Mapping quantitative trait loci for stress induced alterations in porcine leukocyte numbers and functions

Investigating the genetic architecture of disease resilience in pigs by genome-wide association studies of complete blood count traits collected from a natural disease challenge model

Background

Genetic improvement for disease resilience is anticipated to be a practical method to improve efficiency and profitability of the pig industry, as resilient pigs maintain a relatively undepressed level of performance in the face of infection. However, multiple biological functions are known to be involved in disease resilience and this complexity means that the genetic architecture of disease resilience remains largely unknown. Here, we conducted genome-wide association studies (GWAS) of 465,910 autosomal SNPs for complete blood count (CBC) traits that are important in an animal’s disease response. The aim was to identify the genetic control of disease resilience.

Results

Univariate and multivariate single-step GWAS were performed on 15 CBC traits measured from the blood samples of 2743 crossbred (Landrace × Yorkshire) barrows drawn at 2-weeks before, and at 2 and 6-weeks after exposure to a polymicrobial infectious challenge. Overall, at a genome-wise false discovery rate of 0.05, five genomic regions located on Sus scrofa chromosome (SSC) 2, SSC4, SSC9, SSC10, and SSC12, were significantly associated with white blood cell traits in response to the polymicrobial challenge, and nine genomic regions on multiple chromosomes (SSC1, SSC4, SSC5, SSC6, SSC8, SSC9, SSC11, SSC12, SSC17) were significantly associated with red blood cell and platelet traits collected before and after exposure to the challenge. By functional enrichment analyses using Ingenuity Pathway Analysis (IPA) and literature review of previous CBC studies, candidate genes located nearby significant single-nucleotide polymorphisms were found to be involved in immune response, hematopoiesis, red blood cell morphology, and platelet aggregation.

Conclusions

This study helps to improve our understanding of the genetic basis of CBC traits collected before and after exposure to a polymicrobial infectious challenge and provides a step forward to improve disease resilience.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07835-4.

Regulators of Salmonella-host interaction identified by peripheral blood transcriptome profiling: roles of TGFB1 and TRP53 in intracellular Salmonella replication in pigs

Peripheral blood transcriptome is an important intermediate data source for investigating the mechanism of Salmonella invasion, proliferation, and transmission. We challenged 4-week old piglets with Salmonella enterica serovar Typhimurium LT2 and investigated the peripheral blood gene expression profile before treatment (d0) and at 2 and 7 days post-inoculation (dpi) using deep sequencing. Regulator pathways were first predicted in silico and validated by wet-lab experiments. In total, 1255, 765, and 853 genes were differentially expressed between 2 dpi/d0, 7 dpi/d0, and 7 dpi/2 dpi, respectively. Additionally, 1333 genes showed a time effect during the investigated Salmonella infection period. Clustering analysis showed that the differentially expressed genes fell into six distinct expression clusters. Pathway annotation of these gene clusters showed that the innate immune system was first significantly upregulated at 2 dpi and then attenuated at 7 dpi. Toll-like receptor cascades, MyD88 cascade, phagosome pathway, cytokine signaling pathway, and lysosome pathway showed a similar expression pattern. Interestingly, we found that the ribosome pathway was significantly inhibited at 2 and 7 dpi. Gene expression regulation network enrichment analysis identified several candidate factors controlling the expression clusters. Further in vitro study showed that TGFB1 can inhibit Salmonella replication whereas TRP53 can promote Salmonella replication in porcine peripheral blood mononuclear cells and murine macrophages. These results provide new insights into the molecular mechanism of Salmonella-host interactions and clues for the genetic improvement of Salmonella infection resistance in pigs.

The Genetic Architecture of Domestication in Animals

Domestication has been essential to the progress of human civilization, and the process itself has fascinated biologists for hundreds of years. Domestication has led to a series of remarkable changes in a variety of plants and animals, in what is termed the “domestication phenotype.” In domesticated animals, this general phenotype typically consists of similar changes in tameness, behavior, size/morphology, color, brain composition, and adrenal gland size. This domestication phenotype is seen in a range of different animals. However, the genetic basis of these associated changes is still puzzling. The genes for these different traits tend to be grouped together in clusters in the genome, though it is still not clear whether these clusters represent pleiotropic effects, or are in fact linked clusters. This review focuses on what is currently known about the genetic architecture of domesticated animal species, if genes of large effect (often referred to as major genes) are prevalent in driving the domestication phenotype, and whether pleiotropy can explain the loci underpinning these diverse traits being colocated.

Transcriptomic analysis identifies candidate genes and functional networks controlling the response of porcine peripheral blood mononuclear cells to mitogenic stimulation

It is difficult to obtain phenotypic data on disease susceptibility directly from swine in an industry setting. The magnitude of the proliferative response of peripheral blood mononuclear cells (PBMC) to the T cell mitogen concanavalin A (Con A) has long been used as an indirect measure of the responsiveness of the immune system to antigenic stimulation. This trait is known to exhibit moderate heritability in swine, but little is known about the identity of the genes that control the response. In this study, we carried out a time-course microarray experiment to measure gene expression at 3 different stages (3, 20, and 68 h) poststimulation of PBMC with Con A. A total of 46, 452, and 418 differentially expressed (DifEx) genes were identified at each time point, respectively. Expression changes for a subset of these genes were subsequently confirmed by real-time PCR. Functional annotation analyses of the microarray results successfully identified sets of genes involved in processes associated with multiple aspects of cell division, such as DNA and protein synthesis, and control of mitosis. However, the discovery of genes that controlled the response of PBMC to mitogen was limited with this approach, because the drastic changes in the transcriptional program necessitated by cells undergoing division masked changes in smaller immune response gene sets. Pathway and network analyses that focused on immune cells proved to be a more effective strategy for the identification of genes that coordinate aspects of the mitogenic response that are specific to PBMC. The cytokine gene IL15 was shown to be central to the highest scoring network at 20 h and affect the expression of 16 other DifEx genes, including some genes known to regulate T cell activation, such as IL7R, JUN, TNFRSF9, and ZAP70. The IL15 gene maps to a previously identified QTL interval for immune responsiveness to Con A on SSC 8, which also contains the related IL2 gene. At 68 h, a distinct downregulation of major histocompatibility complex class II antigen presentation genes was observed. Overall, the gene expression profile of the Con A-stimulated porcine PBMC points to a Th(1) bias in immune activation. Further work is required to determine whether polymorphisms linked to genes identified in this study affect this immune response trait in pig populations and whether the trait itself correlates with decreased susceptibility to intracellular pathogens in swine.

Health and immune traits of Basque and Large White pigs housed in a conventional or enriched environment

Since decades, production traits such as growth rate, feed efficiency or body composition have been drastically increased in pigs by genetic selection. Whether this selection impacted animal robustness is still unclear. In this study, we compared Large White (LW) pigs, a breed submitted to intense genetic selection for production traits, and Basque (B) pigs, a local rustic breed, reared in two different housing environments (conventional v. enriched). Adaptation to housing conditions among each breed was evaluated at the level of endocrine and immune traits. These are known to be impacted by housing conditions and breed; however, the interaction effects between genotype and environment are less described. Animals (20 per breed and housing environment) entered the experiment at 35 kg of live weight. Levels of cortisol, acute-phase inflammatory proteins, immunoglobulins and hydrogen peroxide, blood formula, lymphocyte proliferation and in-vitro cytokine expression were measured at ∼115 kg of live weight. Animals were checked for skin injuries during the growing period. At slaughter, at the average live weight of 145 kg, carcasses were examined for pathological conditions of the respiratory tract. The major result was that the two breeds exhibited differences in response to the housing environment. Among the 24 sanitary, endocrine or immune traits investigated, the housing conditions affected eight variables in both breeds (salivary cortisol at 0700 and 1900 h, severity of pneumonia at slaughter) or only in B pigs (severe skin lesions) or LW pigs (salivary cortisol at 1500 h, granulocyte numbers and lymphocyte/granulocyte ratio and lymphocyte proliferation). These observations strengthen the hypothesis that selection for high meat production level might be associated with an increased susceptibility of animals to environmental stressors.

Genome-wide association study for T lymphocyte subpopulations in swine

Background

Lymphocytes act as a major component of the adaptive immune system, taking very crucial responsibility for immunity. Differences in proportions of T-cell subpopulations in peripheral blood among individuals under same conditions provide evidence of genetic control on these traits, but little is known about the genetic mechanism of them, especially in swine. Identification of the genetic control on these variants may help the genetic improvement of immune capacity through selection.

Results

To identify genomic regions responsible for these immune traits in swine, a genome-wide association study was conducted. A total of 675 pigs of three breeds were involved in the study. At 21 days of age, all individuals were vaccinated with modified live classical swine fever vaccine. Blood samples were collected when the piglets were 20 and 35 days of age, respectively. Seven traits, including the proportions of CD4+, CD8+, CD4+CD8+, CD4+CD8−, CD4−CD8+, CD4−CD8− and the ratio of CD4+ to CD8+ T cells were measured at the two ages. All the samples were genotyped for 62,163 single nucleotide polymorphisms (SNP) using the Illumina porcineSNP60k BeadChip. 40833 SNPs were selected after quality control for association tests between SNPs and each immune trait considered based on a single-locus regression model. To tackle the issue of multiple testing in GWAS, 10,000 permutations were performed to determine the chromosome-wise and genome-wise significance levels of association tests. In total, 61 SNPs with chromosome-wise significance level and 3 SNPs with genome-wise significance level were identified. 27 significant SNPs were located within the immune-related QTL regions reported in previous studies. Furthermore, several significant SNPs fell into the regions harboring known immunity-related genes, 14 of them fell into the regions which harbor some known T cell-related genes.

Conclusions

Our study demonstrated that genome-wide association studies would be a feasible way for revealing the potential genetics variants affecting T-cell subpopulations. Results herein lay a preliminary foundation for further identifying the causal mutations underlying swine immune capacity in follow-up studies.

Genome-wide association studies for hematological traits in swine

Improving immune capacity may increase the profitability of animal production if it enables animals to better cope with infections. Hematological traits play pivotal roles in animal immune capacity and disease resistance. Thus far, few studies have been conducted using a high-density swine SNP chip panel to unravel the genetic mechanism of the immune capability in domestic animals. In this study, using mixed model-based single-locus regression analyses, we carried out genome-wide association studies, using the Porcine SNP60 BeadChip, for immune responses in piglets for 18 hematological traits (seven leukocyte traits, seven erythrocyte traits, and four platelet traits) after being immunized with classical swine fever vaccine. After adjusting for multiple testing based on permutations, 10, 24, and 77 chromosome-wise significant SNPs were identified for the leukocyte traits, erythrocyte traits, and platelet traits respectively, of which 10 reached genome-wise significance level. Among the 53 SNPs for mean platelet volume, 29 are located in a linkage disequilibrium block between 32.77 and 40.59 Mb on SSC6. Four genes of interest are located within the block, providing genetic evidence that this genomic segment may be considered a candidate region relevant to the platelet traits. Other candidate genes of interest for red blood cell, hemoglobin, and red blood cell volume distribution width also have been found near the significant SNPs. Our genome-wide association study provides a list of significant SNPs and candidate genes that offer valuable information for future dissection of molecular mechanisms regulating hematological traits.

A genome-wide scan for quantitative trait loci affecting respiratory disease and immune capacity in Landrace pigs

Respiratory disease is the most important health concern for the swine industry. Genetic improvement for disease resistance is challenging because of the difficulty in obtaining good phenotypes related with disease resistance; however, identification of genes or markers associated with disease resistance can help in the genetic improvement of pig health. The purpose of our study was to investigate whether quantitative trait loci (QTL) associated with disease resistance were segregated in a purebred population of Landrace pigs that had been selected for meat production traits and mycoplasmal pneumonia of swine (MPS) scores over five generations. We analysed 1395 pigs from the base to the fifth generation of this population. Two respiratory disease traits [MPS scores and atrophic rhinitis (AR) scores] and 11 immune-capacity traits were measured in 630-1332 animals at 7 weeks of age and when the animal's body weight reached 105 kg. Each of the pigs, except sires in the base population, was genotyped using 109 microsatellite markers, and then, QTL analysis of the full-sib family population with a multi-generational pedigree structure was performed. Variance component analysis was used to detect QTL associated with MPS or AR scores, and the logarithm of odds (LOD) score and genotypic heritability of the QTL were estimated. Five significant (LOD > 2.51) and 18 suggestive (LOD > 1.35) QTL for respiratory disease traits and immune-capacity traits were detected. The significant QTL for Log-MPS score, located on S. scrofa chromosome 2, could explain 87% of the genetic variance of this score in this analysis. This is the first report of QTL associated with respiratory disease lesions.

Distinct peripheral blood RNA responses to Salmonella in pigs differing in Salmonella shedding levels: intersection of IFNG, TLR and miRNA pathways

Transcriptomic analysis of the response to bacterial pathogens has been reported for several species, yet few studies have investigated the transcriptional differences in whole blood in subjects that differ in their disease response phenotypes. Salmonella species infect many vertebrate species, and pigs colonized with Salmonella enterica serovar Typhimurium (ST) are usually asymptomatic, making detection of these Salmonella-carrier pigs difficult. The variable fecal shedding of Salmonella is an important cause of foodborne illness and zoonotic disease. To investigate gene pathways and biomarkers associated with the variance in Salmonella shedding following experimental inoculation, we initiated the first analysis of the whole blood transcriptional response induced by Salmonella. A population of pigs (n = 40) was inoculated with ST and peripheral blood and fecal Salmonella counts were collected between 2 and 20 days post-inoculation (dpi). Two groups of pigs with either low shedding (LS) or persistent shedding (PS) phenotypes were identified. Global transcriptional changes in response to ST inoculation were identified by Affymetrix Genechip® analysis of peripheral blood RNA at day 0 and 2 dpi. ST inoculation triggered substantial gene expression changes in the pigs and there was differential expression of many genes between LS and PS pigs. Analysis of the differential profiles of gene expression within and between PS and LS phenotypic classes identified distinct regulatory pathways mediated by IFN-γ, TNF, NF-κB, or one of several miRNAs. We confirmed the activation of two regulatory factors, SPI1 and CEBPB, and demonstrated that expression of miR-155 was decreased specifically in the PS animals. These data provide insight into specific pathways associated with extremes in Salmonella fecal shedding that can be targeted for further exploration on why some animals develop a carrier state. This knowledge can also be used to develop rational manipulations of genetics, pharmaceuticals, nutrition or husbandry methods to decrease Salmonella colonization, shedding and spread.

Mapping quantitative trait loci for T lymphocyte subpopulations in peripheral blood in swine

Background

Increased disease resistance through improved general immune capacity would be beneficial for the welfare and productivity of farm animals. T lymphocyte subpopulations in peripheral blood play an important role in immune capacity and disease resistance in animals. However, very little research to date has focused on quantitative trait loci (QTL) for T lymphocyte subpopulations in peripheral blood in swine.

Results

In the study, experimental animals consist of 446 piglets from three different breed populations. To identify QTL for T lymphocyte subpopulations in peripheral blood in swine, the proportions of CD4+, CD8+, CD4+CD8+, CD4+CD8-, CD4-CD8+, and CD4-CD8- T cells and the ratio of CD4+:CD8+ T cells were measured for all individuals before and after challenge with modified live CSF (classical swine fever) vaccine. Based on the combined data of individuals from three breed populations, genome-wide scanning of QTL for these traits was performed based on a variance component model, and the genome wide significance level for declaring QTL was determined via permutation tests as well as FDR (false discovery rate) correction. A total of 27 QTL (two for CD4+CD8+, one for CD4+CD8-, three for CD4-CD8+, two for CD4-CD8-, nine for CD4+, two for CD8+, and eight for CD4+:CD8+ ratio) were identified with significance level of FDR < 0.10, of which 11 were significant at the level of FDR < 0.05, including the five significant at FDR < 0.01.

Conclusions

Within these QTL regions, a number of known genes having potential relationships with the studied traits may serve as candidate genes for these traits. Our findings herein are helpful for identification of the causal genes underlying these immune-related trait and selection for immune capacity of individuals in swine breeding in the future.

Mapping quantitative trait loci for cytokines in the pig

Increased disease resistance through improved general immune capacity would be beneficial for the welfare and productivity of farm animals. Cytokines are essential diagnostic parameters in veterinary practice. To identify quantitative trait loci (QTL) for cytokine levels in serum in the pig, Interferon-gamma (IFN-γ) and Interleukin 10 (IL-10) levels and the ratio of IFN-γ to IL-10 were measured in a composite pig population, before and after challenge with modified live CSF (classical swine fever) vaccine. Through interval mapping using the variance component approach and the permutation test, 11 QTL (five for IFN-γ, two for IL-10 and four for the ratio of IFN-γ to IL-10) with significance levels of P < 0.10 were identified, of which five were significant at the P < 0.05 level. The most significant QTL (P < 0.01) was found on chromosome 16, with effect on the ratio of IFN-γ to IL-10. Within these QTL regions, a number of known genes were revealed and their potential relationships to the studied traits were discussed. Some of these genes may serve as candidate genes for these traits in swine.

Genetic control of host resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection

This manuscript focuses on the advances made using genomic approaches to identify biomarkers that define genes and pathways that are correlated with swine resistance to infection with porcine reproductive and respiratory syndrome virus (PRRSV), the most economically important swine viral pathogen worldwide. International efforts are underway to assess resistance and susceptibility to infectious pathogens using tools such as gene arrays, single nucleotide polymorphisms (SNPs) chips, genome-wide association studies (GWAS), proteomics, and advanced bioinformatics. These studies should identify new candidate genes and biological pathways associated with host PRRS resistance and alternate viral disease processes and mechanisms; they may unveil biomarkers that account for genetic control of PRRS or, alternately, that reveal new targets for therapeutics or vaccines. Previous genomic approaches have expanded our understanding of quantitative trait loci (QTL) controlling traits of economic importance in pig production, e.g., feed efficiency, meat production, leanness; only recently have these included health traits and disease resistance. Genomic studies should have substantial impact for the pig industry since it is now possible to include the use of biomarkers for basic health traits alongside broader set of markers utilized for selection of pigs for improved performance and reproductive traits, as well as pork quality. Additionally these studies may reveal alternate PRRS control mechanisms that can be exploited for novel drugs, biotherapeutics and vaccine designs.

Detection of quantitative trait loci affecting haematological traits in swine via genome scanning

BACKGROUND

Haematological traits, which consist of mainly three components: leukocyte traits, erythrocyte traits and platelet traits, play extremely important role in animal immune function and disease resistance. But knowledge of the genetic background controlling variability of these traits is very limited, especially in swine.

RESULTS

In the present study, 18 haematological traits (7 leukocyte traits, 7 erythrocyte traits and 4 platelet traits) were measured in a pig resource population consisting of 368 purebred piglets of three breeds (Landrace, Large White and Songliao Black Pig), after inoculation with the swine fever vaccine when the pigs were 21 days old. A whole-genome scan of QTL for these traits was performed using 206 microsatellite markers covering all 18 autosomes and the X chromosome. Using variance component analysis based on a linear mixed model and the false discovery rate (FDR) test, 35 QTL with FDR < 0.10 were identified: 3 for the leukocyte traits, 28 for the erythrocyte traits, and 4 for the platelet traits. Of the 35 QTL, 25 were significant at FDR < 0.05 level, including 9 significant at FDR < 0.01 level.

CONCLUSIONS

Very few QTL were previously identified for hematological traits of pigs and never in purebred populations. Most of the QTL detected here, in particular the QTL for the platelet traits, have not been reported before. Our results lay important foundation for identifying the causal genes underlying the hematological trait variations in pigs.

Mapping of quantitative trait loci for mycoplasma and tetanus antibodies and interferon-gamma in a porcine F(2) Duroc x Pietrain resource population

The aim of the present study was to detect quantitative trait loci (QTL) for innate and adaptive immunity in pigs. For this purpose, a Duroc x Pietrain F(2) resource population (DUPI) with 319 offspring was used to map QTL for the immune traits blood antibodies and interferon-gamma using 122 microsatellites covering all autosomes. Antibodies response to Mycoplasma hyopneumoniae and tetanus toxoid vaccine and the interferon-gamma (IFNG) serum concentration were measured at three different time points and were used as phenotypes. The differences of antibodies and interferon concentration between different time points were also used for the linkage mapping. Line-cross and imprinting QTL analysis, including two-QTL, were performed using QTL Express. A total of 30 QTL (12, 6, and 12 for mycoplasma, tetanus antibody, and IFNG, respectively) were identified at the 5% chromosome-wide-level significant, of which 28 were detected by line-cross and 2 by imprinting model. In addition, two QTL were identified on chromosome 5 using the two-QTL approach where both loci were in repulsion phase. Most QTL were detected on pig chromosomes 2, 5, 11, and 18. Antibodies were increased over time and immune traits were found to be affected by sex, litter size, parity, and month of birth. The results demonstrated that antibody and IFNG concentration are influenced by multiple chromosomal areas. The flanking markers of the QTL identified for IFNG on SSC5 did incorporate the position of the porcine IFNG gene. The detected QTL will allow further research in these QTL regions for candidate genes and their utilization in selection to improve the immune response and disease resistance in pig.

European wild boars and domestic pigs display different polymorphic patterns in the Toll-like receptor (TLR) 1, TLR2, and TLR6 genes

During the last decade, the Toll-like receptors (TLRs) have been extensively studied, and their immense importance in innate immunity is now being unveiled. Here, we report pronounced differences--probably reflecting the domestication process and differences in selective pressure--between wild boars and domestic pigs regarding single nucleotide polymorphisms (SNPs) in TLR genes. The open reading frames of TLR1, TLR2, and TLR6 were sequenced in 25 wild boars, representing three populations, and in 15 unrelated domestic pigs of Hampshire, Landrace, and Large White origin. In total, 20, 27, and 26 SNPs were detected in TLR1, TLR2, and TLR6, respectively. In TLR1 and TLR2, the numbers of SNPs detected were significantly lower (P < or = 0.05, P < or = 0.01) in the wild boars than in the domestic pigs. In the wild boars, one major high frequency haplotype was found in all three genes, while the same pattern was exhibited only by TLR2 in the domestic pigs. The relative frequency of non-synonymous (dN) and synonymous (dS) SNPs was lower for the wild boars than for the domestic pigs in all three genes. In addition, differences in diversity between the genes were revealed: the mean heterozygosity at the polymorphic positions was markedly lower in TLR2 than in TLR1 and TLR6. Because of its localization--in proximity of the bound ligand--one of the non-synonymous SNPs detected in TLR6 may represent species-specific function on the protein level. Furthermore, the codon usage pattern in the genes studied deviated from the general codon usage pattern in Sus scrofa.

Comparative genomics of Toll-like receptor signalling in five species

BACKGROUND

Over the last decade, several studies have identified quantitative trait loci (QTL) affecting variation of immune related traits in mammals. Recent studies in humans and mice suggest that part of this variation may be caused by polymorphisms in genes involved in Toll-like receptor (TLR) signalling. In this project, we used a comparative approach to investigate the importance of TLR-related genes in comparison with other immunologically relevant genes for resistance traits in five species by associating their genomic location with previously published immune-related QTL regions.

RESULTS

We report the genomic localisation of TLR1-10 and ten associated signalling molecules in sheep and pig using in-silico and/or radiation hybrid (RH) mapping techniques and compare their positions with their annotated homologues in the human, cattle and mouse whole genome sequences. We also report medium-density RH maps for porcine chromosomes 8 and 13. A comparative analysis of the positions of previously published relevant QTLs allowed the identification of homologous regions that are associated with similar health traits in several species and which contain TLR related and other immunologically relevant genes. Additional evidence was gathered by examining relevant gene expression and association studies.

CONCLUSION

This comparative genomic approach identified eight genes as potentially causative genes for variations of health related traits. These include susceptibility to clinical mastitis in dairy cattle, general disease resistance in sheep, cattle, humans and mice, and tolerance to protozoan infection in cattle and mice. Four TLR-related genes (TLR1, 6, MyD88, IRF3) appear to be the most likely candidate genes underlying QTL regions which control the resistance to the same or similar pathogens in several species. Further studies are required to investigate the potential role of polymorphisms within these genes.

Molecular genetics of the swine major histocompatibility complex, the SLA complex

The swine major histocompatibility complex (MHC) or swine leukocyte antigen (SLA) complex is one of the most gene-dense regions in the swine genome. It consists of three major gene clusters, the SLA class I, class III and class II regions, that span approximately 1.1, 0.7 and 0.5Mb, respectively, making the swine MHC the smallest among mammalian MHC so far examined and the only one known to span the centromere. This review summarizes recent updates to the Immuno Polymorphism Database-MHC (IPD-MHC) website (http://www.ebi.ac.uk/ipd/mhc/sla/) which serves as the repository for maintaining a list of all SLA recognized genes and their allelic sequences. It reviews the expression of SLA proteins on cell subsets and their role in antigen presentation and regulating immune responses. It concludes by discussing the role of SLA genes in swine models of transplantation, xenotransplantation, cancer and allergy and in swine production traits and responses to infectious disease and vaccines.

Quantitative trait loci for porcine white blood cells and platelet-related traits in a White Duroc x Erhualian F resource population

White blood cell count and platelets are implicated as risk factors for common complex diseases. Genetic factors substantially affect these traits in humans and mice. However, little is known about the genetic architecture of these traits in pigs. To identify quantitative trait loci (QTL) for leucocyte- and platelet-related traits in pigs, the total leucocyte number and differential leucocyte counts including the fraction of basophils, eosinophils, lymphocytes, monocytes, neutrophils, and a series of platelet parameters including platelet count, mean platelet volume, platelet distribution width and plateletcrit were measured in 1033 F(2) animals on 240 days from a White Duroc x Erhualian intercross resource population. A total of 183 informative microsatellites distributed across 19 pig chromosomes (SSC) were genotyped across the entire resource population. Thirty-three QTL were identified for the examined traits, including eight genome-wide significant QTL for white blood cells and differential leucocyte counts on SSC2, 7, 8, 12 and 15 and six significant QTL for platelet-related traits on SSC2, 8, 13 and X. Erhualian or White Duroc alleles were not systematically associated with increased phenotypic values. These results not only confirmed many QTL identified previously in the mouse and swine, but also revealed a number of novel QTL for the traits recorded. Moreover, it is the first time that QTL for platelet-related traits in pigs have been reported.

[Effects of 22 microsatellite DNA markers on stress traits in F2 population of pigs]

In the present study, we analyzed the effects of 22 microsatellite DNA loci on behavior responses and plasma concentration of hormones related to stress and metabolism following transport trial in pigs. These subjects were selected from the segregating F2 generation of a Pietrain (PIE) x Erhualian (EHL) cross, and the two swine strains differ in stress tolerance. A so-called Backtest Score (BS) at 3, 10 and 17 days after birth (BS3, BS10 and BS17) was implemented to assess the behavior responses for each piglet. Plasma concentrations of Insulin, ACTH, Cortisol, T3 and T4 in pigs were measured after the 2 hours' transport. One-way ANOVA was applied to analyze the relation between microsatellite polymorphisms and stress tolerance markers including BS and concentration of hormones. The results revealed that the allelic number was 3-8, heterozygosity was 0.4155-0.7432 and polymorphism information content was 0.3651-0.8150. SW1808 (P<0.01) and SW0320 (P<0.05) had significant effect on ACTH. The effect of SW1303 on Insulin, SW1092 on Cortisol, SW0320 on T3, S0101 on T4, and SW2446 on BS3 reached a significant level at P<0.05, respectively. The effects of SW2446 (P<0.01), SW1816 (P<0.05) and SW0092 (P<0.05) on BS10 were significant, and the effects of SW2108, SW1816 and SW1023 on BS17 were also significant (P<0.05). Our study suggested that these 11 microsatellites in swine were closely associated with behavior responses and stress tolerance in response to transport.

Quantitative trait loci for white blood cell numbers in swine

Differential white blood cell counts are essential diagnostic parameters in veterinary practice but knowledge on the genetic architecture controlling variability of leucocyte numbers and relationships is sparse, especially in swine. Total leucocyte numbers (Leu) and the differential leucocyte counts, i.e. the fractions of lymphocytes (Lym), polymorphonuclear leucocytes [neutrophils (Neu), eosinophils (Eos) and basophils (Bas)] and monocytes (Mon) were measured in 139 F(2) pigs from a Meishan/Pietrain family, before and after challenge with the protozoan pathogen Sarcocystis miescheriana for genome-wide quantitative trait loci (QTL) analysis. After infection, the pigs passed through three stages representing acute disease, reconvalescence and chronic disease. Nine genome-wide significant and 29 putative, single QTL controlling leucocyte traits were identified on 15 chromosomes. Because leucocyte traits varied with health and disease status, QTL influencing the leucocyte phenotypes showed specific health/disease patterns. Regions on SSC1, 8 and 12 contained QTL for baseline leucocyte traits. Other QTL regions reached control on leucocyte traits only at distinct stages of the disease model. Two-thirds of the QTL have not been described before. Single QTL explained up to 19% of the phenotypic variance in the F(2) animals. Related traits were partly under common genetic influence. Our analysis confirms that leucocyte trait variation is associated with multiple chromosomal regions.

Selection for lean growth and food intake leads to correlated changes in innate immune traits in Large White pigs

Genetic selection is well established as a means of improving productivity in pigs, but the effects of continued selection for increased performance on immunity are not well understood, nor are genetic relationships between performance and immunity. This study compared differences in the levels of a range of immune traits between lines of Large White pigs divergently selected for a number of productivity traits. Selection lines compared were highv. low lean growth under restricted feeding (31 high linev. 10 controlv. 38 low line pigs), high v. low lean growth underad libitumfeeding (18 high line v. 10 controlv. 19 low line pigs), and highv. low food intake (24 high linev. 26 low line pigs). Immune traits measured were total white blood cell numbers (WBC), and the numbers of leukocyte subsets: neutrophils, monocytes, eosinophils, lymphocytes, CD4+cells, CD8α+cells, B cells, γδ T cells and CD11R1+Natural killer (NK) cells. CD4+, γδ T cells and CD11R1+cells were subdivided into subpopulations that were positive or negative for the CD8α marker, and conventional CD8αhigh+cytotoxic T cells were also determined. Pigs were tested underad libitumfeeding conditions from 14 to 24 weeks, and immune traits were assessed at ages 18 and 24 weeks. Line differences were estimated using residual maximum likelihood techniques. Consistent differences in immune trait levels were evident between pigs previously selected for high and low lean growth under restricted feeding: at age 24 weeks, high line pigs had higher basal levels of WBC (39·6v. 27·8×106cells per ml, s.e.d. 2·09, for highv. low line pigs) mainly explained by higher levels of lymphocytes (25·5v. 17·3×106cells per ml, s.e.d. 1·54, for highv. low line pigs) with increased numbers of CD8α+cells (8·19v. 5·15×106cells per ml, s.e.d. 0·14) and CD11R1+cells (5·23v. 2·46×106cells per ml, s.e.d. 0·43), predominantly the CD11R1+CD8α?subpopulation ((3·20v. 1·64×106cells per ml, s.e.d. 0·11). High line pigs also had increased numbers of monocytes (2·64v. 1·83×106cells per ml, s.e.d. 0·35). Similar results were obtained at age 18 weeks. There were no consistent differences between divergent lines in pigs selected for lean growth underad libitumfeeding or food intake. This is the first report to demonstrate that selection for some aspects of performance can influence WBC and leukocyte subset numbers in pigs.

Relationship Between Immune Cell Phenotypes and Pig Growth in a Commercial Farm

The objective of this study was to evaluate the relationship between the level and function of circulating immune cells with average daily gain, live and carcass measurements, feed intake, and feed conversion. Production performance was monitored throughout the pig's lifetime. Pigs were moved in weekly batches through the nursery and growing/finishing rooms at specific target weights. Animals were individually weighed at birth and at weaning, and then every two weeks while they were "on test" until they were "off test" and sent to the slaughterhouse. At six to seven weeks of age, the pigs were bled in the nursery. The percentage of immune cell subsets and lymphocyte proliferation was estimated using swine monoclonal antibodies and flow cytometric analysis. The predictive effect of the immune cell subset markers and lymphocyte proliferation on production traits was statistically analyzed. The results indicated that the proportion of several peripheral cell subsets, including CD16+, CD2+/CD16+, and CD8+ lymphocytes, appear to predict growth during the entire productive life of the pig. Larger percentages of lymphocytes expressing CD16+ CD2+/CD16+, and CD8+receptors in blood resulted in a reduction in average daily gain. In addition, high percentages of SLA-DQ+ cells were associated with better carcass weight and feed conversion. The CD16+, CD2+/CD16+, CD8+, and SLA-DQ+/- cell subsets appear to be important biomarkers involved with the inherent ability of the pig to efficiently grow and produce better carcass weight in representative commercial environments.

A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17

Reverse or bidirectional Zoo-FISH suggests that synteny between porcine chromosome 12 (SSC12) and human chromosome 17 (HSA17) is completely conserved. The construction of a high-resolution radiation hybrid (RH) map for SSC12 provides a unique opportunity to determine whether chromosomal synteny is reflected at the molecular level by comparative gene mapping of SSC12 and HSA17. We report an initial, high-resolution RH map of SSC12 on the 12,000-rad IMNpRH2 panel using CarthaGene software. This map contains a total of 320 markers, including 20 microsatellites and 300 ESTs/genes, covering approximately 4836.9 cR12,000. The markers were ordered in 16 linkage groups at LOD 6.0 using framework markers previously mapped on the IMpRH7000-rad SSC12 and porcine genetic maps. Ten linkage groups ordered more than 10 markers, with the largest containing 101 STSs. The resolution of the current RH map is approximately 15.3 kb/cR on SSC12, a significant improvement over the second-generation EST SSC12 RH7000-rad map of 103 ESTs and 15 framework markers covering approximately 2287.2 cR7000. Compared to HSA17, six distinct segments were identified, revealing macro-rearrangements within the apparently complete synteny between SSC12 and HSA17. Further analysis of the order of 245 genes (ESTs) on HSA17 and SSC12 also revealed several micro-rearrangements within a synteny segment. A high-resolution SSC12 RH12,000-rad map will be useful in fine-mapping QTL and as a scaffold for sequencing this chromosome.

Confirmation of QTL on porcine chromosomes 1 and 8 influencing leukocyte numbers, haematological parameters and leukocyte function

A genome wide search in European Wild Boar x Swedish Yorkshire (W x Y) inter-cross pigs has earlier identified quantitative trait loci (QTL) for leucocyte number and function on porcine chromosomes 1 and 8 (SSC 1 and 8). To verify the involvement of these chromosomal regions in the regulation of haematocrit (Hem) and haemoglobin (Hb) levels, leucocyte numbers and in vitro leukocyte functions (mitogen induced proliferation and IL-2 production, virus induced interferon-alpha production and neutrophil phagocytosis), animals of different genetic backgrounds were analysed. The animals comprised a back-cross sire family (n=47) of W x Y pigs and six crossbred [Y x Landrace (L)] sire families (n=191). They were genotyped for 16 genetic markers and an interval analysis was performed. On SSC1, a QTL close to S0082 on the q-arm that influenced numbers of white blood cells in L x Y pigs and numbers of band neutrophils and CD8(+) cells in W x Y pigs was identified (P<or=0.01). An additional SSC1 QTL was identified on the p-arm close to S0008 with influence on numbers of CD2(+) cells in W x Y pigs (P<or=0.05). On SSC8, a QTL influencing Hb (P<or=0.01) and Hem (P<or=0.05) levels was identified close to KIT in the W x Y pigs. For L x Y pigs, a second QTL, distal to KIT and close to S0069, on SSC8 influenced the numbers of MHCII(+) cells and mitogen induced proliferation (P<or=0.05), whilst the QTL close to KIT influenced the number of IgM(+) cells in these pigs (P<or=0.05). The results confirm the involvement of earlier identified regions of SSC1 and SSC8 on porcine immune parameters and some candidate genes were suggested.

Innate immune traits differ between Meishan and Large White pigs

A panel of innate immune traits were compared between Meishan and Large White pigs. These pigs were of similar age and kept under the same environmental conditions to reduce non-genetically derived variation in immune traits. The animals were all apparently healthy and were not experimentally challenged with any pathogen during the study. The measures only required a small blood sample. Total white cell counts were similar between the pig breeds. However, the numbers of lymphocytes, neutrophils and monocytes differed significantly, with Meishans having higher neutrophil and monocyte counts and lower lymphocyte counts. Flow cytometric methods were used to determine quantitatively the characteristics and function of neutrophils and monocytes. Meishan neutrophils were smaller and less complex than Large White neutrophils, and phagocytosis of Escherichia coli and the ensuing oxidative burst was lower in Meishan neutrophils compared to Large White neutrophils. Monocyte phagocytosis of E. coli was significantly less than that of neutrophils in both breeds but the function of Meishan monocytes as measured by phagocytosis and tumour necrosis factor alpha (TNFalpha) release did not differ from that of Large White monocytes. Levels of acute phase proteins also differed between the breeds with a significantly higher proportion of Meishans having elevated serum amyloid A levels. However, Meishans had lower alpha(1)-acid glycoprotein levels than Large Whites and haptoglobin levels were similar. Such differences in innate immune traits may have implications in the resistance to infection by a broad range of pathogens and subsequent disease effects in these breeds. Further studies are warranted to investigate the genes underlying these traits.

Targeted construction of a high-resolution, integrated, comprehensive, and comparative map for a region specific to bovine chromosome 6 based on radiation hybrid mapping

To resolve a candidate chromosome region on the middle part of bovine chromosome 6 (BTA6) containing several different quantitative trait locus (QTL) intervals, we constructed a high-resolution, integrated, comprehensive, and comparative map using a 12,000-rad, whole-genome, cattle-hamster radiation hybrid (RH) panel. The RH map includes a total of 71 loci either selected from bovine and comparative maps or targeted directly from a microdissection library specific for the BTA6 region. All loci typed were placed in one linkage group at a lod score threshold of 4.0. The length of the comprehensive RH map, which is the first high-resolution RH map in cattle, spans 2568.8 cR(12,000). The order of markers obtained principally agrees with the order on published bovine genetic maps. Our RH map integrates markers as well as genes and ESTs available from several physical and genetic maps of BTA6 and the orthologous ovine chromosome 6, human chromosome 4, and mouse chromosomes 5/3. Comparative analysis confirms and refines current knowledge about conservation and rearrangements in corresponding chromosomal regions on BTA6. We identified and localized two new breakpoints for intrachromosomal rearrangements between human chromosome 4 and BTA6. This RH map is a powerful tool in all aspects of genetic, physical, transcript, and comparative mapping. Due to its links to the gene-dense maps of human and mouse, it can serve as a prerequisite to identify possible candidate genes for quantitative trait loci localized in the targeted BTA6 region.