Genome-wide association analysis identified both RNA-seq and DNA variants associated to paratuberculosis in Canadian Holstein cattle ‘in vitro’ experimentally infected macrophages

Citation

Ariel, O., Brouard, J.S., Marete, A., Miglior, F., Ibeagha-Awemu, E., Bissonnette, N. (2021). Genome-wide association analysis identified both RNA-seq and DNA variants associated to paratuberculosis in Canadian Holstein cattle ‘in vitro’ experimentally infected macrophages. BMC Genomics, [online] 22(1), http://dx.doi.org/10.1186/s12864-021-07487-4

Plain language summary

Potential of combining RNA and DNA sequencing to harvest SNP variants using naturally infected macrophages from Johne's diseased Canadian Holstein.
Johne's disease (JD) is an incurable ruminant disease. It causes irreversible economic hardships for dairy farmers because of veterinary costs, culling practices, and lost profits due to the loss of the infected cow's lifetime productivity potential. JD is caused by the bacteria: Mycobacterium avium subspecies paratuberculosis (MAP). The evidence for susceptibility to MAP disease points to multiple interacting factors, including the genetic predisposition to a malfunctioning immune system. Since there is no JD vaccine, a genetic improvement strategy can potentially reduce JD in the population. The first step would be to understand the link between genetic variability and the biological systems that MAP targets during its assault while dominating the specialized cells that detect and destroy bacteria in a cell (i.e., macrophages). A snapshot of all the genes (i.e. the transcriptome from RNA sequencing) at a given time can aid one to measure the response to MAP infection of the macrophages from cows that have been naturally infected and identified as JD positive in the form of single nucleotide polymorphisms (i.e. SNP variants). Such variants identified from a transcriptome analysis could potentially augment the DNA SNP variants, potentially harbouring a variation towards JD. This study identified 22 JD positive cows and 28 healthy (or resistant) cows and sequenced them using RNA sequencing and DNA sequencing techniques.
The complementary strategy allowed the identification of 1,356,248 genetic variants, including 814,168 RNA-seq and 591,220 DNA chip variants. 2,435 RNA-seq genetic variants were predicted to produce a high functional effect on known genes. Furthermore, a genome-wide association study revealed two quantitative traits loci highly associated with JD at chromosome 4 and 11 (P < 5 × 10-7). These variants also showed a potential biological influence on JD susceptibility, notably energy-dependent MTOR gene regulation, which is involved in cell survival, cell proliferation, and cell recycling (i.e. autophagy). This study is important because it identified genetic variants in the macrophages' regulatory pathways that may affect the susceptibility of healthy/resistant cows to MAP infection. The complementary use of RNA-seq data provides an unprecedented opportunity to investigate gene expression and link the genetic variations to biological pathways that MAP normally manipulate during killing macrophages. A strategy incorporating functional markers into genetic selection may significantly improve resistance to an incurable disease. Integrating these research findings into the conventional genetic selection program may allow faster and more lasting improvement in bovine paratuberculosis resistance in dairy cattle.

Abstract

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis, or Johne’s disease (JD), an incurable bovine disease. The evidence for susceptibility to MAP disease points to multiple interacting factors, including the genetic predisposition to a dysregulation of the immune system. The endemic situation in cattle populations can be in part explained by a genetic susceptibility to MAP infection. In order to identify the best genetic improvement strategy that will lead to a significant reduction of JD in the population, we need to understand the link between genetic variability and the biological systems that MAP targets in its assault to dominate macrophages. MAP survives in macrophages where it disseminates. We used next-generation RNA (RNA-Seq) sequencing to study of the transcriptome in response to MAP infection of the macrophages from cows that have been naturally infected and identified as positive for JD (JD (+); n = 22) or negative for JD (healthy/resistant, JD (−); n = 28). In addition to identifying genetic variants from RNA-seq data, SNP variants were also identified using the Bovine SNP50 DNA chip.