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

A comprehensive review of livestock development: insights into domestication, phylogenetics, diversity, and genomic advances

Livestock plays an essential role in sustaining human livelihoods, offering a diverse range of species integral to food security, economic stability, and cultural traditions. The domestication of livestock, which began over 10,000 years ago, has driven significant genetic changes in species such as cattle, buffaloes, sheep, goats, and pigs. Recent advancements in genomic technologies, including next-generation sequencing (NGS), genome-wide association studies (GWAS), and genomic selection, have dramatically enhanced our understanding of these genetic developments. This review brings together key research on the domestication process, phylogenetics, genetic diversity, and selection signatures within major livestock species. It emphasizes the importance of admixture studies and evolutionary forces like natural selection, genetic drift, and gene flow in shaping livestock populations. Additionally, the integration of machine learning with genomic data offers new perspectives on the functional roles of genes in adaptation and evolution. By exploring these genomic advancements, this review provides insights into genetic variation and evolutionary processes that could inform future approaches to improving livestock management and adaptation to environmental challenges, including climate change.

Identification of Nonsynonymous SNPs in Immune-Related Genes Associated with Pneumonia Severity in Pigs

We previously showed that several polymorphisms in genes encoding pattern recognition receptors that cause amino acid substitutions alter pathogen recognition ability and disease susceptibility in pigs. In this study, we expanded our analysis to a wide range of immune-related genes and investigated polymorphism distribution and its influence on pneumonia in multiple commercial pig populations. Among the polymorphisms in 42 genes causing 634 amino acid substitutions extracted from the swine genome database, 80 in 24 genes were found to have a minor allele frequency of at least 10% in Japanese breeding stock pigs via targeted resequencing. Of these, 62 single nucleotide polymorphisms (SNPs) in 23 genes were successfully genotyped in 862 pigs belonging to four populations with data on pneumonia severity. Association analysis using a generalized linear mixed model revealed that 12 SNPs in nine genes were associated with pneumonia severity. In particular, SNPs in the cellular receptor for immunoglobulin G FCGR2B and the intracellular nucleic acid sensors IFI16 and LRRFIP1 were found to be associated with mycoplasmal pneumonia of swine or porcine pleuropneumonia in multiple populations and may therefore have wide applications in the improvement of disease resistance in pigs. Functional analyses at the cellular and animal levels are required to clarify the mechanisms underlying the effects of these SNPs on disease susceptibility.

Elucidation of novel SNPs affecting immune response to classical swine fever vaccination in pigs using immunogenomics approach

The host genetic makeup plays a significant role in causing the within-breed variation among individuals after vaccination. The present study was undertaken to elucidate the genetic basis of differential immune response between high and low responder Landlly (Landrace X Ghurrah) piglets vis-à-vis CSF vaccination. For the purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measure of humoral immune response. Double-digestion restriction associated DNA (ddRAD) sequencing was undertaken on 96 randomly chosen Landlly piglets using Illumina HiSeq platform. SNP markers were called using standard methodology. Genome-wide association study (GWAS) was undertaken in PLINK program to identify the informative SNP markers significantly associated with differential immune response. The results revealed significant SNPs associated with E2 antibody response against CSF vaccination. The genome-wide informative SNPs for the humoral immune response against CSF vaccination were located on SSC10, SSC17, SSC9, SSC2, SSC3 and SSC6. The overlapping and flanking genes (500Kb upstream and downstream) of significant SNPs were CYB5R1, PCMTD2, WT1, IL9R, CD101, TMEM64, TLR6, PIGG, ADIPOR1, PRSS37, EIF3M, and DNAJC24. Functional enrichment and annotation analysis were undertaken for these genes in order to gain maximum insights into the association of these genes with immune system functionality in pigs. The genetic makeup was associated with differential immune response against CSF vaccination in Landlly piglets while the identified informative SNPs may be used as suitable markers for determining variation in host immune response against CSF vaccination in pigs.

Genomic Association Analysis of Growth and Backfat Traits in Large White Pigs

The pig industry is significantly influenced by complex traits such as growth rate and fat deposition, which have substantial implications for economic returns. Over the years, remarkable genetic advancements have been achieved through intense artificial selection to enhance these traits in pigs. In this study, we aimed to investigate the genetic factors that contribute to growth efficiency and lean meat percentages in Large White pigs. Specifically, we focused on analyzing two key traits: age at 100 kg live weight (AGE100) and backfat thickness at 100 kg (BF100), in three distinct Large White pig populations-500 Canadian, 295 Danish, and 1500 American Large White pigs. By employing population genomic techniques, we observed significant population stratification among these pig populations. Utilizing imputed whole-genome sequencing data, we conducted single population genome-wide association studies (GWAS) as well as a combined meta-analysis across the three populations to identify genetic markers associated with the aforementioned traits. Our analyses highlighted several candidate genes, such as CNTN1-which has been linked to weight loss in mice and is potentially influential for AGE100-and MC4R, which is associated with obesity and appetite and may impact both traits. Additionally, we identified other genes-namely, PDZRN4, LIPM, and ANKRD22-which play a partial role in fat growth. Our findings provide valuable insights into the genetic basis of these important traits in Large White pigs, which may inform breeding strategies for improved production efficiency and meat quality.

Polymorphisms in Pattern Recognition Receptor Genes Are Associated with Respiratory Disease Severity in Pig Farms

Reduced productivity caused by infections, particularly respiratory diseases, is a serious problem in pig farming. We have previously reported polymorphisms in porcine pattern recognition receptor genes affecting molecular functions and demonstrated that the 2197A/C polymorphism in the nucleotide-binding oligomerization domain containing 2 (NOD2) gene influences porcine circovirus 2-induced mortality. Here, we investigated how these polymorphisms affect respiratory disease-induced lesions, using samples from a slaughterhouse dealing with pigs from two farms. Lung lesions were evaluated using two scoring systems, Goodwin (GW) and slaughterhouse pleuritis evaluation system (SPES), to determine the influence of Mycoplasma hyopneumoniae (Mhp) and Actinobacillus pleuropneumoniae (App), respectively. SPES scores were significantly higher when the 1205T allele of Toll-like receptor 5 (TLR5-1205T), rather than TLR5-1205C, was present. On the farm with more severe Mhp invasion, lower GW lesion scores were significantly associated with the presence of the NOD-like receptor family pyrin domain containing 3 (NLRP3)-2906G allele; where App invasion was worse, lower SPES scores were significantly associated with the presence of the NOD2-2197C allele. Combinations of polymorphisms in pattern recognition receptor genes can therefore be utilized for breeding for resistance against respiratory diseases in pigs. DNA markers of these polymorphisms can thus be used to improve productivity by reducing respiratory diseases due to bacterial pathogens in pig livestock.

GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data

Total number born (TNB), number of stillborn (NSB), and gestation length (GL) are economically important traits in pig production, and disentangling the molecular mechanisms associated with traits can provide valuable insights into their genetic structure. Genotype imputation can be used as a practical tool to improve the marker density of single-nucleotide polymorphism (SNP) chips based on sequence data, thereby dramatically improving the power of genome-wide association studies (GWAS). In this study, we applied Beagle software to impute the 50 K chip data to the whole-genome sequencing (WGS) data with average imputation accuracy (R2) of 0.876. The target pigs, 2655 Large White pigs introduced from Canadian and French lines, were genotyped by a GeneSeek Porcine 50K chip. The 30 Large White reference pigs were the key ancestral individuals sequenced by whole-genome resequencing. To avoid population stratification, we identified genetic variants associated with reproductive traits by performing within-population GWAS and cross-population meta-analyses with data before and after imputation. Finally, several genes were detected and regarded as potential candidate genes for each of the traits: for the TNB trait: NOTCH2, KLF3, PLXDC2, NDUFV1, TLR10, CDC14A, EPC2, ORC4, ACVR2A, and GSC; for the NSB trait: NUB1, TGFBR3, ZDHHC14, FGF14, BAIAP2L1, EVI5, TAF1B, and BCAR3; for the GL trait: PPP2R2B, AMBP, MALRD1, HOXA11, and BICC1. In conclusion, expanding the size of the reference population and finding an optimal imputation strategy to ensure that more loci are obtained for GWAS under high imputation accuracy will contribute to the identification of causal mutations in pig breeding.

[Opportunities and risks of the use of genetic resistances to infectious diseases in pigs - an overview]

Demands for health, performance and welfare in pigs, as well as the desire for consumer protection and reduced antibiotic use, require optimal measures in advance of disease development. This includes, in principle, the use of genetically more resistant lines and breeding animals, whose existence has been proven for a wide range of pathogen-host interactions. In addition, attempts are being made to identify the gene variants responsible for disease resistance in order to force the selection of suitable populations, also using modern biotechnical technics. The present work is intended to provide an overview of the research status achieved in this context and to highlight opportunities and risks for the future.The evaluation of the international literature shows that genetic disease resistance exist in many areas of swine diseases. However, polygenic inheritance, lack of animal models and the influence of environmental factors during evaluation render their implementation in practical breeding programs demanding. This is where modern molecular genetic methods, such as Gene Editing, come into play. Both approaches possess their pros and cons, which are discussed in this paper. The most important infectious diseases in pigs, including general diseases and epizootics, diseases of the respiratory and digestive tract and diseases of the immune system are taken into account.

Genome-wide association studies for production, respiratory disease, and immune-related traits in Landrace pigs

Identification of a quantitative trait locus (QTL) related to a chronic respiratory disease such as Mycoplasmal pneumonia of swine (MPS) and immune-related traits is important for the genetic improvement of disease resistance in pigs. The objective of this study was to detect a novel QTL for a total of 22 production, respiratory disease, and immune-related traits in Landrace pigs. A total of 874 Landrace purebred pigs, which were selected based on MPS resistance, were genotyped using the Illumina PorcineSNP60 BeadChip. We performed single nucleotide polymorphism (SNP)-based and haplotype-based genome-wide association studies (GWAS) to detect a novel QTL and to evaluate the possibility of a pleiotropic QTL for these traits. SNP-based GWAS detected a total of six significant regions in backfat thickness, ratio of granular leucocytes to lymphatic cells, plasma concentration of cortisol at different ages, and complement alternative pathway activity in serum. The significant region detected by haplotype-based GWAS was overlapped across the region detected by SNP-based GWAS. Most of these detected QTL regions were novel regions with some candidate genes located in them. With regard to a pleiotropic QTL among traits, only three of these detected QTL regions overlapped among traits, and many detected regions independently affected the traits.

A specific promoter-type in ribonuclease L gene is associated with phagocytic activity in pigs

We have previously generated Large White pigs with high immune competence using a selection strategy based on phagocytic activity (PA), capacity of alternative complement pathway, and antibody response after vaccination against swine erysipelas. In this study, to identify the genetic changes caused by the immune selection pressure, we compared gene expression and polymorphisms in the promoter region between pigs subjected to the immune selection (immune-selected pigs) and those that were not (non-selected pigs). After lipid A stimulation, using a microarray analysis, 37 genes related to immune function and transcription factor activity showed a greater than three-fold difference in expression between macrophages derived from immune-selected and non-selected pigs. We further performed a polymorphic analysis of the promoter region of the differentially expressed genes, and elucidated the predominant promoter-types in the immune-selected and non-selected pigs, respectively, in the genes encoding ribonuclease L (RNASEL), sterile α motif and histidine-aspartate domain containing deoxynucleoside triphosphate triphosphohydrolase 1, signal transducer and activator of transcription 3, and tripartite motif containing 21. Analysis of the association between these promoter genotypes and the immune phenotypes revealed that the immune-selected promoter-type in RNASEL was associated with increased PA and was inherited recessively. Considering that RNASEL has been reported to be involved in antimicrobial immune response of mice, it may be possible to enhance the PA of macrophages and improve disease resistance in pig populations using RNASEL promoter-type as a DNA marker for selection.

A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders

Simple Summary

This study is a comprehensive review of genomic regions associated with animal behavior in farmed mammals (beef and dairy cattle, pigs, and sheep) which contributes to a better understanding of the biological mechanisms influencing the target indicator trait and to gene expression studies by suggesting genes likely controlling the trait, and it will be useful in optimizing genomic predictions of breeding values incorporating biological information. Behavioral mechanisms are complex traits, genetically controlled by multiple genes spread across the whole genome. The majority of the genes identified in cattle, pigs, and sheep in association with a plethora of behavioral measurements (e.g., temperament, terrain use, milking speed, tail biting, and sucking reflex) are likely controlling stimuli reception (e.g., olfactory), internal recognition of stimuli (e.g., neuroactive ligand–receptor interaction), and body response to a stimulus (e.g., blood pressure, fatty acidy metabolism, hormone signaling, and inflammatory pathways). Six genes were commonly identified between cattle and pigs. About half of the genes for behavior identified in farmed mammals were also identified in humans for behavioral, mental, and neuronal disorders. Our findings indicate that the majority of the genes identified are likely controlling animal behavioral outcomes because their biological functions as well as potentially differing allele frequencies between two breed groups (subjectively) clustered based on their temperament characteristics.

Abstract

The main objectives of this study were to perform a systematic review of genomic regions associated with various behavioral traits in the main farmed mammals and identify key candidate genes and potential causal mutations by contrasting the frequency of polymorphisms in cattle breeds with divergent behavioral traits (based on a subjective clustering approach). A total of 687 (cattle), 1391 (pigs), and 148 (sheep) genomic regions associated with 37 (cattle), 55 (pigs), and 22 (sheep) behavioral traits were identified in the literature. In total, 383, 317, and 15 genes overlap with genomic regions identified for cattle, pigs, and sheep, respectively. Six common genes (e.g., NR3C2, PITPNM3, RERG, SPNS3, U6, and ZFAT) were found for cattle and pigs. A combined gene-set of 634 human genes was produced through identified homologous genes. A total of 313 out of 634 genes have previously been associated with behavioral, mental, and neurologic disorders (e.g., anxiety and schizophrenia) in humans. Additionally, a total of 491 candidate genes had at least one statistically significant polymorphism (p-value < 0.05). Out of those, 110 genes were defined as having polymorphic regions differing in greater than 50% of exon regions. Therefore, conserved genomic regions controlling behavior were found across farmed mammal species and humans.

A 1.6 Mb region on SSC2 is associated with antibody response to classical swine fever vaccination in a mixed pig population

Classical Swine Fever (CSF) is a contagious viral disease of pigs which is endemic in several parts of the world, including India. Prophylactic vaccination using live attenuated vaccine is the preferred method of control. However, there is significant inter-individual variation in the antibody response to vaccination. In this study, we measured the E2 antibody blocking percentage after 21 days of CSF vaccination in a mixed pig population consisting of Landrace, indigenous Ghurrah pigs, and their crossbreds. A Genome Wide Association Study (GWAS) carried out using single-SNP and haplotype based methods detected a 1.6 Mb region on SSC2 (28.92-30.52 Mb) as significantly associated with antibody response to CSF vaccination. The significant region and 1 Mb flanking sequences encompass 3 genes - EIF3M, DNAJC24 and ARL14EP, which code for proteins involved in Pestivirus replication and host immune response system. Our results combined with previous studies on immune response of pigs present this region as a suitable candidate for future functional investigations.

Genomic Analysis of IgG Antibody Response to Common Pathogens in Commercial Sows in Health-Challenged Herds

Losses due to infectious diseases are one of the main factors affecting productivity in the swine industry, motivating the investigation of disease resilience-related traits for genetic selection. However, these traits are not expected to be expressed in the nucleus herds, where selection is performed. One alternative is to use information from the commercial level to identify and select nucleus animals genetically superior for coping with pathogen challenges. In this study, we analyzed the genetic basis of antibody (Ab) response to common infectious pathogens in health-challenged commercial swine herds as potential indicator traits for disease resilience, including Ab response to influenza A virus of swine (IAV), Mycoplasma hyopneumoniae (MH), porcine circovirus (PCV2), and Actinobacillus pleuropneumoniae (APP; different serotypes). Ab response was measured in blood at entry into gilt rearing, post-acclimation (∼40 days after entering the commercial herd), and parities 1 and 2. Heritability estimates for Ab response to IAV, MH, and PCV2 ranged from 0 to 0.76. Ab response to APP ranged from 0 to 0.40. The genetic correlation (r _G ) of Ab response to IAV with MH, PCV2, PRRSV, and APP_mean (average Ab responses for all serotypes of APP) were positive (>0.29) at entry. APP_mean was negatively correlated with PCV2 and MH at entry and parity 2 but positively correlated with MH at post-acclimation and parity 1. Genomic regions associated with Ab response to different APP serotypes were identified on 13 chromosomes. The region on chromosome 14 (2 Mb) was associated with several serotypes of APP, explaining up to 4.3% of the genetic variance of Ab to APP7 at entry. In general, genomic prediction accuracies for Ab response were low to moderate, except average Ab response to all infectious pathogens evaluated. These results suggest that genetic selection of Ab response in commercial sows is possible, but with variable success depending on the trait and the time-point of collection. Future work is needed to determine genetic correlations of Ab response with disease resilience, reproductive performance, and other production traits.

Omics Application in Animal Science-A Special Emphasis on Stress Response and Damaging Behaviour in Pigs

Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to record adequate phenotypes under field conditions. Second, damaging behaviours and stress susceptibility are complex traits, and their biology is not yet well understood. Dissecting complex traits into biologically better defined, heritable and easily measurable proxy traits and developing biomarkers will facilitate recording these traits in large numbers. High-throughput molecular technologies (“omics”) study the entirety of molecules and their interactions in a single analysis step. They can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways. Here, we provide a general overview of different omics approaches and we give examples of how these techniques could be applied to discover biomarkers. We discuss the genetic dissection of the stress response by different omics techniques and we provide examples and outline potential applications of omics tools to understand and prevent outbreaks of damaging behaviours.

Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs

BACKGROUND

Porcine respiratory disease is one of the most important health problems which causes significant economic losses.

OBJECTIVE

To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 SNPs in a total of 249 individuals based on genome-wide sequencing data.

METHODS

Genome comparison of three susceptibility to swine EP pig breeds (Jinhua, Erhualian and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using XP-EHH and FST statistical approaches identified 691 positively selected genes. Based on QTLs, GO terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma.

RESULTS

Most of these genes were tested by several methods including transcription analysis and candidated genes association study. Among these genes: CYP1A1 and CTNNB1 are involved in fertility; TGFBR3 plays a role in meat quality traits; WNT2, CTNNB1 and TCF7 take part in adipogenesis and fat deposition simultaneously; PLAUR (completely linked to AXL, r2=1) plays an essential role in the successful ovulation of matured oocytes in pigs; CLPSL2 (strongly linked to SPDEF, r2=0.848) is involved in male fertility.

CONCLUSION

These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provide insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

RNA-seq transcriptome profiling of porcine lung from two pig breeds in response to Mycoplasma hyopneumoniae infection

Background

Mycoplasma hyopneumoniae (Mhp) is the main pathogen causing respiratory disease in the swine industry. Mhp infection rates differ across pig breeds, with Chinese native pig breeds that exhibit high fecundity (e.g., Jiangquhai, Meishan, Erhualian) more sensitive than Duroc, Landrace, and other imported pig breeds. However, the genetic basis of the immune response to Mhp infection in different pig breeds is largely unknown.

Aims

The aims of this study were to determine the relative Mhp susceptibility of the Chinese native Jiangquhai breed compared to the Duroc breed, and identify molecular mechanisms of differentially expressed genes (DEGs) using an RNA-sequencing (RNA-seq) approach.

Methods

Jiangquhai and Duroc pigs were artificially infected with the same Mhp dose. The entire experiment lasted 28 days. Daily weight gain, Mhp-specific antibody levels, and lung lesion scores were measured to evaluate the Mhp infection susceptibility of different breeds. Experimental pigs were slaughtered on the 28th day. Lung tissues were collected for total RNA extraction. RNA-seq was performed to identify DEGs, which were enriched by gene ontology (GO) and the Kyoto Encyclopedia annotation of Genes and Genomes (KEGG) databases. DEGs were validated with real-time quantitative polymerase chain reaction (RT-qPCR).

Results

Infection with the same Mhp dose produced a more serious condition in Jiangquhai pigs than in Duroc pigs. Jiangquhai pigs showed poorer growth, higher Mhp antibody levels, and more serious lung lesions compared with Duroc pigs. RNA-seq identified 2,250 and 3,526 DEGs in lung tissue from Jiangquhai and Duroc pigs, respectively. The two breeds shared 1,669 DEGs, which were involved in immune-relevant pathways including cytokine-cytokine receptor interaction, PI3K-Akt signaling pathway, and chemokine signaling pathway. Compared to Jiangquhai pigs, more chemokines, interferon response factors, and interleukins were specifically activated in Duroc pigs; CXCL10, CCL4, IL6 and IFNG genes were significantly up-regulated, which may help Duroc pigs enhance immune response and reduce Mhp susceptibility.

Conclusion

This study demonstrated differential immune-related DEGs in lung tissue from the two breeds, and revealed an important role of genetics in the immune response to Mhp infection. The biological functions of these important DEGs should be further confirmed and maybe applied as molecular markers that improve pig health.

New insights into host adaptation to swine respiratory disease revealed by genetic differentiation and RNA sequencing analyses

Swine respiratory disease (SRD) causes massive economic losses in the swine industry and is difficult to control and eradicate on pig farms. Here, we employed population genetics and transcriptomics approaches to decipher the molecular mechanism of host adaptation to swine respiratory disease. We recorded two SRD-related traits, the enzootic pneumonia-like (EPL) score and lung lesion (LL) levels, and performed four body weight measurements, at ages of 150, 180, 240, and 300 days, in a Chinese Bamaxiang pig herd (n = 314) raised under consistent indoor rearing conditions. We divided these animals into disease-resistant and disease-susceptible groups based on the most likely effects of both SRD-related traits on their weight gain, and performed genetic differentiation analyses in these two groups. Significant loci showing the top 1% of genetic differentiation values, exceeding the threshold of p = 0.005 set based on 1,000-times permutation tests, were defined as candidate regions related to host resistance or susceptibility to SRD. We identified 107 candidate genes within these regions, which are mainly involved in the biological processes of immune response, fatty acid metabolism, lipid metabolism, and growth factor signaling pathways. Among these candidate genes, TRAF6, CD44, CD22, TGFB1, CYP2B6, and SNRPA were highlighted due to their central regulatory roles in host immune response or fat metabolism and their differential expression between healthy lung tissues and lung lesions. These findings advance our understanding of the molecular mechanisms of host resistance or susceptibility to respiratory disease in pigs and are of significance for the breeding pigs resistant to respiratory disease in the swine industry.

Genomewide association of piglet responses to infection with one of two porcine reproductive and respiratory syndrome virus isolates

Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease in the swine industry. Identification of host genetic factors that enable selection for improved performance during PRRS virus (PRRSV) infection would reduce the impact of this disease on animal welfare and production efficiency. We conducted genomewide association study (GWAS) analyses of data from 13 trials of approximately 200 commercial crossbred nursery-age piglets that were experimentally infected with 1 of 2 type 2 isolates of PRRSV (NVSL 97-7985 [NVSL] and KS2006-72109 [KS06]). Phenotypes analyzed were viral load (VL) in blood during the first 21 d after infection (dpi) and weight gain (WG) from 0 to 42 dpi. We accounted for the previously identified QTL in the region on SSC4 in our models to increase power to identify additional regions. Many regions identified by single-SNP analyses were not identified using Bayes-B, but both analyses identified the same regions on SSC3 and SSC5 to be associated with VL in the KS06 trials and on SSC6 in the NVSL trials ( < 5 × 10); for WG, regions on SSC5 and SSC17 were associated in the NVSL trials ( < 3 × 10). No regions were identified with either method for WG in the KS06 trials. Except for the region on SSC4, which was associated with VL for both isolates (but only with WG for NVSL), identified regions did not overlap between the 2 PRRSV isolate data sets, despite high estimates of the genetic correlation between isolates for traits based on these data. We also identified genomic regions whose associations with VL or WG interacted with either PRRSV isolate or with genotype at the SSC4 QTL. Gene ontology (GO) annotation terms for genes located near moderately associated SNP ( < 0.003) were enriched for multiple immunologically (VL) and metabolism- (WG) related GO terms. The biological relevance of these regions suggests that, although it may increase the number of false positives, the use of single-SNP analyses and a relaxed threshold also increased the identification of true positives. In conclusion, although only the SSC4 QTL was associated with response to both PRRSV isolates, genes near associated SNP were enriched for the same GO terms across PRRSV isolates, suggesting that host responses to these 2 isolates are affected by the actions of many genes that function together in similar biological processes.

Genome-wide association studies identify susceptibility loci affecting respiratory disease in Chinese Erhualian pigs under natural conditions

Prevalence of swine respiratory disease causes poor growth performance in and serious economic losses to the swine industry. In this study, a categorical trait of enzootic pneumonia-like (EPL) score representing the infection gradient of a respiratory disease, more likely enzootic pneumonia, was recorded in a herd of 332 Chinese Erhualian pigs. According to their EPL scores and the disease effect on weight gains, these pigs were grouped into controls (EPL score ≤ 1) and cases (EPL score > 1). The weight gain of the case group reduced significantly at days 180, 210, 240 and 300 as compared to the control group. The heritability of EPL score was estimated to be 0.24 based on the pedigree information using a linear mixed model. All 332 Erhualian pigs and their nine sire parents were genotyped with Illumina Porcine 60K SNP chips. Two genome-wide association studies were performed under a generalized linear mixed model and a case-control model respectively. In total, five loci surpassed the suggestive significance level (P = 2.98 × 10^-5 ) on chromosomes 2, 8, 12 and 14. CXCL6, CXCL8, KIT and CTBP2 were highlighted as candidate genes that might play important roles in determining resistance/susceptibility to swine EP-like respiratory disease. The findings advance understanding of the genetic basis of resistance/susceptibility to respiratory disease in pigs.

Association of swine leukocyte antigen class II haplotypes and immune-related traits in a swine line selected for resistance to mycoplasmal pneumonia

By selective breeding for five generations, a Landrace line has been recently established to improve resistance to mycoplasmal pneumonia of swine (MPS), daily gain (DG), back fat thickness (BF), and plasma cortisol concentrations (COR). To clarify the involvement of swine leukocyte antigen (SLA) polymorphisms in the selection process, we investigated possible associations of 11 SLA-class II haplotypes with selected traits or immune parameters. Pigs with the low-resolution SLA haplotype Lr-0.23 or Lr-0.13, which increased in frequency with the passage of generations, had less severe pathological lesions of MPS, increased leukocyte phagocytic activity, and higher white blood cell counts. In contrast, Lr-0.12 and Lr-0.2, which decreased in subsequent generations, were weakly associated with more severe pathological lesions of MPS. Therefore, in the studied Landrace line, the Lr-0.23 and Lr-0.13 haplotypes are potentially useful genetic markers for selecting and breeding animals with less severe pathological lesions of MPS.

Emerging Role of Corticosteroid-Binding Globulin in Glucocorticoid-Driven Metabolic Disorders

Glucocorticoid hormones (GCs) are critical for survival since they ensure the energy supply necessary to the body in an ever challenging environment. GCs are known to act on appetite, glucose metabolism, fatty acid metabolism, and storage. However, to be beneficial to the body, GC levels should be maintained in an optimal window of concentrations. Not surprisingly, conditions of GC excess or deficiency, e.g., Cushing's syndrome or Addison's disease, are associated with severe alterations of energy metabolism. Corticosteroid-binding globulin (CBG), through its high specific affinity for GCs, plays a critical role in regulating plasma GC levels and their access to target cells. Genetic studies in various species including humans have revealed that CBG is the major factor influencing interindividual genetic variability of plasma GC levels, both in basal and stress conditions. Some, but not all, of these genetic studies have also provided data linking CBG levels to body composition and insulin levels. The examination of CBG-deficient mice submitted to hyperlipidic diets unveiled specific roles for CBG in lipid storage and metabolism. An influence of CBG on appetite has not been reported but remains to be more finely analyzed. Finally, only male mice have been examined under high-fat diet, while obesity is affecting women even more than men. Overall, a role of CBG in GC-driven metabolic disorders is emerging in recent studies. Although subtle, the influence of CBG in these diseases could open the way to new therapeutic interventions since CBG is easily accessible in the blood.

Correlated responses of respiratory disease and immune capacity traits of Landrace pigs selected for Mycoplasmal pneumonia of swine (MPS) lesion

Five generations of Landrace pigs selected for average daily gain, backfat thickness, Mycoplasmal pneumonia of swine (MPS) lesion score, and plasma cortisol levels, was executed to decrease the MPS lesion score. Genetic parameters and correlated genetic responses for respiratory disease and peripheral blood immune traits were estimated in 1395 Landrace pigs. We estimated the negative genetic correlation of MPS lesion score with phagocytic activity (PA) at 7 weeks of age (-0.67). The breeding values of PA at 7 weeks of age and 105 kg body weight and the correlated selection response of the ratio of granular leukocytes to lymphocytes at 105 kg body weight were significantly increased, and sheep red blood cell-specific antibody production (AP) was significantly decreased in a selection-dependent manner. Increasing of natural immunological indicators (e.g. PA) and decreasing of humoral immunological indicator (e.g. AP) were observed due to genetically decreasing MPS lesion score.

Analysis of non-synonymous SNPs of the porcine SERPINA6 gene as potential causal variants for a QTL affecting plasma cortisol levels on SSC7

Recently, the SERPINA6 gene encoding corticosteroid-binding globulin (CBG) has been proposed as a candidate gene for a quantitative trait locus (QTL) affecting cortisol level on pig chromosome 7. The QTL was repeatedly detected in different lines, including a Piétrain × (German Landrace × German Large White) cross (PiF1) and purebred German Landrace (LR). In this study, we investigated whether the known non-synonymous polymorphisms c.44G>T, c.622C>T, c.770C>T, c.793G>A, c.832G>A and c.919G>A of SERPINA6 are sufficient to explain the QTL in these two populations. Our investigations revealed that SNPs c.44G>T, c.622C>T, c.793G>A and c.919G>A are associated with cortisol level in PiF1 (P < 0.01). Haplotype analysis showed that these associations are largely attributable to differences between a major haplotype carrying SNPs c.793G>A and c.919G>A and a haplotype carrying SNPs c.44G>T and c.622C>T. Furthermore, some SNPs, particularly c.44G>T and c.622C>T and the carrier haplotype, showed association with meat quality traits including pH and conductivity (P < 0.05). In LR, the non-synonymous SNPs segregate at very low frequency (<5%) and/or show only weak association with cortisol level (SNPs c.832G>A and c.919G>A; P < 0.05). These findings suggest that the non-synonymous SNPs are not sufficient to explain the QTL across different breeds. Therefore, we examined whether the expression of SERPINA6 is affected by cis-regulatory polymorphisms in liver, the major organ for CBG production. We found allelic expression imbalance of SERPINA6, which suggests that its expression is indeed affected by genetic variation in cis-acting elements. This represents candidate causal variation for future studies of the molecular background of the QTL.

Genetics of upper and lower airway diseases in the horse

Genetic predispositions for guttural pouch tympany, recurrent laryngeal neuropathy and recurrent airway obstruction (RAO) are well documented. There is also evidence that exercise-induced pulmonary haemorrhage and infectious diseases of the respiratory tract in horses have a genetic component. The clinical expression of equine respiratory diseases with a genetic basis results from complex interactions between the environment and the genetic make-up of each individual horse. The genetic effects are likely to be due to variations in several genes, i.e. they are polygenic. It is therefore unlikely that single gene tests will be diagnostically useful in these disorders. Genetic profiling panels, combining several genetic factors with an assessment of environmental risk factors, may have greater value, but much work is still needed to uncover diagnostically useful genetic markers or even causative variants for equine respiratory diseases. Nonetheless, chromosomal regions associated with guttural pouch tympany, recurrent laryngeal neuropathy and RAO have been identified. The association of RAO with other hypersensitivities and with resistance to intestinal parasites requires further study. This review aims to provide an overview of the available data and current thoughts on the genetics of equine airway diseases.

Characterization of the liver-macrophages isolated from a mixed primary culture of neonatal swine hepatocytes

We recently developed a novel procedure to obtain liver-macrophages in sufficient number and purity using a mixed primary culture of rat and bovine hepatocytes. In this study, we aim to apply this method to the neonatal swine liver. Swine parenchymal hepatocytes were isolated by a two-step collagenase perfusion method and cultured in T75 culture flasks. Similar to the rat and bovine cells, the swine hepatocytes retained an epithelial cell morphology for only a few days and progressively changed into fibroblastic cells. After 5–13 days of culture, macrophage-like cells actively proliferated on the mixed fibroblastic cell sheet. Gentle shaking of the culture flask followed by the transfer and brief incubation of the culture supernatant resulted in a quick and selective adhesion of macrophage-like cells to a plastic dish surface. After rinsing dishes with saline, the attached macrophage-like cells were collected at a yield of 10⁶ cells per T75 culture flask at 2–3 day intervals for more than 3 weeks. The isolated cells displayed a typical macrophage morphology and were strongly positive for macrophage markers, such as CD172a, Iba-1 and KT022, but negative for cytokeratin, desmin and a-smooth muscle actin, indicating a highly purified macrophage population. The isolated cells exhibited phagocytosis of polystyrene microbeads and a release of inflammatory cytokines upon lipopolysaccharide stimulation. This shaking and attachment method is applicable to the swine liver and provides a sufficient number of macrophages without any need of complex laboratory equipments.