, and F. Miglior. 2018. Discovery of expression quantitative trait loci associated with Johne’s disease using both RNA-seq and DNA variants. 11th World Congress on Genetics Applied to Livestock Production. February 10th-16th 2018, Auckland, New-Zealand.

Plain language summary

The bacterium that causes Johne's disease (JD), also known as paratuberculosis, is a mycobacterium. It can infect ruminants around the world. This infection is incurable and chronic. No treatment is currently available.

Genetic resistance to mycobacteria, including tuberculosis, has been reported. Genetic improvement is a slow, long-term process, but the results are permanent. The genetic gains made in a generation remain in future generations. The objective of this study was to identify genetic variations associated with susceptibility to paratuberculosis.

In this study, we sought to understand the mechanisms that cause the bacteria to take the cow's immune system hostage to hide and multiply. We spent a lot of time studying macrophages. This is a type of cell in which the bacteria is hiding to multiply. It has been said that since the mycobacterium takes the macrophage hostage and that genetic resistance exists, it would be wise to study the genetic variations of the macrophage. To do so, we read all the gene activity of these macrophages of cows negative and positive to the disease. This reading was performed with a new generation of high throughput sequencing. Thus, there are 1.2 million variations. It is very powerful. Of these variations, 161K have never been reported. Of the genetic variations seen in macrophages, 2,700 would have a significant impact on gene function. The genetic association study identified 288 markers associated with the disease.
Other tools allowed us to list the genes associated with these variations. It was thus possible to highlight various mechanisms that would be involved in the cell, including effects on the mitochondria, the energy engine of the cell. Thus, genetic variation would promote the persistence of the pathogen by influencing the behavior of macrophages in the long term. This study is the prayer of the genre.
In summary, genetic variations associated with bovine paratuberculosis have been identified in the immune cells of dairy cows. Our results contribute to a better understanding of immune cell control and survival mechanisms of mycobacteria.


Johne’s disease (JD) is a debilitating chronic disease in ruminants caused by Mycobacterium avium ssp. paratuberculosis (MAP) which manipulates gut macrophages as survival strategies and for its dissemination. The endemic situation of JD can be in part explained by the lack of genetic resistance to MAP infection in cattle populations. A successful genetic improvement strategy results from a comprehensive understanding of the genetic variability associated with disease susceptibility/resistance, while providing information about the affected biological pathways. In this functional genomics study, accurate phenotypic data (e.g. diagnosis records) for JD were used to identify 22 MAP-infected (JD(+)) and 28 healthy/resistant (JD(–)) cows. The transcriptome of their blood circulating primary macrophages were analysed using the next-generation RNA sequencing (RNA-Seq) technology. DNA genotypes were also identified using a complementary strategy: the BovineSNP50 DNAchip imputed to the high density (HD) DNAchip. More than 60% of the 1,356,248 variants (call rate ≥ 0.2, minor allele frequency ≥ 0.05) were identified by RNA-seq, among which 12% (161,951) were novel variants. Genome-wide association study identified two major expression quantitative trait loci (eQTL) on BTA4 and 11 at –log10 (P) ≥ 7. Interestingly, 2,435 RNA-seq variants are predicted to produce high functional effect on known genes, while only 33 DNA genotypes (HD) were found in this category. Network and pathway analysis using BovineMine from JD(+/–) macrophages revealed interesting cue regarding pathways that deserved further investigation (e.g. STAT transcription factor). RNA-Seq is an effective strategy to identify eQTL and thus increases the power to detect functional genetic variants. In the present study, we succeeded to identify eQTL and the regulatory pathways that discriminate MAP infected from healthy/resistant cows. Genetic variations in susceptible cows allow MAP to proliferate and escape the normal mycobacterial killing process of the macrophages. This strategy is thus highly relevant in genetic selection, as it may reduce disease susceptibility. An integration of the findings of this research (genomic information), into the conventional young sire selection and progeny testing program could yield a better, more accurate and rapid genetic improvement of resistance to bovine paratuberculosis in Canadian dairy herds.