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Background: Gut microbial composition and its metabolites are crucial for livestock production performance. Metabolite profiles from autopsied biospecimens provide vital information on the basic mechanisms that affect the overall health and production traits in livestock animals. However, the role of the host breed in the gut microbiome and fecal metabolome of commercial pigs remains unclear. In this work, differences in microbiota composition among three commercial pig breeds Duroc, Yorkshire, and Landrace were measured by 16S rRNA gene sequencing. Fecal metabolite compositions of the three pig breeds were detected using untargeted metabolomics. Results: There were significant differences in the gut microbiomes of the three species, indicating that host breed affects the diversity and structure of gut microbiota. Several breed-associated microorganisms were identified at different taxonomic levels. Notely, most microbial taxa were annotated as Lactobacillacea, Muribaculaceae, and Oscillospiraceae. Several bacteria, including Lactobacillus, Subdoligranulum, Faecalibacterium, Oscillospira, Oscillospiraceae_UCG-002, and Christensenellaceae_R-7_group, could be considered as biomarkers for improving the backfat thickness (BF) for commercial pigs. Additionally, KEGG analysis of gut microbiota further revealed that arginine biosynthesis, pyruvate metabolism, and fatty acid biosynthesis varied greatly among pig breeds. Multiple gut bacterial metabolites (e.g., spermidine, estradiol, and palmitic acid) were identified as breed-associated. Mediation analysis ultimately revealed the cross-talk among gut microbiota, metabolites, and BF thickness, proclaiming that the microbial and metabolic biomarkers identified in this study could be used as biomarkers for improving BF phenotype. Conclusions: This work provides vital insights into breed effects on gut microbiota and metabolite compositions of commercial pigs and uncovers potential biomarkers that are significant for pig breed improvement. [ABSTRACT FROM AUTHOR]

Abstract Background Gut microbial composition and its metabolites are crucial for livestock production performance. Metabolite profiles from autopsied biospecimens provide vital information on the basic mechanisms that affect the overall health and production traits in livestock animals. However, the role of the host breed in the gut microbiome and fecal metabolome of commercial pigs remains unclear. In this work, differences in microbiota composition among three commercial pig breeds Duroc, Yorkshire, and Landrace were measured by 16S rRNA gene sequencing. Fecal metabolite compositions of the three pig breeds were detected using untargeted metabolomics. Results There were significant differences in the gut microbiomes of the three species, indicating that host breed affects the diversity and structure of gut microbiota. Several breed-associated microorganisms were identified at different taxonomic levels. Notely, most microbial taxa were annotated as Lactobacillacea , Muribaculaceae, and Oscillospiraceae. Several bacteria, including Lactobacillus, Subdoligranulum, Faecalibacterium, Oscillospira, Oscillospiraceae_UCG-002, and Christensenellaceae_R-7_group, could be considered as biomarkers for improving the backfat thickness (BF) for commercial pigs. Additionally, KEGG analysis of gut microbiota further revealed that arginine biosynthesis, pyruvate metabolism, and fatty acid biosynthesis varied greatly among pig breeds. Multiple gut bacterial metabolites (e.g., spermidine, estradiol, and palmitic acid) were identified as breed-associated. Mediation analysis ultimately revealed the cross-talk among gut microbiota, metabolites, and BF thickness, proclaiming that the microbial and metabolic biomarkers identified in this study could be used as biomarkers for improving BF phenotype. Conclusions This work provides vital insights into breed effects on gut microbiota and metabolite compositions of commercial pigs and uncovers potential biomarkers that are significant for pig breed improvement.

Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68–98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.

Simple Summary: It is well known that hematologic and biochemical reference intervals (RIs) play a major role in defining the health state of an animal. China is home to over 50% of the world pig population, but the assessment of hematologic and biochemical parameters for healthy commercial pigs has not yet been well studied in China. Adopting hematologic and biochemical RIs from other regions may lead to misjudgments by clinicians or researchers. Therefore, the aim of this study was to evaluate the correlations between hematologic and biochemical parameters and to provide a basic reference for the establishment of blood RIs for commercial pigs in China. Since most hematologic and biochemical parameters were significantly different between nursery pigs and sows, we preliminarily established hematologic and biochemical RIs for nursery pigs and sows, respectively. Our results are useful for better assessing the health conditions of commercial pigs in China. Hematologic and biochemical data are useful for indicating disease diagnosis and growth performance in swine. However, the assessment of these parameters in healthy commercial pigs is rare in China. Thus, blood samples were collected from 107 nursery pigs and 87 sows and were analyzed for 25 hematologic and 14 biochemical variables. After the rejection of the outliers and the detection of the data distribution, the correlations between the blood parameters were analyzed and the hematologic/biochemical RIs were preliminarily established using the 95% percentile RI. Correlation analysis showed that albumin was the hub parameter among the blood parameters investigated, and genes overlapping with key correlated variables were discovered. Most of the hematologic and biochemical parameters were significantly different between nursery pigs and sows. The 95% RIs of white blood cells and red blood cells were 7.18–24.52 × 109/L and 5.62–7.84 × 1012/L, respectively, for nursery pigs, but 9.34–23.84 × 109/L and 4.98–8.29 × 1012/L for sows. The 95% RIs of total protein and albumin were 43.16–61.23 g/dL and 19.35–37.86 g/dL, respectively, for nursery pigs, but 64.96–88.68 g/dL and 31.91–43.28 g/dL for sows. In conclusion, our study highlights the variability in blood parameters between nursery pigs and sows and provides fundamental data for the health monitoring of commercial pigs in China. [ABSTRACT FROM AUTHOR]

Our objective was to determine the effects of increasing dietary standardized ileal digestible lysine levels on the growth performance of PIC 337 × Camborough commercial pigs that were sired by highindex boars. A total of 2,200 barrows and gilts (PIC 337 × Camborough) were used in six experiments covering body weight ranges of 11-25 kg (Exp.1), 26-46 kg (Exp.2), 45-66 kg (Exp.3), 63-85 kg (Exp.4), 86-110 kg (Exp.5), and 108-134 kg (Exp.6). Pigs were placed in two rooms with 45 pens in Room 1 and 43 pens in Room 2, and there were 25 pigs/pen (12 or 13 gilts and 13 or 12 barrows) for both rooms. Room 1 was used in Exp. 1, 3, and 5; Room 2 was used in Exp. 2, 4, and 6. At the beginning of each trial, on-test pens were blocked by body weight and randomly allotted to one of five treatments (90, 100, 105, 110, or 120% of PIC SID Lys recommendations for Exp.1 to Exp. 5; whereas 80, 90, 100, 110, or 120% of PIC SID Lys recommendations for Exp. 6) in a randomized complete block design. Off-test pens were fed a common wash-out diet between trials, and common diets were formulated to meet PIC nutrient requirements according to the specific weight range. Data were analyzed using generalized linear mixed model with pen as the experimental unit in R Studio (Version 3.5.2, R Core Team; Vienna, Austria). Dietary SID Lys levels were included as fixed effects, and weight block was included as random effects in the model. All data are reported as least square means and considered statistically significant at P < 0.05 and marginally significant at P < 0.10. Increasing SID Lys improved average daily gain (ADG; linear, P = 0.003) and gain-to-feed ratio (G:F; quadratic, P = 0.007) in Exp.1; improved ADG (quadratic, P = 0.045) in Exp.4; improved ADG (quadratic, P = 0.009) and G:F (quadratic, P = 0.002) in Exp.5; and improved ADG (linear, P = 0.037) and G:F (linear, P = 0.030) in Exp.6 (Table 1). However, there was no evidence for difference among treatments on growth performance in Exp.2 and 3. With increasing dietary SID Lys levels, gram of SID Lys per kilogram of bodyweight gain and 5 (P = 0.002); and increased in a linear manner in Exp.2, 3, 4, and 6 (P < 0.001). In conclusion, increasing dietary SID Lys levels improved the growth performance of PIC 337 × Camborough commercial pigs sired by high-index boars when the bodyweight was below 25 kg or beyond 63 kg. [ABSTRACT FROM AUTHOR]

Hematologic and biochemical data are useful for indicating disease diagnosis and growth performance in swine. However, the assessment of these parameters in healthy commercial pigs is rare in China. Thus, blood samples were collected from 107 nursery pigs and 87 sows and were analyzed for 25 hematologic and 14 biochemical variables. After the rejection of the outliers and the detection of the data distribution, the correlations between the blood parameters were analyzed and the hematologic/biochemical RIs were preliminarily established using the 95% percentile RI. Correlation analysis showed that albumin was the hub parameter among the blood parameters investigated, and genes overlapping with key correlated variables were discovered. Most of the hematologic and biochemical parameters were significantly different between nursery pigs and sows. The 95% RIs of white blood cells and red blood cells were 7.18–24.52 × 109/L and 5.62–7.84 × 1012/L, respectively, for nursery pigs, but 9.34–23.84 × 109/L and 4.98–8.29 × 1012/L for sows. The 95% RIs of total protein and albumin were 43.16–61.23 g/dL and 19.35–37.86 g/dL, respectively, for nursery pigs, but 64.96–88.68 g/dL and 31.91–43.28 g/dL for sows. In conclusion, our study highlights the variability in blood parameters between nursery pigs and sows and provides fundamental data for the health monitoring of commercial pigs in China.

Porcine circovirus type 2 (PCV2) is recognized as one of the most important agents of reproductive disorders in gilts and sows worldwide. It is associated with considerable economic losses in the swine industry due to the unthriftiness, and variable morbidity and mortality it causes in pigs. In spite of the devastation caused by this virus to the global pig industry, there is little or no report of its occurrence in Nigeria. Hence, a slaughterhouse based survey was conducted to determine the prevalence of PCV2 infections in pigs in Ibadan, southwest Nigeria. Using a commercial ELISA kit, 364 pig sera collected from a major abattoir were screened for IgG antibodies against PCV2. The overall prevalence of anti-PCV2 antibodies in the pigs was 1.4 % (5/364), with more female pigs (4/237, 1.7 %) being seropositive than males (1/127, 0.8 %). Since there is no routine vaccination against this swine disease in Nigeria, thus the antibodies detected in the pig sera indicated a natural exposure to the virus. The absence of clinical disease in the pigs also suggests the possibility of a carrier status for these animals and shows that they could serve as hosts for the perpetuation of the disease. These findings underscore the need for continuous surveillance for PCV2 among pigs in Nigeria in order to determine its contribution to production losses incurred in the Nigerian swine industry and aid the development of prevention and control strategies against the disease.

Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine parvovirus (PPV) infections cause significant economic losses to the pig industry and are considered the most economically important viral diseases of intensive swine production. Despite numerous reports on both diseases in several countries worldwide, the status of PRRSV and PPV in Nigeria remains largely unknown. Thus, a serological survey was conducted to determine the prevalence of PRRSV and PPV infections in pigs in Southwest Nigeria. Using commercial ELISA kits, 368 pig sera were screened for antibodies against PRRSV (types I and II) and PPV. Significantly higher antibody prevalence was obtained for PRRSV (53.8%) compared to PPV (36.1%). Since there is no vaccination against both diseases in the country, the findings of this study suggest that PRRSV and PPV are present in the pig population in southwest Nigeria. There should be continuous monitoring of pigs for these diseases in Nigeria since both viruses are associated with major economic losses in the swine industry, affecting all stages of production. This will help to ascertain the actual burden and increase awareness of both diseases to facilitate early detection in order to institute appropriate control measures in the country.

Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68-98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Peng, Derks, Groenen, Zhao and Bosse.)

Among swine genetic markers, the highly polymorphic swine leukocyte antigen (SLA) is one of the key determinants, associated with not only immune responses but also reproductive performance and meat quality. The objective of this study was to characterize the SLA class I and II diversities in the commercial pig populations. In this study, a total number of 158 pigs (126 gilts and 32 boars) were randomly selected from different breeding herds of five major pig-producing companies, which covered ~70% of Thai swine production. The results indicate that a moderate level of SLA diversity was maintained in the Thai swine population, despite the performance-oriented breeding scheme. The highly common SLA class I alleles were SLA-1 * 08:XX, SLA-2 * 02:XX, and SLA-3 * 04:XX at a combined frequency of 30.1, 18.4, and 34.5%, respectively, whereas DRB1 * 04:XX, DQB1 * 02:XX and DQA * 02:XX were the common class II alleles at 22.8, 33.3, and 38.6%, respectively. The haplotype Lr-32.0 (SLA-1 * 07:XX, SLA-2 * 02:XX, and SLA-3 * 04:XX) and Lr-0.23 (DRB1 * 10:XX, DQB1 * 06:XX, DQA * 01:XX) was the most common SLA class I and II haplotype, at 15.5 and 14.6%, respectively. Common class I and II haplotypes were also observed, which Lr-22.15 was the most predominant at 11.1%, followed by Lr-32.12 and Lr-4.2 at 10.8 and 7.9%, respectively. To our knowledge, this is the first report of SLA class I and II diversities in the commercial pigs in Southeast Asia. The information of the common SLA allele(s) in the population could facilitate swine genetic improvement and future vaccine design., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Techakriengkrai, Nedumpun, Golde and Suradhat.)

In the pig industry, purebred animals are raised in nucleus herds and selected to produce crossbred progeny to perform in commercial environments. Crossbred and purebred performances are different, correlated traits. All purebreds in a pen have their performance assessed together at the end of a performance test. However, only selected crossbreds are removed (based on visual inspection) and measured at different times creating many small contemporary groups (CGs). This may reduce estimated breeding value (EBV) prediction accuracies. Considering this sequential recording of crossbreds, the objective was to investigate the impact of different CG definitions on genetic parameters and EBV prediction accuracy for crossbred traits. Growth rate (GP) and ultrasound backfat (BFP) records were available for purebreds. Lifetime growth (GX) and backfat (BFX) were recorded on crossbreds. Different CGs were tested: CG&#95;all included farm, sex, birth year, and birth week; CG&#95;week added slaughter week; and CG&#95;day used slaughter day instead of week. Data of 124,709 crossbreds were used. The purebred phenotypes (62,274 animals) included three generations of purebred ancestors of these crossbreds and their CG mates. Variance components for four-trait models with different CG definitions were estimated with average information restricted maximum likelihood. Purebred traits' variance components remained stable across CG definitions and varied slightly for BFX. Additive genetic variances (and heritabilities) for GX fluctuated more: 812 ± 36 (0.28 ± 0.01), 257 ± 15 (0.17 ± 0.01), and 204 ± 13 (0.15 ± 0.01) for CG&#95;all, CG&#95;week, and CG&#95;day, respectively. Age at slaughter (AAS) and hot carcass weight (HCW) adjusted for age were investigated as alternatives for GX. Both have potential for selection but lower heritabilities compared with GX: 0.21 ± 0.01 (0.18 ± 0.01), 0.16 ± 0.02 (0.16 + 0.01), and 0.10 ± 0.01 (0.14 ± 0.01) for AAS (HCW) using CG&#95;all, CG&#95;week, and CG&#95;day, respectively. The predictive ability, linear regression (LR) accuracy, bias, and dispersion of crossbred traits in crossbreds favored CG&#95;day, but correlations with unadjusted phenotypes favored CG&#95;all. In purebreds, CG&#95;all showed the best LR accuracy, while showing small relative differences in bias and dispersion. Different CG scenarios showed no relevant impact on BFX EBV. This study shows that different CG definitions may affect evaluation stability and animal ranking. Results suggest that ignoring slaughter dates in CG is more appropriate for estimating crossbred trait EBV for purebred animals., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Society of Animal Science.)