Genome-wide association analysis for porcine reproductive and respiratory syndrome virus susceptibility traits in two genetic populations of pigs1

Candidate markers for enhanced host response to PRRS have scarce adverse effects on pigs' growth and production

BACKGROUND

Porcine Reproductive and Respiratory Syndrome (PRRS) is one of the most challenging viral diseases that cause substantial economic losses in the pig industry worldwide. The clinical signs of PRRS depend on, among others, the immunomodulatory properties of the PRRS virus strain, farm health status, herd immunity, and host genetics. The high virulence and mutation rate of PRRS virus limit the efficacy of vaccination programs. In recent years, several candidate genetic markers associated with PRRS resilience have been identified, and selective breeding was suggested as an additional approach to control PRRS under field conditions. Even so, it is essential to investigate the effects of these genetic markers on pigs' productivity. Our study aimed to assess the association between seven previously reported candidate genetic markers for host response to PRRS (rs80800372 in GBP1, rs340943904 in GBP5, rs322187731 in GBP6, rs1107556229 in CD163, rs338508371 in SGK1, rs80928141 in TAP1, and a 275-bp insertion in the promoter of MX1) and production traits in pigs under non-challenging conditions.

RESULTS

About 600 high-health Duroc pigs were genotyped for the selected genetic markers and their effects on production traits (live body weight, carcass weight, backfat thickness, intramuscular fat content and composition) were assessed using a linear model. The genetic markers GBP5_rs340943904, GBP6_rs322187731, CD163_rs1107556229, and the 275-bp insertion at the promoter of MX1 showed no relevant associations with growth and carcass traits at slaughter. Regarding GBP1_rs80800372 (WUR1000125), the favourable G allele for PRRS resilience displayed significant additive effects on backfat thickness (+ 1.18 ± 0.42 mm; p = 0.005) and lean content (-1.72 ± 0.56%; p ≤ 0.01) at slaughter. In addition, the genetic markers SGK1_rs338508371 and TAP1_rs8092814 were associated with the palmitoleic content in gluteus medius, without affecting the total of the monounsaturated fatty acids.

CONCLUSIONS

Our results indicate that genetic markers for PRRS resilience have no relevant effects on growth and carcass traits in pigs reared under non-challenging conditions, except for GBP1_rs80800372 where the favourable allele for PRRS response has a negative impact on lean content. Therefore, since the effects of GBP1_rs80800372 were attributed to the causal variant GBP5_rs340943904, it seems beneficial to select pigs for the genetic marker at GBP5 instead of GBP1. Overall, pigs might be selected for enhanced PRRS resilience without compromising their overall productivity.

PRRSV-Vaccinated, Seronegative Sows and Maternally Derived Antibodies (I): Impact on PRRSV-1 Challenge Outcomes in Piglets

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) remains an infectious agent with high importance in the swine industry. In this study, the influence of maternally derived antibodies (MDAs) on an experimental PRRSV-1 challenge is investigated. Piglets included in the study (n = 36) originated from a Belgian farrow-to-finish herd in which the sow population was routinely vaccinated with a modified live vaccine against PRRSV. Eighteen piglets were born from three PRRSV-seropositive sows (responders to vaccination) and had a clear presence of PRRSV-specific MDAs (E+ piglets). The other eighteen piglets were born from three PRRSV-seronegative sows (non-responders to vaccination) and did not have PRRSV-specific MDAs (E- piglets). In each group, twelve piglets were intranasally challenged with a high dose of the heterologous PRRSV-1 07V063 strain, the remaining piglets were mock-challenged (PBS) and served as controls. During the first days after infection, higher serum viremia and nasal shedding were observed in the challenged E- piglets compared to the challenged E+ piglets. However, at 10 days post-infection, the peak serum viremia was significantly higher in the E+ piglets in comparison to the E- piglets and serum viremia remained slightly higher in this group until the end of the study. Additionally, the two challenged groups had a different immune response to the PRRSV infection. The E- challenged piglets showed an earlier and more intense seroconversion, leading to significantly higher antibody titers at 10 dpi compared to the E+ challenged piglets. Furthermore, a trend towards both higher induction of serum IFN-γ and higher induction of IFN-γ secreting cells was observed in the E- challenged piglets. In contrast, a significantly higher induction of serum TNF-α at 7 dpi was seen in the E+ challenged piglets compared to the E- challenged piglets. The results gathered in this study suggest that PRRSV-specific MDAs induce partial protection during the early stages of infection but are not sufficient to protect against a high challenge dose. The presence of piglets lacking PRRSV-specific MDAs might pose a risk for PRRSV infection and enhanced transmission in pig farms in young piglets.

Role of genetic factors in different swine breeds exhibiting varying levels of resistance/susceptibility to PRRSV

Porcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), is an economically significant contagious disease. Traditional approaches based on vaccines or medicines were challenging to control PRRSV due to the diversity of viruses. Different breeds of pigs infected with PRRSV have been reported to have different immune responses. However, due to the complexity of interaction mechanism between host and PRRSV, the genetic mechanism leading to PRRSV susceptibility/resistance in various pig breeds is still unclear. Herein, the role of host genetic components in PRRSV susceptibility is systematically described, and the molecular mechanisms by which host genetic factors such as SNPs, cytokines, receptor molecules, intestinal flora, and non-coding RNAs regulate PRRSV susceptibility/resistance. Therefore, improving the resistance to disease of individual animals through disease-resistance breeding technology is of profound significance for uplifting the sustainable and healthy development of the pig industry.

Integrated time-series transcriptomic and metabolomic analyses reveal different inflammatory and adaptive immune responses contributing to host resistance to PRRSV

Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly contagious disease that affects the global pig industry. To understand mechanisms of susceptibility/resistance to PRRSV, this study profiled the time-serial white blood cells transcriptomic and serum metabolomic responses to PRRSV in piglets from a crossbred population of PRRSV-resistant Tongcheng pigs and PRRSV-susceptible Large White pigs. Gene set enrichment analysis (GSEA) illustrated that PRRSV infection up-regulated the expression levels of marker genes of dendritic cells, monocytes and neutrophils and inflammatory response, but down-regulated T cells, B cells and NK cells markers. CIBERSORT analysis confirmed the higher T cells proportion in resistant pigs during PRRSV infection. Resistant pigs showed a significantly higher level of T cell activation and lower expression levels of monocyte surface signatures post infection than susceptible pigs, corresponding to more severe suppression of T cell immunity and inflammatory response in susceptible pigs. Differentially expressed genes between resistant/susceptible pigs during the course of infection were significantly enriched in oxidative stress, innate immunity and humoral immunity, cell cycle, biotic stimulated cellular response, wounding response and behavior related pathways. Fourteen of these genes were distributed in 5 different QTL regions associated with PRRSV-related traits. Chemokine CXCL10 levels post PRRSV infection were differentially expressed between resistant pigs and susceptible pigs and can be a promising marker for susceptibility/resistance to PRRSV. Furthermore, the metabolomics dataset indicated differences in amino acid pathways and lipid metabolism between pre-infection/post-infection and resistant/susceptible pigs. The majority of metabolites levels were also down-regulated after PRRSV infection and were significantly positively correlated to the expression levels of marker genes in adaptive immune response. The integration of transcriptome and metabolome revealed concerted molecular events triggered by the infection, notably involving inflammatory response, adaptive immunity and G protein-coupled receptor downstream signaling. This study has increased our knowledge of the immune response differences induced by PRRSV infection and susceptibility differences at the transcriptomic and metabolomic levels, providing the basis for the PRRSV resistance mechanism and effective PRRS control.

Transcriptional Analysis for Tuberculosis in Pregnant Women From the PRegnancy Associated Changes In Tuberculosis Immunology (PRACHITi) Study

A new tuberculosis (TB) diagnostic cartridge assay, which detects a 3-gene TB signature in whole blood, was not diagnostic in women with maternal TB disease in India (area under the curve [AUC] = 0.72). In a cohort of pregnant women, we identified a novel gene set for TB diagnosis (AUC = 0.97) and one for TB progression (AUC = 0.96).

Importance of the Major Histocompatibility Complex (Swine Leukocyte Antigen) in Swine Health and Biomedical Research

In pigs, the major histocompatibility complex (MHC), or swine leukocyte antigen (SLA) complex, maps to Sus scrofa chromosome 7. It consists of three regions, the class I and class III regions mapping to 7p1.1 and the class II region mapping to 7q1.1. The swine MHC is divided by the centromere, which is unique among mammals studied to date. The SLA complexspans between 2.4 and 2.7 Mb, depending on haplotype, and encodes approximately 150 loci, with at least 120 genes predicted to be functional. Here we update the whole SLA complex based on the Sscrofa11.1 build and annotate the organization for all recognized SLA genes and their allelic sequences. We present SLA nomenclature and typing methods and discuss the expression of SLA proteins, as well as their role in antigen presentation and immune, disease, and vaccine responses. Finally, we explore the role of SLA genes in transplantation and xenotransplantation and their importance in swine biomedical models.