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

Abstract

Background 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. Results The complementary strategy allowed the identification of 1,356,248 genetic variants, including 814,168 RNA-seq and 591,220 DNA chip variants. Annotation using SnpEff predicted that the 2435 RNA-seq genetic variants would produce high functional effect on known genes in comparison to the 33 DNA chip variants. Significant variants from JD(+/−) macrophages were identified by genome-wide association study and revealed two quantitative traits loci: BTA4 and 11 at (P < 5 × 10− 7). Using BovineMine, gene expression levels together with significant genomic variants revealed pathways that potentially influence JD susceptibility, notably the energy-dependent regulation of mTOR by LKB1-AMPK and the metabolism of lipids. Conclusion In the present study, we succeeded in identifying genetic variants in regulatory pathways of the macrophages that may affect the susceptibility of cows that are healthy/resistant to MAP infection. RNA-seq provides an unprecedented opportunity to investigate gene expression and to link the genetic variations to biological pathways that MAP normally manipulate during the process of killing macrophages. A strategy incorporating functional markers into genetic selection may have a considerable impact in improving resistance to an incurable disease. Integrating the findings of this research into the conventional genetic selection program may allow faster and more lasting improvement in resistance to bovine paratuberculosis in dairy cattle.

Modeling Paratuberculosis in Laboratory Animals, Cells or Tissues: Focus on Their Applications for Pathogenesis, Diagnosis, Vaccines and Therapies Studies

“…The importance of host genetics has been further demonstrated in studies that have showed that the ability of MDMs to limit MAP viability is associated with specific genetic profiles [75]. Many studies have identified genetic variants in the regulatory pathways of the macrophages that may affect the susceptibility of cows that are healthy/resistant to MAP infection [76,77]. All these studies support the use of genomic and transcriptomic approaches to enable the identification of the markers associated particularly with susceptibility to MAP infection.…”

Complete Genome Sequence of Lacticaseibacillus paracasei Strain VHProbi O44, Isolated from Feces from a Healthy Baby

“…Strain VHProbi O44 was cultured using the same method as for isolation to extract genomic DNA. Total DNA was extracted using a genomic DNA purification kit (Promega, USA) ( 2 ). DNA samples were quality controlled using a TBS-380 fluorometer (Turner BioSystems Inc.), and high-quality DNA was used for further research ( 3 ).…”

Response to Oxidative Burst-Induced Hypoxia Is Associated With Macrophage Inflammatory Profiles as Revealed by Cellular Genome-Wide Association

“…This concept in human studies is known as familial GWAS or GWAS on isolated population (62). In cattle, 50 samples and less were successfully used in a genome-wide eQTL mapping analysis and GWAS (63,64).…”