The Role of the MYL4 Gene in Porcine Muscle Development and Its Molecular Regulatory Mechanisms

Muscle growth stands as a pivotal economic trait within pig production, governed by a complex interplay of multiple genes, each playing a role in its quantitative manifestation. Understanding the intricate regulatory mechanisms of porcine muscle development is crucial for enhancing both pork yield and quality. This study used the GSE99749 dataset downloaded from the GEO database, conducting a detailed analysis of the RNA-seq results from the longissimus dorsi muscle (LD) of Tibetan pigs (TP), Wujin pigs (WJ) and large white pigs (LW) at 60 days of gestation, representing diverse body sizes and growth rates. Comparative analyses between TPvsWJ and TPvsLW, along with differential gene expression (DEG) analysis, functional enrichment analysis, and protein-protein interaction (PPI) network analysis, revealed 1048 and 1157 significantly differentially expressed genes (p < 0.001) in TPvsWJ and TPvsLW, respectively. With stricter screening criteria, 37 DEGs were found to overlap between the 2 groups. PPI analysis identified MYL5, MYL4, and ACTC1 as the three core genes. This article focuses on exploring the MYL4 gene. Molecular-level experimental validation, through overexpression and interference of the MYL4 gene combined with EDU staining experiments, demonstrated that overexpression of MYL4 significantly promoted the proliferation of porcine skeletal muscle satellite cells (PSMSC), while interference with MYL4 inhibited their proliferation. Furthermore, by examining the effects of overexpressing and interfering with the MYL4 gene on the muscle hypertrophy marker Fst gene and the muscle degradation marker FOXO3 gene, the pivotal role of the MYL4 gene in promoting muscle growth and preventing muscle degradation was further confirmed. These findings offer a new perspective on the molecular mechanisms behind porcine muscle growth and development, furnishing valuable data and insights for muscle biology research.

Exploring the role of the CapG gene in hypoxia adaptation in Tibetan pigs

Introduction: The CapG gene, which is an actin-binding protein, is prevalent in eukaryotic cells and is abundantly present in various pathways associated with plateau hypoxia adaptation. Tibetan pigs, which have inhabited high altitudes for extended periods, provide an excellent research population for investigating plateau hypoxia adaptation. Results: This study focused on Tibetan pigs and Yorkshire pigs residing in Nyingchi, Tibet. The blood physiological data of Tibetan pigs were found to be significantly higher than those of Yorkshire pigs, including RBC, HGB, HCT, MCH, and MCHC. The SNP analysis of the CapG gene identified six sites with mutations only present in Tibetan pigs. Notably, the transcription factors at sites C-489T, C-274T, and A-212G were found to be altered, and these sites are known to be associated with hypoxia adaptation and blood oxygen transportation. The mRNA expression of the CapG gene exhibited highly significant differences in several tissues, with the target proteins predominantly higher in the Yorkshire pig compared to the Tibetan pig. Specifically, a notable difference was observed in the lung tissues. Immunohistochemistry analysis revealed high expression levels of CapG proteins in the lung tissues of both Tibetan and Yorkshire pigs, primarily localized in the cytoplasm and cell membrane. Conclusion: The CapG gene plays a significant role in regulating hypoxia adaptation in Tibetan pigs. This study provides a theoretical basis for the conservation and utilization of Tibetan pig resources, the breeding of highland breeds, epidemic prevention and control, and holds great importance for the development of the highland livestock economy.

Prevalence of hepatitis E virus genotype 4 of probable human origin in Tibetan pigs from the Qinghai-Tibetan Plateau, China

Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide. In 2018-2022, we investigated the presence of HEV RNA in 1233 stool samples collected in the Qinghai-Tibetan Plateau, including humans (16), Tibetan pigs (624), yaks (312), sheep (267), and dogs (14). HEV RNA was only detected in Tibetan pig faecal samples (18.27%, 114/624). To perform molecular characterization of HEV strains in Tibetan pigs, we obtained 21 complete HEV genome sequences between 2018 and 2022. Sequence comparisons showed that 21 HEV strains from Tibetan pigs shared the mean nucleotide identities with the reference HEV strains ranging between 82.9% and 94.9% and 89.3% and 92.1% similarities with human HEV strains. Phylogenetic analysis confirmed that all HEV strains were genotype 4, closely related to human HEV strains. Sequence recombinant analysis showed five potential recombinant strains identified in this study, of which SWU/D18/2018 (GenBank No. MK410044) was recombinant with human and swine HEV strains, located 6509-6878 nt from the recombination point. Based on the Bayesian evolutionary trees, we found that most HEV strains diverged later than human HEV (16 Tibetan pig HEV strains diverged later than 1979, and seven human HEV strains diverged earlier than 1979). Therefore, we speculated that the prevalence of HEV 4 in Tibetan pigs possibly originated from humans in the Qinghai-Tibetan Plateau.

Comparative evaluation of the fecal microbiota of adult hybrid pigs and Tibetan pigs, and dynamic changes in the fecal microbiota of hybrid pigs

The breed of pig can affect the diversity and composition of fecal microbiota, but there is a lack of research on the fecal microbiota of hybrid pigs. In this study, feces samples from Chuanxiang black pigs (a hybrid of Tibetan and Duroc pigs) aged 3 days (n = 24), 70 days (n = 31), 10 months (n = 13) and 2 years (n = 30) and Tibetan pigs aged 10 months (n = 14) and 2 years (n = 15) were collected and sequenced by 16S rRNA gene sequencing technology. We also measured the weight of all the tested pigs and found that the 10-month-old and two-year-old Chuanxiang black pigs weighed about three times the weight of Tibetan pigs of the same age. After comparing the genus-level microbiota composition of Tibetan pigs and Chuanxiang black pigs at 10 months and two years of age, we found that Treponema and Streptococcus were the two most abundant bacteria in Chuanxiang black pigs, while Treponema and Chirstensenellaceae_R.7_group were the two most abundant bacteria in Tibetan pigs. Prediction of microbial community function in adult Chuanxiang black pigs and Tibetan pigs showed changes in nutrient absorption, disease resistance, and coarse feeding tolerance. In addition, we also studied the changes in fecal microbiota in Chuanxiang black pigs at 3 days, 70 days, 10 months, and 2 years of age. We found that the ecologically dominant bacteria in fecal microbiota of Chuanxiang black pigs changed across developmental stages. For example, the highest relative abundance of 70-day-old Chuanxiang black pigs at the genus level was Prevotella. We identified specific microbiota with high abundance at different ages for Chuanxiang black pigs, and revealed that the potential functions of these specific microbiota were related to the dominant phenotype such as fast growth rate and strong disease resistance. Our findings help to expand the understanding of the fecal microbiota of hybrid pigs and provide a reference for future breeding and management of hybrid pigs.

Drug Susceptibility Test and Analysis of Quinolone Resistance Genes in Mycoplasma hyopneumoniae Vaccine Strains and Field Isolates from China

Background

Enrofloxacin is a commonly used animal-specific drug in veterinary clinics. However, this drug has no epidemiological cutoff values (ECVs/ECOFFs) for Mycoplasma hyopneumoniae in CLSI and EUCAST. Defining the epidemiological cutoff values (ECOFFs) of enrofloxacine to Mycoplasma hyopneumoniae (M. hyo) can inform an early detection of bacterial resistance to better manage the resistance prevention and also help in establishing drug resistance breakpoints;.

Methods

We determined the susceptibility breakpoint of M. hyo to enrofloxacin by the American Clinical and Laboratory Standards Institute (CLSI) standard method based on the PCR of vaccine strains and wild strains drug resistance genes;.

Results

Eighty strains of M.hyo isolated in Tibet were moderately sensitive (S) to tetracycline, florfenicol, spiramycin, erythromycin thiocyanate, tilmicosin, tiamulin, lincomycin, clindamycin, ofloxacin, enrofloxacin, gentamicin, amikacin, with MICs below 0.5 μg/mL. For vaccine 168L, RM48, and J strains, the susceptibility to the same antibacterial drugs was lower compared to the Tibetan isolates. The resistance of J strain to erythromycin thiocyanate was confirmed. Gene point mutation was confirmed in Quinolone Resistance Determining Regions (QRDR) of HNSH strain Topoisomerase IV subunit A, this finding is compared with the sequencing results of 168L strain reference sequence (Accession number: CP003131). Arg-Lys amino acid mutation (G921A and G1179A) was confirmed for the increase of MIC value involved in M.hyo to enrofloxacine;.

Conclusion

The cut-off value of M.hyo to enrofloxacin was set as 1 μg/mLby ECOFFinder XL 2010 V2.1.

Cryptosporidium infection induced the dropping of SCFAS and dysbiosis in intestinal microbiome of Tibetan pigs

The infection of Cryptosporidium in pigs causes digestive system ailments, diarrhea and weight loss serving as an economic burden, especially in newborn animals. The bacterial fermentation products of short-chain fatty acids have important roles in immune function, microbiota regulation, osmotic balance and metabolism. However, till now little knowledge is available about the effect of Cryptosporidium infection on microbiota and SCFAs in plateau pigs. Hence, we performed this study to explore the response of microbiota and SCFAs in the natural infection of Cryptosporidium in Tibetan pigs. Cryptosporidium positive (infected, G) and negative samples (healthy, J) in our previous study were used for high throughputsequencing and Gas Chromatography-Mass Spectrometer analysis. Over 81 000 and 74 000 filtered sequences were detected in healthy and infected Tibetan pigs, respectively. Lower sample richness and evenness were observed in Cryptosporidium infection, as alpha diversity analysis found that chao1 (p < 0.05), faith_pd (p < 0.05), and observed_features in group G were significantly lower than pigs in group J. A total of 4 and 27 significant different phyla and genera were found between group G and J. The changed genera were Psychrobacter, Desemzia, Succiniclasticum, Treponema, Campylobacter, Atopobium, Olsenella, Pediococcus, Peptococcus, Sharpea, Desulfovibrio, Acinetobacter, Rhodococcus, Anaerostipes, Turicibacter, Lactobacillus, RFN20, Phascolarctobacterium, Roseburia, Megasphaera, Streptococcus, Blautia, Lachnospira, rc4_4, Gemmiger, Dorea, Oribacterium and Prevotella, which affected the microbiota functions with 360 abundance changed enzymes, and pathways in L1, L2 and L3 levels of KEGG. The concentration of acetic acid (p < 0.01), butyric acid (p < 0.05) and caproic acid (p < 0.01) were lower in group G. In conclusion, the present study herein uncovered that the host responses to Cryptosporidium infection in Tibetan pigs with 27 of significantly changed genera decreased SCFAs in pigs, which may provide insights in further developing novel therapy against this protozoan.

Different feeding patterns affect meat quality of Tibetan pigs associated with intestinal microbiota alterations

This study aimed to investigate the effects of different feeding patterns on meat quality, gut microbiota and its metabolites of Tibetan pigs. Tibetan pigs with similar body weight were fed the high energy diets (HEP, 20 pigs) and the regular diets (RFP, 20 pigs), and free-ranging Tibetan pigs (FRP, 20 pigs) were selected as the reference. After 6 weeks of experiment, meat quality indexes of semitendinosus muscle (SM) and cecal microbiota were measured. The results of meat quality demonstrated that the shear force of pig SM in FRP group was higher than that in HEP and RFP groups (p < 0.001); the pH-value of SM in HEP pigs was higher at 45 min (p < 0.05) and lower at 24 h (p < 0.01) after slaughter than that in FRP and RFP groups; the SM lightness (L* value) of FRP pigs increased compared with RFP and HEP groups (p < 0.001), while the SM redness (a* value) of FRP pigs was higher than that of RFP group (p < 0.05). The free fatty acid (FA) profile exhibited that the total FAs and unsaturated FAs of pig SM in HEP and RFP groups were higher than those in FRP group (p < 0.05); the RFP pigs had more reasonable FA composition with higher n-3 polyunsaturated FAs (PUFAs) and lower n-6/n-3 PUFA ratio than HEP pigs (p < 0.05). Based on that, we observed that Tibetan pigs fed high energy diets (HEP) had lower microbial α-diversity in cecum (p < 0.05), and distinct feeding patterns exhibited a different microbial cluster. Simultaneously, the short-chain FA levels in cecum of FRP and RFP pigs were higher compared with HEP pigs (p < 0.05). A total of 11 genera related to muscle lipid metabolism or meat quality, including Alistipes, Anaerovibrio, Acetitomaculun, etc., were identified under different feeding patterns (p < 0.05). Spearman correlation analysis demonstrated that alterations of free FAs in SM were affected by the genera Prevotellaceae_NK3B31_group, Prevotellaceae UCG-003 and Christensenellaceae_R-7_group (p < 0.05). Taken together, distinct feeding patterns affected meat quality of Tibetan pigs related to gut microbiota alterations.

Alterations in gut microbiota improve SCFA production and fiber utilization in Tibetan pigs fed alfalfa diet

Tibetan pigs were thought to have good performances of rough feeding tolerance, which may be related to the gut microbiota. This study was conducted to investigate the changes of colonic microbiota contribute to fiber utilization in Tibetan pigs fed alfalfa supplementation diet compared with basal diet, and verified whether the microbial community in Tibetan pigs fed alfalfa diet was beneficial to utilize fiber using in vitro fermentation. A total of 40 Tibetan pigs were allocated into two groups and fed with a corn-soybean meal basal diet (CD) or a 50% alfalfa supplementation diet (AD) for 42d. Our results showed pigs fed CD diet improved carcass weight compared to pigs fed AD diet (p < 0.05), yet reduced the bacterial diversity (p < 0.05). Tibetan pigs fed CD diet increased certain pathogenic bacteria (Streptococcus) abundance (FDR < 0.05). Alfalfa consumption increased fiber-degrading bacteria abundance (UCG-005, Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, Alloprevotella, Marvinbryantia, and Anaerovibrio) in the colonic digesta (FDR < 0.05) and improved concentrations of acetate, propionate, butyrate, and total SCFA in colonic content (p < 0.05). Higher fermentation capacity of fecal microbiota from pig fed AD diet was verified by in vitro fermentation. Collectively, our results indicated that alfalfa supplementation in diets improved the abundance of fiber-degrading bacteria and SCFA production in the hindgut of Tibetan pig, as well as enhanced the fermentation capacity of fecal microbiota.

The Effects of Dietary Inclusion of Mulberry Leaf Powder on Growth Performance, Carcass Traits and Meat Quality of Tibetan Pigs

This research was conducted to study the effects of dietary inclusion of mulberry leaf powder (MLP) on growth performance, meat quality, antioxidant activity, and carcass traits of Tibetan pigs. Eighteen Tibetan pigs (33.8 ± 1.1 kg) were assigned to two treatment groups randomly and received either the control diet (CON) or a basal diet containing 8% MLP (MLP) for two months. After the two-month feeding trial, the MLP group showed lower backfat thickness while a higher lean percentage. Compared with CON pigs, MLP pigs had higher serum CAT activity. In addition, dietary MLP supplementation significantly decreased the muscle shear force. Muscle fiber morphology analysis showed that MLP pigs had larger muscle fiber density while smaller muscle fiber cross-sectional area. Up-regulated gene expression of myosin heavy chain (MyHC)IIa was also observed in MLP pigs. These results indicate that the enhanced antioxidant activity and altered muscle fiber type and morphology appeared to contribute to the improvement of meat quality in Tibetan pigs fed diets containing MLP.

Complete genome sequencing and investigation on the fiber-degrading potential of Bacillus amyloliquefaciens strain TL106 from the tibetan pig

Background

Cellulolytic microorganisms are considered a key player in the degradation of feed fiber. These microorganisms can be isolated from various resources, such as animal gut, plant surfaces, soil and oceans. A new strain of Bacillus amyloliquefaciens, TL106, was isolated from faeces of a healthy Tibetan pigs. This strain can produce cellulase and shows strong antimicrobial activity in mice. Thus, in this study, to better understand the strain of B. amyloliquefaciens TL106 on degradation of cellulose, the genome of the strain TL106 was completely sequenced and analyzed. In addition, we also explored the cellulose degradation ability of strain TL106 in vitro.

Results

TL106 was completely sequenced with the third generation high-throughput DNA sequencing. In vitro analysis with enzymatic hydrolysis identified the activity of cellulose degradation. TL106 consisted of one circular chromosome with 3,980,960 bp and one plasmid with 16,916 bp, the genome total length was 3.99 Mb and total of 4,130 genes were predicted. Several genes of cellulases and hemicellulase were blasted in Genbank, including β-glucosidase, endoglucanase, ß-glucanase and xylanase genes. Additionally, the activities of amylase (20.25 U/mL), cellulase (20.86 U/mL), xylanase (39.71 U/mL) and β-glucanase (36.13 U/mL) in the fermentation supernatant of strain TL106 were higher. In the study of degradation characteristics, we found that strain TL106 had a better degradation effect on crude fiber, neutral detergent fiber, acid detergent fiber, starch, arabinoxylan and β-glucan of wheat and highland barley .

Conclusions

The genome of B. amyloliquefaciens TL106 contained several genes of cellulases and hemicellulases, can produce carbohydrate-active enzymes, amylase, cellulase, xylanase and β-glucanase. The supernatant of fermented had activities of strain TL106. It could degrade the fiber fraction and non-starch polysaccharides (arabinoxylans and β-glucan) of wheat and highland barley. The present study demonstrated that the degradation activity of TL106 to crude fiber which can potentially be applied as a feed additive to potentiate the digestion of plant feed by monogastric animals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02599-7.

Plateau Adaptation Gene Analyses Reveal Transcriptomic, Proteomic, and Dual Omics Expression in the Lung Tissues of Tibetan and Yorkshire Pigs

Elevated environments such as plateaus are often classified as low oxygen environments. The hypoxic adaptation mechanisms utilized by organisms in these conditions are not well understood. To address this, the differentially expressed genes (DEGs) involved in hypoxia adaptation were assessed using two pig breeds (Tibetan pig [TP] and Yorkshire sow [YY]). Genes related to lung tissue responses to hypoxia were assessed using transcriptomic (using RNA-seq) and proteomic (using iTRAQ) analysis. A total of 1021 DEGs were screened out. In the iTRAQ omics data, a total of 22,100 peptides were obtained and 4518 proteins were found after filtering. A total of 271 differentially expressed proteins [DEPs] were screened using the conditions of p < 0.05; FC ≤ 0.833; and FC ≥ 1.2. A total of 14 DEGs at the mRNA and protein levels were identified and found to be associated with regulation of the inflammatory response; blood particles; and MAPK cascade response regulation. Among the DEGs, six were associated with hypoxia adaptation function (mitochondria and glycolysis) in pigs. The results of this study identify novel candidate genes involved in porcine hypoxia adaptation mechanisms.

Post-transcriptional regulation through alternative splicing in the lungs of Tibetan pigs under hypoxia

In multicellular organisms, alternative splicing (AS) is central to the regulation of multiple biological processes. To further elucidate the adaptive strategy of AS in the lungs of Tibetan pigs in response to hypoxia, we identified and analyzed five basic AS types and 59,930 AS events in 18,179 genes. We found that approximately 65.10% of the total expressed genes underwent AS in the lungs of Tibetan pigs at a high altitude (TH). The frequencies of AS events were similar among the different groups (5.06-5.30 events in each gene on average). Skipped exons (SEs) were the predominant type of AS event, followed by mutually exclusive exons (MXEs), alternative 3' splice sites (A3SSs) and alternative 5' splice sites (A5SSs). Retained introns (RIs), the remaining type of AS event, showed lower frequencies. Further comparison analysis of differentially expressed genes (DEGs) and differentially spliced genes (DSGs) identified 2,209 differential splicing events in the above 18,000 expressed genes, including 918 increased and 1,291 decreased splicing events between the TH and Tibetan pigs at a low altitude (TL) groups. We identified 227 hypoxia-related genes involved in lung development that were differentially regulated through AS. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis clearly identified many DEGs and DSGs at high or low altitude. Seven pathways in the top 20 enriched KEGG terms overlapped for the DEGs and DSGs, including the chemokine signaling pathway, B cell receptor signaling pathway, and cytokine-cytokine receptor interaction, which exert many immunoregulatory and inflammatory actions critical to the lung under hypoxia. Twelve pathways overlapped in hypoxic DEGs and DSGs and included antigen processing, presentation and biosynthesis. ​GO analysis of the DEGs and DSGs among the four groups showed that numerous GO terms were enriched in the biological category, and the proportion of genes with downregulated expression was greater among 227 hypoxic genes than that of all genes. The results suggest that AS plays an essential role in the regulation of gene expression during hypoxia and that numerous genes involved in lung development are differentially regulated through AS.

Molecular detection and phylogenetic analysis of porcine circovirus type 3 in Tibetan pigs on the Qinghai-Tibet Plateau of China

Background

Porcine circovirus type 3 (PCV3) has been confirmed to infect pigs, posing a health risk and making pigs more susceptible to other pathogens. After the first report of PCV3 infection in the United States, its prevalence was determined in pigs suffering from clinical digestive or respiratory diseases in several other regions, including the Sichuan and Gansu provinces of China. In this study, we describe the frequency of PCV3 detection in Tibetan pigs inhabiting three different provinces surrounding the Qinghai-Tibet Plateau of China.

Methods

A total of 316 samples from diarrheic animals and 182 samples from healthy animals were collected in a randomized manner. Conventional PCR was applied for PCV3 DNA detection. The conserved regions of the PCV3 gene were analyzed with MEGA 7.1 software to design specific primers to sequence entire Cap genes in PCV3 strains, and the sequences were then used to confirm the subtypes of PCV3 in the positive samples. Prediction of the amino acid sequences by nucleotide sequence translation was also performed to compare the point mutations in the entire Cap protein. Twenty PCV3 whole-genomic sequences were used for genome phylogenetic analyses of PCV3 and sequence alignments with 22 other reference strains.

Results

We found that the prevalence of the virus was significantly higher in samples from pigs with diarrhoea than that in samples from healthy pigs. Phylogenetic analysis of Cap proteins demonstrated that the 20 PCV3 strains formed three clades, including PCV3a (8/20, 40.00%), PCV3b (5/20, 25%) and PCV3c (7/20, 35.00%). The complete genome sequence revealed that these strains formed one branch in the phylogenetic tree. Sequence analysis showed that the Cap proteins of the 20 different viral strains shared between 95.84 and 99.18% nucleotide identity. Cap protein sequence analyses showed that the positivity rate of PCV3a was highest in the samples from pigs with diarrhoea. In comparison, PCV3c was the most elevated subtype in the healthy samples. There was no mutation at a specific site in the amino acid sequences of the entire Cap protein from different PCV3 subtype strains from heathy samples. There was a mutation at site 113 in PCV3a, site 129 in PCV3b, and site 116 in PCV3c.

Conclusion

Our present data provide evidence that PCV3 is prevalent in Tibetan pigs at high altitudes in China, and the higher prevalence rates of the PCV3a and PCV3b subtypes in samples from pigs with diarrhoea further indicate that the genotypes should not be neglected during surveys of the pathogenicity of PCV3. Phylogenetic and genetic diversity analyses suggested that the continuous evolution, adaptation and mechanisms of pathogenicity of PCV3 in Tibetan pigs living in this special environment should be further studied.

The Expression Regulatory Network in the Lung Tissue of Tibetan Pigs Provides Insight Into Hypoxia-Sensitive Pathways in High-Altitude Hypoxia

To adapt to a low-oxygen environment, Tibetan pigs have developed a series of unique characteristics and can transport oxygen more effectively; however, the regulation of the associated processes in high-altitude animals remains elusive. We performed mRNA-seq and miRNA-seq, and we constructed coexpression regulatory networks of the lung tissues of Tibetan and Landrace pigs. HBB, AGT, COL1A2, and EPHX1 were identified as major regulators of hypoxia-induced genes that regulate blood pressure and circulation, and they were enriched in pathways related to signal transduction and angiogenesis, such as HIF-1, PI3K-Akt, mTOR, and AMPK. HBB may promote the combination of hemoglobin and oxygen as well as angiogenesis for high-altitude adaptation in Tibetan pigs. The expression of MMP2 showed a similar tendency of alveolar septum thickness among the four groups. These results indicated that MMP2 activity may lead to widening of the alveolar wall and septum, alveolar structure damage, and collapse of alveolar space with remarkable fibrosis. These findings provide a perspective on hypoxia-adaptive genes in the lungs in addition to insights into potential candidate genes in Tibetan pigs for further research in the field of high-altitude adaptation.

Vascular characteristics and expression of hypoxia genes in Tibetan pigs' hearts

Background

Tibetan pigs have exhibited unique characteristics from low‐altitudes pigs and adapted well to the Qinghai‐Tibet Plateau.

Objectives

The current study was undertaken to investigate the hypoxic adaptation of heart in Tibetan pigs.

Methods

The hearts of Tibetan pigs and Landrace pigs raised at high or low altitudes were compared using 3D casting technology, scanning electron microscopy and real‐time quantitative PCR (qRT‐PCR).

Results

We found that the ratio of the major axis to the minor axis and the density of the heart were significantly higher in Tibetan pigs than in Landrace pigs (p < 0.05). Tibetan pigs had larger diameters and higher densities of arterioles than Landrace pigs (p < 0.05), and these features have a similar variation with the expression of vascular endothelial growth factor (VEGF). The cardiac expression levels of hypoxia‐inducible factor‐1α (HIF‐1α) and endothelial nitric oxide synthase (eNOS) were significantly higher in pigs reared at high altitudes than in those reared at low altitudes (p < 0.05). In contrast, Egl nine homolog 1 (EGLN1) had the opposite trend with respect to HIF‐1α and eNOS and was related to red blood cell (RBC) counts. Notably, the expressions of erythropoietin (EPO) and endothelial PAS domain‐containing protein 1 (EPAS1) were significantly higher in Landrace pigs kept at high altitudes than in the others (p < 0.05) and were associated with haemoglobin.

Conclusions

These findings show that the regulation of the heart function of Tibetan pigs in a hypoxic environment is manifested at various levels to ensure the circulation of blood under extreme environmental conditions.

Primary characterization of the immune responses in Tibetan pigs infected with Chinese Tibet isolate of Trichinella spiralis

Background

Trichinellosis, caused by Trichinella spiralis, is a serious foodborne parasitic zoonosis. Tibetan pig is an infrequent, endemic plateau pig species, mainly distributed in Tibet Plateau, China. Because of the free-range system, Tibetan pigs are at risk of infection with Trichinella. The present study aimed to primarily profile the characteristics of T. spiralis infection in Tibetan pigs, including IgG levels, larvae burdens, and cytokines.

Results

The immune responses to Chinese Tibet T. spiralis isolate infection in Tibetan pigs with different doses were investigated in a tracking duration of 49 days. The muscle larvae per gram (lpg) were evaluated at 105 days post-infection (dpi). The results showed that the mean larval number of T. spiralis in Tibetan pigs increased with infective dose, with average lpg values of 3.5, 50.4 and 115.6 for Tibetan pigs infected with 200, 2,000, and 20,000 muscle larvae (ML) of T. spiralis. The anti-Trichinella IgG increased with inoculum dose and dpi, and peaked at 49 dpi. The kinetics of cytokines in the sera was detected by microarray, including interferon-γ (IFN-γ), interleukin (IL)-1β, IL-8, IL-12, IL-4, IL-6, IL-10, Granulocyte-macrophage Colony Stimulating Factor (GM-CSF), tumor necrosis factor (TNF)-α and transforming growth factor (TGF)-β1. The Th1/Th2 mixed cytokines were detectable in all samples. Interleukin-12 demonstrated the highest concentration compared to other cytokines and peaked at 42 dpi. Almost all cytokines were maintained at a high level at 42 dpi. Additionally, we also report a Trichinella seropositive rate of 43.9 % (18 out of 41) from field samples of Tibetan pigs.

Conclusions

The present study showed an increased Th1/Th2 mixed cytokines in Tibetan pigs elicited by T. spiralis. The high seroprevalence of Trichinella infection in field samples of Tibetan pigs further raises serious concern for the prevention and control of trichinellosis in this host for public health safety.

Composition of chemical elements in the edible viscera of Tibetan pigs and its correlation with environment and feed

The main purpose of this research was to evaluate the element distribution in the edible viscera of Tibetan pigs and to clarify its correlation with soils, drinking water and feed. A total of 55 chemical elements were simultaneously quantified. P, K, Na, Mg, Ca, Fe and Zn were the most abundant elements in the analyzed viscera. The general distribution of all element concentrations in the viscera of Tibetan pigs was such that liver > kidney > small intestine > heart = lung = large intestine > stomach. Comparison with national and international allowable limits of toxic elements indicates that consumption of Tibetan pig viscera presents potential health risks. Spearman correlation analysis reveals that significantly (p < 0.0001) positive relationships exist between the element profiles of viscera and drinking water, soils as well as feed. For all edible viscera, the largest values of correlation coefficient were observed to be with corn feed. Our research provides a relatively comprehensive investigation of the elemental composition in Tibetan pig viscera. The correlation data would be helpful for the local farm to reformulate the feed for Tibetan pigs to improve the quality and safety of the viscera.

Prevalence and genetic characterization of Enterocytozoon bieneusi and Giardia duodenalis in Tibetan pigs in Tibet, China

Enterocytozoon bieneusi and Giardia duodenalis are important opportunistic enteric zoonotic pathogens that cause diarrhoea and intestinal diseases in animals and humans. China is the largest producer of pigs, but whether Tibetan pigs, a unique pig breed in Tibet, are infected with E. bieneusi and G. duodenalis is unknown. Therefore, we conducted a molecular epidemiological survey to determine the prevalence of E. bieneusi and G. duodenalis in Tibetan pigs in Tibet, China, and identified the genotypes of these causative agents. A total of 345 faecal specimens were collected from Tibetan pigs from three Tibet counties (Milin, Cuona and Gongbujiangda), examined by nested PCR and sequenced utilizing genetic markers in the ribosomal internal transcribed spacer (ITS) region of the rRNA and glutamate dehydrogenase (gdh) gene for E. bieneusi and G. duodenalis, respectively. Moreover, using multilocus sequence typing, the subtypes of E. bieneusi were identified based on four loci (MS1, MS3, MS4 and MS7). A total of 41 (11.88%) faecal samples from Tibetan pigs were E. bieneusi-positive, and 2 (0.58%) were G. duodenalis-positive. The multivariate logistic regression analysis showed that age was considered a risk factor for Tibetan pig infection of E. bieneusi. Two novel (GB11, GB31) and four known E. bieneusi genotypes (EbpC, EbpD, PigEBITS5 and CHS12) were identified and were all classified as zoonotic group 1 according to the phylogenetic analysis. Two MLGs (MLGI and MLGII) were further identified in the E. bieneusi EbpC genotype by multilocus sequence typing analysis. In addition, two G. duodenalis assemblages (D and E) were found in the present study. To our knowledge, the current study is the first to detect the prevalence and perform genetic characterization of G. duodenalis in Tibetan pigs in Tibet, China. The results could provide essential data for controlling E. bieneusi and G. duodenalis infections in Tibetan pigs that are in contact with other animals and humans, as Tibetan pigs could be a potential source for human infection by these pathogens.

In-depth mapping of the proteome of Tibetan pig tenderloin (longissimus dorsi) using offline high-pH reversed-phase fractionation and LC-MS/MS

In recent years, Tibetan pig breeding and meat processing have developed rapidly. However, the basic physiological and biochemical characteristics of Tibetan pork have not been systematically explored. The present study conducted a high-throughput analysis of the tenderloin (longissimus dorsi) proteome of the Tibetan pigs and performed a functional annotation and bioinformatics analysis of the identified proteins. Based on offline two-dimensional liquid chromatography fractionation and MS/MS identification, a total of 1,723 proteins were identified in the tenderloin of Tibetan pigs. Gene ontology analysis and pathway enrichment analysis revealed that the proteins involved in respiration (oxidative phosphorylation, glycolysis/gluconeogenesis, citric acid cycle, and pyruvate metabolism) and protein synthesis and metabolism (proteasome, amino acid biosynthesis, endoplasmic reticulum protein processing, and ribosomes) were significantly enriched, indicating that the energy production and protein metabolism are the most important physiological processes in Tibetan pig tenderloin. Practical applications The in-depth mapping of the tenderloin (longissimus dorsi) proteome of the Tibetan pigs gives a panoramic perspective at the protein molecular level and provides important information on the mechanisms of postmortem muscle physiology and meat quality formation. Furthermore, the development of Tibetan pork storage and processing technologies would also benefit from the characterization of the biochemical properties of Tibetan pork.

Natural selection on TMPRSS6 associated with the blunted erythropoiesis and improved blood viscosity in Tibetan pigs

Tibetan pigs, indigenous to Tibetan plateau, are well adapted to hypoxia. So far, there have been not any definitively described genes and functional sites responsible for hypoxia adaptation for the Tibetan pig. The whole genome-wide association studies in human suggested that genetic variations in TMPRSS6 was associated with hemoglobin concentration (HGB) and red cell counts (RBC). Here we conducted resequencing of the nearly entire genomic region (40.1 kb) of the candidate gene TMPRSS6 in 40 domestic pigs and 40 wild boars along continuous altitudes and identified 708 SNPs, in addition to an indel (CGTG/----) in the intron 10. We conduct the CGTG indel in 838 domestic pigs, both the CGTG deletion frequency and the pairwise r² linkage disequilibrium showed an increase with elevated altitudes, suggesting that TMPRSS6 has been under Darwinian positive selection. As the conserved core sequence of hypoxia-response elements (HREs), the deletion of CGTG in Tibetan pigs decreased the expression levels of TMPRSS6 mRNA and protein in the liver revealed by real-time quantitative PCR and western blot, respectively. We compared domestic pigs and Tibetan pigs living continuous altitudes, found that the blood-related traits with the increase of altitude, however, the HGB did not increase with the elevation in Tibetan pigs. Genotype association analysis results dissected a genetic effect on reducing HGB by 13.25 g/L in Gongbo'gyamda Tibetan pigs, decreasing mean corpuscular volume (MCV) by 4.79 fl in Diqing Tibetan pigs. In conclusion, the CGTG deletion of TMPRSS6 resulted in lower HGB and smaller MCV, which could reflect a blunting erythropoiesis and improving blood viscosity as well as erythrocyte deformability. It remains to be determined whether a blunting of erythropoiesis for TMPRSS6 or others genetic effects are the physiological adaptations among Tibetan pigs.

Molecular Detection of Indigenous Hepatitis E Virus (HEV) from Tibetan Pigs in Tibet, China

Hepatitis E is an important public health concern throughout the world. Many molecular and serological surveys have reported the prevalence and genotypic characteristics of HEV in humans and animals worldwide. However, the genotypic characterization of this virus is very limited in Tibetan pigs. Hence, we aimed to explore the genotype of HEV, prevailing among Tibetan pigs in China. For this purpose, 253 bile samples of Tibetan pigs (free-range animals) were collected from different slaughterhouses during 2017-2018 and subsequently tested for HEV RNA by RT-nPCR. A total of 11 out of 253 (4.35%) samples tested were positive for HEV RNA. Based on the sequence alignment and phylogenetic analysis, all the isolated HEV strains belonged to genotype 4 and clustered into subtype 4b by sharing more than 84.8-95.2% identities with other reported strains. Our results concluded that HEV genotype 4 is prevailing among Tibetan pigs in Tibet, China.

Porcine epidemic diarrhea: an emerging disease in Tibetan pigs in Tibet, China

Porcine epidemic diarrhea virus (PEDV) is a devastating cause of diarrhea in pigs worldwide, and has caused enormous economic losses in the pork industry. To date, however, it is still unclear whether Tibetan pigs from the Tibetan Plateau of China are exposed to PED. This study was to investigate the seroprevalence of PED in Tibetan pigs in Tibet, China. A total of 364 serum samples were collected from Tibetan pigs in Nyingchi in 2014 and 2015. Each sample was assayed for PED antibodies by commercial enzyme-linked immunosorbent assay (ELISA) kits. Our results showed that the seroprevalence of PED in Tibetan pigs was 39.56% with the further distribution of 26.37% and 52.75% in Nyingchi and Mainling (odds ratio was more commonly affected in Mainling than Nyingchi), respectively. Moreover, the seroprevalence of PED was 65.28%, 35.83%, and 28.57% in juveniles, sub adults, and adults, respectively. The prevalence was found as 40.63% in males and 38.37% in females. The present survey indicated that the infection of PED in Tibetan pigs was widely spread in Tibet, which should arouse public concern of the threat to the health of Tibetan pigs and the development of breeding industry in this unique region of the world.

Characterization of the complete mitochondrial genome of Metastrongylus salmi (M. salmi) derived from Tibetan pigs in Tibet, China

The present study was designed to determine and analyze the mt genomes of Metastrongylus salmi (M. salmi), and reveal the phylogenetic relationships of this parasite using mt DNA sequences. Results showed that the complete mt genome of M. salmi was 13722 bp containing 12 protein-coding genes (cox1-3, nad1-6, nad4L, atp6 and cytb), 22 transfer RNA genes, and 2 ribosomal RNA genes (rrnL and rrnS). The overall A+T content was 73.54% and the nucleotide composition was A (23.52%), C (6.14%), G (19.60%), T (50.02%), and N (UCAG) (0.73%). A total of 4237 amino acids are encoded from the Tibetan isolates of M. salmi mt genomes. The ATA was predicted as the most common starting codon with 41.7% (5/12 protein genes); and 11 of the 12 protein genes were found to have a TAG or TAA translation termination codon. By clustering together the phylogenetic trees of Tibetan M. salmi and Austrian M. salmi, the M. salmi isolated from Tibetan pigs was found to be highly homological with that stemmed from Austrian one. This information provides meaningful insights into the phylogenetic position of the M. salmi China isolate and represents a useful resource for selecting molecular markers for diagnosis and population studies.

Detection and genetic characterization of porcine deltacoronavirus in Tibetan pigs surrounding the Qinghai-Tibet Plateau of China

Porcine deltacoronavirus (PDCoV) is a recently discovered RNA virus that belongs to the family Coronaviridae and genus Deltacoronavirus. This virus causes enteric disease in piglets that is characterized by enteritis and diarrhoea. In our present investigation, 189 diarrhoeic samples were collected between July 2016 and May 2017 from Tibetan pigs inhabiting in three different provinces surrounding the Qinghai–Tibet Plateau of China. We then applied the molecular‐based method of reverse transcription polymerase chain reactions (RT‐PCRs) to detect the presence of PDCoV in collected samples, and RT‐PCR indicated that the prevalence of PDCoV was 3.70% (7/189) in Tibetan pigs. Four of 7 PDCoV‐positive pigs were monoinfections of PDCoV, three samples were co‐infections of PDCoV with porcine epidemic diarrhoea virus (PEDV), and 52 (27.51%) samples were positive for PEDV. Four strains with different full‐length genomes were identified (CHN/GS/2016/1, CHN/GS/2016/2, CHN/GS‐/2017/1 and CHN/QH/2017/1), and their genomes were used to analyse the characteristics of PDCoV currently prevalent in Tibetan pigs. We found a 3‐nt insertion in the spike gene in four strains in Tibetan pigs. Phylogenetic analysis of the complete genome and spike and nucleocapsid gene sequences revealed that these strains shared ancestors with the strain CHN‐AH‐2004, which was found in pigs from the Anhui province of China mainland. However, PDCoV strains from Tibetan pigs formed different branches within the same cluster, implying continuous evolution in the field. Our present findings highlight the importance of epidemiologic surveillance to limit the spread of PDCoV in livestock at high altitudes in China.

Seroprevalence and risk factors associated with Pseudorabies virus infection in Tibetan pigs in Tibet

Background

Pseudorabies (PR) is an important emerging infectious disease that is characterized by fever, extreme itching and encephalomyelitis. However, it is still unclear whether Tibetan pigs are exposed to Pseudorabies virus (PRV) or not.

The present study was conducted to investigate the seroprevalence of PRV infection in Tibetan pigs in Nyingchi area of Tibet through enzyme-linked immunosorbent assay (ELISA). A total of 368 serum samples from Tibetan pigs were collected during 2015.

Results

Results showed that 58 (15.76%) samples were found positive for PRV antibodies with further distribution of 18.23%, 13.42% and 6.25% from Nyingchi, Mainling and Gongbo’gyamda areas on the Tibetan plateau, respectively; along with 12.10%, 17.71% and 17.57% prevalence of PRV in juveniles, sub-adults and adults, respectively. The prevalence of PRV infection between male (14.61%) and female (16.84%) showed non-significant difference (P > 0.05). The risk factors of infection were found to be associated with feed type, age and altitude.

Conclusions

The present study depicts a serious concern with a new emerging infectious disease in Tibetan pigs in Tibet, China.

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs

While the skin microbiome has been shown to play important roles in health and disease in several species, the effects of altitude on the skin microbiome and how high-altitude skin microbiomes may be associated with health and disease states remains largely unknown. Using 16S rRNA marker gene sequencing, we characterized the skin microbiomes of people from two racial groups (the Tibetans and the Hans) and of three local pig breeds (Tibetan pig, Rongchang pig, and Qingyu pig) at high and low altitudes. The skin microbial communities of low-altitude pigs and humans were distinct from those of high-altitude pigs and humans, with five bacterial taxa (Arthrobacter, Paenibacillus, Carnobacterium, and two unclassified genera in families Cellulomonadaceae and Xanthomonadaceae) consistently enriched in both pigs and humans at high altitude. Alpha diversity was also significantly lower in skin samples collected from individuals living at high altitude compared to individuals at low altitude. Several of the taxa unique to high-altitude humans and pigs are known extremophiles adapted to harsh environments such as those found at high altitude. Altogether our data reveal that altitude has a significant effect on the skin microbiome of pigs and humans.

Seroprevalence and risk factors associated with hepatitis E virus infections among people and pigs in Tibet, China

Hepatitis E virus (HEV), the causative agent of hepatitis E, is an important public health problem throughout the world. There is little information available on the autochthonous HEV infection in highland inhabitants (Tibet, average elevation >3000m) of China. Therefore, we conducted a cross-sectional survey to determine the sero-prevalence of Hepatitis E and association of different risk factors in local people and pigs in Tibet, China. For this purpose, serum samples were collected from 600 local volunteers and 453 Tibetan pigs from July 2014 to August 2015. All the samples were examined for the presence of anti-HEV IgG antibodies by using enzyme-linked immunosorbent assay (ELISA). While socio-demographic and behavioral characteristics were also obtained through questionnaire. The present survey found a close relationship among the HEV of Tibetan people and pigs. The prevalence of anti-HEV IgG was detected 39.33% (236/600) and 42.38% (192/453) in local people and pigs, respectively. There was a significance association of different age groups, ethnic groups, people having contact with pigs or consuming uncooked meat, and gender of Tibetan pigs. Our findings confirmed the presence of autochthonous HEV among people and pigs in Tibet, China. Therefore, effective measures should be taken to prevent and control HEV infection in Tibet, China.

Seroprevalence and risk factors associated with Haemophilus parasuis infection in Tibetan pigs in Tibet

Haemophilus parasuis is the causative agent of Glässer's disease, an important emerging infectious disease, but little is known of H. parasuis infection in Tibetan pigs in Tibet. The objective of the present investigation was to examine H. parasuis seroprevalence in Tibetan pigs in Tibet, China. Serum samples from 423 Tibetan pigs in Nyingchi, Tibet, China from April to December in 2010 were examined independently for the presence of antibodies against H. parasuis. A total of 147 (34.75%, 95% confidence interval [CI] 30.21-39.29) Tibetan pigs were tested positive for H. parasuis antibodies by the indirect hemagglutination assay (IHA) using a kit commercially available. 80 of 231 in Nyingchi (34.63%, 95% CI 28.50-40.77) and 67 of 192 in Mainling (34.89%, 95% CI 28.15-41.64) were tested positive, but the difference was not statistically significant (P>0.05, χ(2)=0.003). The prevalence ranged from 19.72% (95% CI 10.46-28.97) to 75.00% (95% CI 32.57-100) varying in different age groups, with higher prevalence in breeding boars than in piglets, and the difference was statistically significant (P<0.05). The prevalence of H. parasuis infection in males (45.03%, 95% CI 37.57-52.49) was significantly higher than that in the female (30%, 95% CI 22.41-37.59) pigs (P<0.05, χ(2)=7.361). Gender of Tibetan pigs was the main risk factor associated with H. parasuis infection. The results of the present survey indicated a wide distribution of H. parasuis among Tibetan pigs in Tibet, China and further investigation should better assess circulation of H. parasuis in Tibetan pigs. To the best of our knowledge, the present study represents the first report of H. parasuis infection in Tibetan pigs in China.