Evaluation of the Chinese indigenous pig breed Dahe and crossbred Dawu for growth and carcass characteristics, organ weight, meat quality and intramuscular fatty acid and amino acid composition

Single-nucleus RNA sequencing and lipidomics reveal characteristics of transcriptional and lipid composition in porcine longissimus dorsi muscle

BACKGROUND

Global per capita meat consumption continues to rise, especially pork. Meat quality is influenced by the content of intramuscular fat (IMF) as a key factor. The longissimus dorsi muscle of Dahe pigs (DHM, IMF: 7.98% ± 1.96%) and Dahe black pigs (DHBM, IMF: 3.30% ± 0.64%) was studied to explore cellular heterogeneity and differentially expressed genes (DEGs) associated with IMF deposition using single-nucleus RNA sequencing (snRNA-seq). The lipid composition was then analyzed using non-targeted lipidomics.

RESULTS

A total of seven cell subpopulations were identified, including myocytes, fibroblast/fibro/adipogenic progenitors (FAPs), satellite cells, endothelial cells, macrophages, pericytes, and adipocytes. Among them, FAPs and adipocytes were more focused because they could be associated with lipid deposition. 1623 DEGs in the FAPs subpopulation of DHBM were up-regulated compared with DHM, while 1535 were down-regulated. These DEGs enriched in the glycolysis/gluconeogenesis pathway. 109 DEGs were up-regulated and 806 were down-regulated in the adipocyte subpopulation of DHBM compared with DHM, which were mainly enriched in the PPAR signaling pathway and fatty acid (FA) biosynthesis. The expression level of PPARG, ABP4, LEP, and ACSL1 genes in DHM was higher than that in DHBM. Lipidomics reveals porcine lipid composition characteristics of muscle tissue. A total of 41 lipid classes and 2699 lipid species were identified in DHM and DHBM groups. The top ten relative peak areas of lipid classes in DHM and DHBM were triglyceride (TG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), diglyceride (DG), cardiolipin (CL), ceramides (Cer), Simple Glc series (Hex1Cer), sphingomyelin (phSM), and phosphatidylinositol (PI). The relative peak areas of 35 lipid species in DHM were lower than DHBM, and 28 lipid species that were higher. There was a significant increase in the TG fatty acyl chains C6:0, C17:0, and C11:4, and a significant decrease in C16:0, C18:1, C18:2, and C22:4 in DHBM (p < 0.05).

CONCLUSIONS

C16:0 FA may downregulate the expression level of PPARG gene, which leads to the downregulation of fat metabolism-related genes such as ACSL, PLIN2, and FABP4 in DHBM compared with DHM. This may be the reason that the lipid deposition ability of Dahe pigs is stronger than that of Dahe black pigs, which need further investigation.

Development of small intestinal barrier function and underlying mechanism in Chinese indigenous and Duroc piglets during suckling and weaning periods

This study explored the developmental changes in small intestinal barrier function and the potential regulatory roles of intestinal microbiota and metabolites in different breeds of piglets during suckling and weaning periods. Taoyuan black (TB), Xiangcun black (XB), and Duroc (DR) piglets (10 litters per breed; half male and half female) were selected for sampling to evaluate the intestinal barrier-related indexes and intestinal microbiota and metabolites at 1, 10, 21 (weaned), and 24 (3 d after weaning) d old. The results showed that weaning led to severe shedding of small intestinal microvilli and sparse microvilli arrangement. D-lactate level in the ileum of TB and XB piglets during suckling and weaning periods was lower (P < 0.01) than that of DR piglets, as well as the ileal diamine oxidase level at 1 d old. The expression level of mucin 1 was higher (P < 0.05) in the ileum of TB and XB piglets than that of DR piglets, and it was the highest in the ileum of TB piglets at 21 d old. The expression levels of mucin 2 and mucin 13 were higher (P < 0.10) in TB and XB piglets than those of DR piglets at 21 d old, whereas mucin 2 and mucin 13 in the ileum of TB and XB piglets were higher (P < 0.05) than those of DR piglets at 24 d old. TB and XB piglets had a lower relative abundance of Escherichia_Shigella at 21 and 24 d old, but they had higher Streptococcus at 1 and 24 d old than DR piglets (P < 0.01). Differential metabolites between the three breeds of piglets were mainly related to oxidative phosphorylation, steroid biosynthesis, and bile acid synthesis. Collectively, these findings suggest that different pig breeds present differences in the development of the small intestinal barrier function. Compared with DR piglets, TB and XB piglets had higher intestinal permeability during the suckling period and a stronger intestinal mechanical barrier after weaning. Moreover, intestinal microbiota and metabolites are the key factors for developing small intestinal barrier functions in different breeds of piglets.

Investigation on muscle fiber types and meat quality and estimation of their heritability and correlation coefficients with each other in four pig populations

The aim of this study was to investigate the muscle fiber types and meat quality in four populations and estimate the heritability and correlation coefficients of those traits in Shanxia long black pig (SX). In this study, a total of 318 pigs were recorded for 16 traits of the muscle fiber types and meat quality in four populations, including 256 individuals from the new breed SX. The population had a significant effect on all recorded traits, and the meat quality of the Lulai black pig was better than the remaining populations. The heritability (h2 ) of meat quality traits was from 0.06 (pH at 24 h) to 0.47 (shearing force), and the muscle fiber types belonged to the traits with low to medium heritability. The density of total fiber had the highest h2 (0.40), while the percentage of type IIA had the lowest h2 (0.04). Most traits are phenotypically correlated with each other, but only a small proportion of traits are genetically correlated with each other. None fiber type genetically correlated with meat quality significantly, because the genetic correlation coefficients had large standard errors. These results provided some insights into genetic improvements for the meat quality in pig breeds and also indicated that the parameters of muscle fiber characteristics can explain parts of the variation in meat quality.

Single-nucleus transcriptome sequencing reveals hepatic cell atlas in pigs

BACKGROUND

As the largest substantive organ of animals, the liver plays an essential role in the physiological processes of digestive metabolism and immune defense. However, the cellular composition of the pig liver remains poorly understood. This investigation used single-nucleus RNA sequencing technology to identify cell types from liver tissues of pigs, providing a theoretical basis for further investigating liver cell types in pigs.

RESULTS

The analysis revealed 13 cells clusters which were further identified 7 cell types including endothelial cells, T cells, hepatocytes, Kupffer cells, stellate cells, B cells, and cholangiocytes. The dominant cell types were endothelial cells, T cells and hepatocytes in the liver tissue of Dahe pigs and Dahe black pigs, which accounts for about 85.76% and 82.74%, respectively. The number of endothelial cells was higher in the liver tissue of Dahe pigs compared to Dahe black pigs, while the opposite tendency was observed for T cells. Moreover, functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic endothelial cells were significantly enriched in the protein processing in endoplasmic reticulum, MAPK signaling pathway, and FoxO signaling pathway. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic T cells were significantly enriched in the thyroid hormone signaling pathway, B cell receptor signaling pathway, and focal adhesion. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic hepatocytes were significantly enriched in the metabolic pathways.

CONCLUSIONS

In summary, this study provides a comprehensive cell atlas of porcine hepatic tissue. The number, gene expression level and functional characteristics of each cell type in pig liver tissue varied between breeds.

Postmortem calpain changes in longissimus muscle from Lanyu native and Kaohsiung crossbred black pigs

The purpose of this study was to compare postmortem calpain changes in porcine muscle between Lanyu native (n = 10) and Kaohsiung crossbred (50% Meishan and 50% Duroc, n = 10) black pigs. Longissimus dorsi (LM) muscles (4th to 10th ribs) from both sides of carcasses were hot-sectioned in 30 min postmortem, vacuum-packaged, and stored at 5°C. LM samples from the left side of carcasses were sampled at 0 (30 min postmortem), 3, 6, 12, 24, 48, and 72 h of storage. The 24 and 72 h samples of shear force measurement were taken from the LM at the 8th and 10th ribs of the right side of carcasses, respectively. Our results showed that the decreases in calpain-1 activity, desmin content, and shear force were slower (P < 0.05) in Lanyu native black pig than in Kaohsiung crossbred black pig samples. Therefore, postmortem proteolysis and tenderization were more limited in LM from Lanyu native pigs than from Kaohsiung crossbred pigs.

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.

Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing

To investigate the difference of microbial communities among Diannan small-ear (DNSE), Dahe black (DHB) and Yorkshire (YS) pigs, we compared the microbial taxonomic and functional composition using a metagenomic approach. A total of 1,002,362 non-redundant microbial genes were identified, DHB and YS pigs had more similar genetic makeup compared with DNSE pigs. Bacteroidetes, Firmicutes and Spirochetes were the three most abundant phyla for all pig breeds, and DNSE pigs had a higher abundance of Prevotella genus than DHB and YS pigs. The functional profiles varied among the three pig breeds, DNSE pigs had more active carbohydrate metabolism and more abundant antibiotic resistance genes than the other two pig breeds. Moreover, we found that peptide and macrolide resistances genes in DNSE pigs were more abundant than that in DHB pigs (p < 0.05). This study will help to provide a theoretical basis for the development of native pig breeds in Yunnan Province, China.

Evaluation of coat color inheritance and production performance for crossbreed from Chinese indigenous Chenghua pig crossbred with Berkshire

Objective

This work was to determine coat inheritance and evaluate production performance for crossbred pigs from Berkshire×Chenghua (BC) compared with Chinese indigenous Chenghua (CH) pigs.

Methods

The coat color phenotypes were recorded for more than 16,000 pigs, and the genotypes of melanocortin 1 receptor (MCIR) gene were identified by sequencing. The reproductive performance of 927 crossbred BC F4 gilts and 320 purebred CH gilts was recorded. Sixty pigs of each breed were randomly selected at approximately 60 days of age to determine growth performance during fattening period, which lasted for 150 days for BC pigs and 240 days for CH pigs. At the end of the fattening period, 30 pigs of each breed were slaughtered to determine carcass composition and meat quality.

Results

The coat color of BC pigs exhibits a “dominant black” hereditary pattern, and all piglets derived from boars or sows genotyped E^D1E^D1 homozygous for MC1R gene showed a uniform black coat phenotype. The BC F4 gilts displayed a good reproductive performance, showing a higher litter and tear size and were heavier at farrowing litter and at weaning litter than the CH gilts, but they reached puberty later than the CH gilts. BC F4 pigs exhibited improved growth and carcass characteristics with a higher average daily live weight gain, lower feed-to-gain ratio, and higher carcass lean meat rate than CH pigs. Like CH pigs, BC F4 pigs produced superior meat-quality characteristics, showing ideal pH and meat-color values, high intramuscular fat content and water-holding capacity, and acceptable muscle-fiber parameters. C18:1, C16:0, C18:0, and C18:2 were the main fatty acids in M. longissimus lumborum in the two breeds, and a remarkably high polyunsaturated/saturated fatty acid ratio of ~0.39 was observed in the BC F4 pigs.

Conclusion

The BC F4 pigs exhibit a uniform black coat pattern and acceptable total production performance.

Carcass Composition and Physicochemical Characteristics of Meat from Pork Chains Based on Native and Hybrid Pigs

The purpose of the research was to investigate the carcass composition, meat quality and chemical composition of pigs from two pork chains for the production of traditional dry/cured products in Croatia. The trial involved 24 Black Slavonian barrows reared outdoors (NAT chain) and 24 PIC hybrid barrows kept under industrial conditions (INT chain); all animals were raised to 160 kg of live weight. After slaughter, carcass and meat quality traits were measured and samples for chemical composition were taken. After that, a full dissection of the carcasses was performed. The pigs from the INT pork chain had leaner carcasses, higher bone percentages, and lower fatness levels than the NAT carcasses. Pigs from the NAT chain exhibited a more desirable meat quality. No differences were found in moisture, and samples from the INT chain exhibited higher collagen and protein percentage. Muscles from the NAT chain had higher IMF and MUFA levels, and the SFA content was lower than in INT pork. Despite the superior carcass traits of the pigs from the INT chain, pigs from the NAT chain demonstrated better suitability for the production of dry/cured products.

Dietary Betaine Addition Alters Carcass Traits, Meat Quality, and Nitrogen Metabolism of Bama Mini-Pigs

Betaine is widely used as feed additives in animal husbandry as it can cause many benefits such as improving antioxidant ability, growth performance, and carcass traits. However, there are limited studies about the effects of betaine on the Bama mini-pigs. The present study was conducted to evaluate the effects of dietary betaine on carcass traits, meat quality, and nitrogen metabolism of pigs. Twenty-six pregnant Bama mini-pigs and then 104 weaned piglets were assigned for experimental treatments. The plasma and muscle samples were collected at 65-, 95-, and 125-d-old pigs, respectively. The results showed that betaine addition in the sow-offspring diets increased the lean meat rate in the 65-d-old pigs, whereas carcass weight, carcass yield, and loin-eye area were increased in the 95-d-old pigs, and carcass weight and backfat thickness in the 125-d-old pigs. Dietary betaine addition in the sow-offspring diets increased the contents of plasma Asp of 65-d-old, Met of 95- and 125-d-old, and Sar of 125-d-old pigs. Moreover, betaine addition increased the contents of Met, His, Ile, and Phe in Longissimus thoracis et lumborum, whereas those contents were decreased in biceps femoris and psoas major muscles at different stages. Betaine addition in the sow and piglets' diets regulated the muscle fiber-type and myogenic regulatory gene expressions. In summary, betaine addition in the sow and sow-offspring diets could improve the carcass traits and meat quality by altering the plasma biochemical parameters, amino acid composition, and gene expressions of skeletal muscle.

Comparative characterization of lipids and volatile compounds of Beijing Heiliu and Laiwu Chinese black pork as markers

Chinese black pork is preferred by consumers due to its unique organoleptic characteristics, which are closely related to lipids and volatiles. The primary aim of this study was to reveal key lipids and volatiles for the differentiation of Duroc × (Landrace × Yorkshire) (DLY), and Beijing Heiliu and Laiwu black (BHLB) pork. Here, lipid and volatile profiles were comprehensively characterized and compared using untargeted lipidomic and volatilomic analysis. The BHLB pork showed higher intramuscular fat content (p < 0.05). The content of total monounsaturated fatty acids, along with C16:1, C17:1, C18:1, and C20:1, was higher in BHLB pork compared with DLY pork (p < 0.05). Lipidomic analysis showed that DLY and BHLB pork significantly differed in lipids at the class and molecular levels. The BHLB pork had significantly more triglyceride and less lysophosphatidylcholine compared with DLY pork (p < 0.05). In positive and negative modes, 34 and 21 potential lipid markers, respectively, were selected for the discrimination of DLY and BHLB pork. In addition, volatilomic analysis showed that DLY and BHLB pork were well distinguished, and 13 volatiles were considered as potential discriminatory markers. Our findings provide a comprehensive lipidomic and volatilomic profiles characteristic of BHLB pork and will hopefully provide an important basis for the effective identification of Chinese black pork.

Composition and functional diversity of fecal bacterial community of wild boar, commercial pig and domestic native pig as revealed by 16S rRNA gene sequencing

The bacterial community in mammalian gastrointestinal tract is abundant and complex. To date, little is known about the gut microbiota of wild boar. This study aimed to investigate the fecal bacterial diversity of wild boar and compare with commercial pig and domestic native pig. The diet composition showed that the diets of wild boar, commercial pig and domestic native pig were different from each other. More than 1,760,000 quality-filtered sequences were obtained, and the results revealed distinct compositions and diversity of fecal microbiota in three groups. PCoA and NMDS analyses showed that fecal bacterial communities of wild boar, commercial pig and domestic native pig formed distinctly different clusters. Although the three groups shared a large size of OTUs comprising a core microbiota community, a strong distinction existed at family and genus levels. Ruminococcaceae, Prevotellaceae and Christensenellaceae were more abundant in the feces of wild boar than in domestic native pig and commercial pig. At the genus level, the proportion of unidentified Christensenellaceae was remarkably higher in wild boar group, while commercial pig and domestic native pig group had a higher abundance of Streptococcus and Lactobacillus. Tax4Fun predictions of metagenome function showed statistically significant differences in the functions of fecal microbiota in three groups. There were more bacteria genes with amino acid metabolism, cell growth and death, cell motility, energy metabolism, immune system and environmental adaptation observed in wild boar feces, while commercial pig feces contained more bacteria genes with carbohydrate metabolism, drug resistance, aging, infectious diseases, lipid metabolism, endocrine and metabolic diseases. These results indicated that the fecal microbial ecosystem of the wild boar is significantly different from that of domestic native pig and commercial pig, suggesting that diet is an important factor leading to differences in bacterial abundance and diversity in feces.

Evaluation of the four breeds in synthetic line of Jiaxing Black Pigs and Berkshire for meat quality traits, carcass characteristics, and flavor substances

To investigate breed characteristics and the effect of hybridization of Jiaxing Black Pig (JBP) with Western breeds, the carcass and meat quality traits and flavor substances such as inosinic acids (IMP), intramuscular fat (IMF) in longissimus muscle (LM) from five breeds including JBP, Berkshire, Berkshire × JBP (BJBP), Duroc × Berkshire × JBP (DBJBP), Duroc × Landrace × JBP (DLJBP) were compared in this study. It was found that water holding capacity (WHC) of LM in JBP was significantly higher than that in the other strains (p < 0.01). Dressing out percentage and lean percentage of JBP were both significantly lower than those in the others (p < 0.01) in connection with their lighter carcass weight and higher subcutaneous fat percentage (p < 0.01). Heterosis was realized in DJBP, DBJBP, and DLJBP since their carcass weight, lean percentage, and loin eye muscle area (LEMA) were markedly higher when compared to JBP, whereas lower than those in Berkshire. Among the breeds, the content of IMF and IMP in the LM of JBP were the highest. These traits were also palpably improved in the crossbreds, especially for DBJBP, of which pork was considered outstanding for containing the most abundant essential amino acids (EAA) and total amino acids (TAA).

Growth, carcass characteristics and meat quality of Chinese indigenous Yanan pig crossbred with Duroc and Berkshire genotypes

The objective of the present study was to evaluate the effects of crossbreeding on the growth, carcass characteristics and meat quality of Chinese native Yanan (YN) pig breed and related crossbreeds, including Duroc × Yanan (DY) and Duroc × (Berkshire × Yanan) (DBY). In total, 60 pigs (20 per breed) were used in the study. The results showed that both crossbreeds, especially DBY pigs, exhibited improved growth and carcass characteristics compared with those of purebred YN pigs. Moreover, the two crossbreeds, especially DBY pigs, produced acceptable meat-quality characteristics (normal pH and meat-colour values, high intramuscular fat content and water-holding capacity, acceptable muscle-fibre parameters, and strong pork flavour) similar to those of YN pigs. M. longissimus lumborum contained eight essential amino acids, with high contents in all pigs. C18:1, C16:0, C18:0, and C18:2 were the main fatty acids in M. longissimus lumborum in the three breeds, and a polyunsaturated:saturated fatty acid ratio of ~0.2 was observed in DBY and YN pigs. These results indicated that DBY pigs exhibit an acceptable total production performance and could be extensively used in commercial pig production to provide high-quality niche products.

Dynamic transcriptome and DNA methylome analyses on longissimus dorsi to identify genes underlying intramuscular fat content in pigs

Background

The intramuscular fat content (IMF) refers to the amount of fat within muscles, including the sum of phospholipids mainly found in cell membranes, triglycerides and cholesterol, and is determined both by hyperplasia and hypertrophy of adipocyte during the development of pigs. The IMF content is an important economic trait that is genetically controlled by multiple genes. The Laiwu pig is an indigenous fatty pig breed distributed in North China, characterized by excessively higher level of IMF content (9%~12%), therefore, is suitable for the identification of genes controlling IMF variations. To identify genes underlying IMF deposition, we performed genome-wide transcriptome and methylome analyses on longissimus dorsi (LD) muscle in Laiwu pigs across four developmental stages.

Results

A total of 22,524 expressed genes were detected and 1158 differentially expressed genes (DEGs) were hierarchically clustered in the LD muscle over four developmental stages from 60 d to 400 d. These genes were significantly clustered into four temporal expression profiles, and genes participating in fat cell differentiation and lipid biosynthesis processes were identified. From 120 d to 240 d, the period with the maximum IMF deposition rate, the lipid biosynthesis related genes (FOSL1, FAM213B and G0S2), transcription factors (TFs) (EGR1, KLF5, SREBF2, TP53 and TWIST1) and enriched pathways (steroid biosynthesis and fatty acid biosynthesis) were revealed; and fat biosynthesis relevant genes showing differences in DNA methylation in gene body or intergenic region were detected, such as FASN, PVALB, ID2, SH3PXD2B and EGR1.

Conclusions

This study provides a comprehensive landscape of transcriptome of the LD muscle in Laiwu pigs ranging from 60 to 400 days old, and methylome of the LD muscle in 120 d and 240 d Laiwu pigs. A set of candidate genes and TFs involved in fat biosynthesis process were identified, which were probably responsible for IMF deposition. The results from this study would provide a reference for the identification of genes controlling IMF variation, and for exploring molecular mechanisms underlying IMF deposition in pigs.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4201-9) contains supplementary material, which is available to authorized users.

Correlation between three glycometabolic-related hormones and muscle glycolysis, as well as meat quality, in three pig breeds

BACKGROUND

The present study aimed to evaluate the correlations among muscle concentrations of three glycometabolic-related hormones (insulin, epinephrine and glucagon), muscle glycolysis and meat quality in representative muscles of either glycolytic or oxidative types. Moreover, the relative glycometabolic-related gene expression was measured. One Western crossbreed DLY (Duroc × (Landrace × Yorkshire)), one crossbreed with half-Chinese native-pig origin DL (Duroc × LiangShan) and one pure Chinese native pig TP (Tibetan pig) were used in the present study.

RESULTS

Among the three breeds, DLY had the greatest glucagon and epinephrine (P < 0.01). Compared with DLY, TP and DL had lower lactic acid concentrations, showing lower glycolytic potentials (GP), greater ultimate pH values (P < 0.01) and lower relative expression levels of glycometabolic-related genes (GYS1, PRKAG3 and PKM2). Compared with the glycolytic muscle (musculus longissimus dorsi), oxidative muscle PM (musculus psoas major) had lower glucagon and epinephrine contents, lower GP and better meat quality. The concentration of glycometabolic-related hormones in the muscle had significant correlations with muscle glycolysis, meat pH and lightness.

CONCLUSION

The results obtained in the present study imply that glucagon and epinephrine levels could be used to indicate early glycolytic metabolism during postmortem. These findings may be helpful in identifying pork with undesirable quality traits. 2016 Society of Chemical Industry.

Intestinal microbiota could transfer host Gut characteristics from pigs to mice

BACKGROUND

The present study was conducted to compare the differences in gut microbiota composition and gut-phenotypes among pig breeds, and determine whether these differences would transmit to mice colonized with fecal microbiota of different pig breeds. A total of 24 1-day-old germ-free BALB/C mice were divided into 3 groups (TFM, YFM and RFM), which were transplanted with intact fecal microbiota of Tibetan pig (TP), Yorkshire pig (YP) and Rongchang pig (RP), respectively.

RESULTS

Results showed that different pig breeds exhibited distinct gut microbiota profile based on high-throughput pyrosequencing. YP exhibited a lower Firmicutes/Bacteroidetes ratio and apparent genera differences compared with RP and TP, and higher levels of bacteria from Spirochaetes were observed in TP compared with RP and YP (P < 0.05). Transplanted porcine microbiota into GF mice replicated the phenotypes of pig donors. Moreover, the three groups of donor pigs and their mice recipients exhibited different intestinal index and morphology. TP and RP had higher intestinal weight and relative CDX2 mRNA expression in ileum than YP, and longer intestine, higher villus height of duodenum and jejunum were observed in TP compared with YP and RP (P < 0.05). TP exhibited higher GLP-2 mRNA expression in duodenum and jejunum than RP (P < 0.05). Similarly, YFM had lower intestine weight and CDX2 mRNA expression in ileum than TFM and RFM (P < 0.05). The intestine length in TFM was longer than that in RFM, and TFM had higher villus height in duodenum and jejunum and GLP-2 mRNA expression in ileum than the other two groups (P < 0.05). Besides, the digestive and absorptive ability was different among the three groups in donor pigs and mice recipients. YP had higher jejunal lactase and maltase activities than TP and RP, while TP had higher activities of jejunal ATPase, γ-GT, and relative SGLT1 mRNA expression in duodenum and jejunum than YP and RP (P < 0.05). Likewise, YFM had higher jejunal sucrase and maltase activities than TFM and RFM, whereas higher jejunal γ-GT activity and relative SGLT1 mRNA expression in duodenum and ileum were observed in TFM compared with YFM and RFM (P < 0.05). In addition, Tibetan pigs-derived microbiota improved gut barrier in mice recipients. The concentration of MDA in YP was higher than that in TP and RP (P = 0.078), and the relative ZO-1 mRNA expression in ileum in TP was higher than that in YP (P < 0.05). Likely, compared with TFM and RFM, YFM exhibited increasing MDA concentration in jejunum (P = 0.098), and the relative ZO-1 mRNA expression in duodenum and ileum in TFM were higher than that in YFM (P < 0.05).

CONCLUSIONS

There were huge differences in gut microbiota composition and gut characteristics among pig breeds, and gut microbiota could partially convey host gut characteristics from pigs to mice.

Transcriptome Analysis of Liangshan Pig Muscle Development at the Growth Curve Inflection Point and Asymptotic Stages Using Digital Gene Expression Profiling

Animal growth curves can provide essential information for animal breeders to optimize feeding and management strategies. However, the genetic mechanism underlying the phenotypic differentiation between the inflection point and asymptotic stages of the growth curve is not well characterized. Here, we employed Liangshan pigs in stages of growth at the inflection point (under inflection point: UIP) and the two asymptotic stages (before the inflection point: BIP, after the inflection point: AIP) as models to survey global gene expression in the longissimus dorsi muscle using digital gene expression (DGE) tag profiling. We found Liangshan pigs reached maximum growth rate (UIP) at 163.6 days of age and a weight of 134.6 kg. The DGE libraries generated 117 million reads of 5.89 gigabases in length. 21,331, 20,996 and 20,139 expressed transcripts were identified BIP, UIP and AIP, respectively. Among them, we identified 757 differentially expressed genes (DEGs) between BIP and UIP, and 271 DEGs between AIP and UIP. An enrichment analysis of DEGs proved the immune system was strengthened in the AIP stage. Energy metabolism rate, global transcriptional activity and bone development intensity were highest UIP. Meat from Liangshan pigs had the highest intramuscular fat content and most favorable fatty acid composition in the AIP. Three hundred eighty (27.70%) specific expression genes were highly enriched in QTL regions for growth and meat quality traits. This study completed a comprehensive analysis of diverse genetic mechanisms underlying the inflection point and asymptotic stages of growth. Our findings will serve as an important resource in the understanding of animal growth and development in indigenous pig breeds.

Copy number variation detection using SNP genotyping arrays in three Chinese pig breeds

We performed genome-wide CNV detection based on SNP genotyping data of 96 Chinese-native Tibetan, Dahe and Wuzhishan pigs. These pigs are particularly interesting because of their excellent adaptation to hypoxia or small body size, which facilitates the use of them as models of different human diseases in addition to valuable agricultural animals. A total of 105 CNV regions (CNVRs) were identified, encompassing 16.71 Mb of the pig genome. Seven of 10 (70%) CNVRs selected randomly were validated by quantitative real-time PCR. Comparison with previous studies revealed 25 (23.81%) novel CNVRs, indicating that CNV coverage of the pig genome is still incomplete and there exists large diversity between pig breeds. Functional analysis of genes located in these CNVRs confirmed the high representation of genes involved in sensory perception, neurological system processes and other basic metabolic processes. In addition, the majority of these CNVRs were detected to span reported pig QTL that affect various traits, which highlighted three biologically interesting genes with copy number changes (i.e., ANKRD34B, FAM110B and ABCG1). These genes may have economic importance in pig breeding and are worth being further investigated. We also obtained some CNVRs harboring genes that had human orthologs involved in human diseases such as cardiovascular disease and Alzheimer's disease. The findings of this study are a significant extension of the coverage of CNVRs in the pig genome and provide valuable resources for follow-up-associated studies of CNVs in pig complex traits as well as important implications of human diseases.

Comparison of the meat quality, post-mortem muscle energy metabolism, and the expression of glycogen synthesis-related genes in three pig crossbreeds

Post-mortem muscle energy metabolism plays an important role in pork quality. To analyse the differences of meat quality and energy metabolism, three commercial pig crossbreeds frequently used in China were studied, they were DT (Duroc × Taihu; n = 16), PIC (five-way crossbreed from Pig Improvement Co., UK; n = 29) and DLY (Duroc × (Landrace × Yorkshire); n = 19) pigs. The results showed that DT pigs had a higher post-mortem pH45 min and pH24 h, lower shear force and drip loss, higher muscle free-glucose and glycogen contents, and lower lactic acid content than did PIC and DLY pigs. Post-mortem muscle free-glucose content of these three pig crossbreeds changed little, from 45 min to 96 h post-mortem. The expression levels of PRKAG3 (encoding a regulatory subunit of the AMP-activated protein kinase) and GYS1 (encoding muscle glycogen synthase) genes of DT pigs were significantly lower than those of PIC and DLY pigs. DT pigs had a higher expression level of glycogenin-1-like (encoding glycogenin) gene than did PIC and DLY pigs. In conclusion, DT pigs had better meat quality than did the other two pig crossbreeds. We deduced that the post-mortem muscle energy status and metabolism of DT pigs might be an important reason for their good meat quality, and future research should focus on the molecular and physiological mechanism of post-mortem muscle energy metabolism to find ways to improve meat quality.

Comparison of faecal microbial community of lantang, bama, erhualian, meishan, xiaomeishan, duroc, landrace, and yorkshire sows

The objective of this study was to investigate differences in the faecal microbial composition among Lantang, Bama, Erhualian, Meishan, Xiaomeishan, Duroc, Landrace, and Yorkshire sows and to explore the possible link of the pig breed with the gut microbial community. Among the sows, the Meishan, Landrace, Duroc, and Yorkshire sows were from the same breeding farm with the same feed. Fresh faeces were collected from three sows of each purebred breed for microbiota analysis and volatile fatty acid (VFA) determination. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that samples from Bama, Erhualian, and Xiaomeishan sows, which from different farms, were generally grouped in one cluster, with similarity higher than 67.2%, and those from Duroc, Landrace, and Yorkshire sows were grouped in another cluster. Principal component analysis of the DGGE profile showed that samples from the foreign breeds and the samples from the Chinese indigenous breeds were scattered in two different groups, irrespective of the farm origin. Faecal VFA concentrations were significantly affected by the pig breed. The proportion of acetate was higher in the Bama sows than in the other breeds. The real-time PCR analysis showed that 16S rRNA gene copies of total bacteria, Firmicutes and Bacteroidetes were significantly higher in the Bama sows compared to Xiaomeishan and Duroc sows. Both Meishan and Erhualian sows had higher numbers of total bacteria, Firmicutes, Bacteroidetes and sulphate-reducing bacteria as compared to Duroc sows. The results suggest that the pig breed affects the composition of gut microbiota. The microbial composition is different with different breeds, especially between overseas breeds (lean type) and Chinese breeds (relatively obese type).

Distinctive genes determine different intramuscular fat and muscle fiber ratios of the longissimus dorsi muscles in Jinhua and landrace pigs

Meat quality is determined by properties such as carcass color, tenderness and drip loss. These properties are closely associated with meat composition, which includes the types of muscle fiber and content of intramuscular fat (IMF). Muscle fibers are the main contributors to meat mass, while IMF not only contributes to the sensory properties but also to the plethora of physical, chemical and technological properties of meat. However, little is known about the molecular mechanisms that determine meat composition in different pig breeds. In this report we show that Jinhua pigs, a Chinese breed, contains much higher levels of IMF than do Landrace pigs, a Danish breed. We analyzed global gene expression profiles in the longissimus dorsi muscles in Jinhua and Landrace breeds at the ages of 30, 90 and 150 days. Cross-comparison analysis revealed that genes that regulate fatty acid biosynthesis (e.g., fatty acid synthase and stearoyl-CoA desaturase) are expressed at higher levels in Jinhua pigs whereas those that regulate myogenesis (e.g., myogenic factor 6 and forkhead box O1) are expressed at higher levels in Landrace pigs. Among those genes which are highly expressed in Jinhua pigs at 90 days (d90), we identified a novel gene porcine FLJ36031 (pFLJ), which functions as a positive regulator of fat deposition in cultured intramuscular adipocytes. In summary, our data showed that the up-regulation of fatty acid biosynthesis regulatory genes such as pFLJ and myogenesis inhibitory genes such as myostatin in the longissimus dorsi muscles of Jinhua pigs could explain why this local breed produces meat with high levels of IMF.

Effect of replacing soybean protein by taro leaf (Colocasia esculenta (L.) Schott) protein on growth performance of exotic (Landrace × Yorkshire) and native (Moo Lath) Lao pigs

The impact of replacing soybean crude protein (CP) with CP from ensiled taro leaves (ET) on growth performance, carcass traits, and organ weights in Landrace × Yorkshire (LY) and Moo Lath (ML) Lao pigs was studied. Twenty-four castrated male pigs, 12 of each breed, were allocated to the treatments according to a completely randomized 3 × 2 factorial (three levels of ET × two breeds) arrangement with four pigs per treatment. The pigs were kept in individual pens and were fed at 4 % dry matter of body weight for 105 days. The control diet (ET0) was formulated with soybean meal as the main CP source, and in the other two diets, soybean CP was replaced to 25 % (ET25) and 50 % (ET50), respectively, with CP from ensiled taro leaves. Calculated metabolizable energy intake decreased with increasing replacement of soybean CP in the diet, while dry matter intake (DMI), CP intake (CPI), average daily gain (ADG), and feed conversion ratio (FCR) were unaffected. Carcass weight, back fat thickness, and dressing percentage were unaffected by soybean CP replacement, while organ weights (except for spleen) increased (P < 0.001) when soybean CP was replaced by CP from ensiled taro leaves in the diet. LY pigs had higher (P < 0.001) DMI, CPI, and ADG and better (P < 0.001) FCR than ML pigs. LY pigs had higher carcass weight (P < 0.001), lower back fat thickness (P < 0.001), and higher organ weights (P < 0.05-0.001) than the ML pigs. In conclusion, taro leaf silage can replace up to 50 % of soybean CP in the diet of growing Lao LY and ML pigs without negative effects on performance and carcass traits.

Carcass and meat quality traits of four commercial pig crossbreeds in China

We evaluated carcass and meat quality traits of two Chinese native crossbreeds Landrace x Meishan (LM) and Duroc x (Landrace x Meishan) (DLM) and two foreign crossbreeds Duroc x (Landrace x Yorkshire) (DLY) and PIC (an imported five-way crossbreed). One hundred and twenty weaned pigs (half castrated males and half females) were reared and slaughtered at a predestinated slaughter age. The general carcass and meat quality traits were measured and analyzed. The DLY and PIC crosses had significantly heavier live weights (93.39 and 96.33 kg, P < 0.01), significantly higher dressing percentages (80.65 and 79.39%, P < 0.05), significantly bigger loin areas (42.69 and 43.91 cm(2), P < 0.001), and significantly more lean carcasses (65.78 and 66.40%, P < 0.001) than LM and DLM. On the other hand, LM had a significantly lower live weight (70.29 kg, P < 0.01), significantly thicker back fat (3.54 cm, P < 0.001), significantly less lean carcasses (46.82%, P < 0.001), and significantly less ham and breech (26.53%, P < 0.05) than the other crossbreeds. Among meat quality parameters, LM had the highest intramuscular fat content (5.02%, P < 0.001) and the smallest fiber area (3126.45 μm(2), P < 0.01). However, PIC showed the lowest pH(1) (5.82, P < 0.01) and pH(2) (5.63, P < 0.01), the highest drip loss (2.89%, P < 0.01), and the lowest intramuscular fat (1.35%, P < 0.001). We concluded that LM and DLM had good meat quality traits but poorer carcass traits than DLY and PIC; DLY had good carcass and meat quality traits; PIC had good carcass traits, but it had less intramuscular fat, lower pH and higher drip loss.

Effect of replacing soybean protein with protein from ensiled stylo (Stylosanthes guianensis (Aubl.) Sw. var. guianensis) on growth performance, carcass traits and organ weights of exotic (Landrace × Yorkshire) and native (Moo Lath) Lao pigs

The present study examined the impact of replacing crude protein (CP) from soybean with CP from ensiled stylo (ES) on growth performance, carcass traits and organ weights in Landrace × Yorkshire (LY) and Moo Lath (ML) native Lao pigs. Twenty-four castrated male pigs, 12 of each breed, were allocated to the diet treatments according to a completely randomised 3 × 2 factorial (three ES levels × two breeds) arrangement, with four pigs per diet treatment. Pigs were kept in individual pens and fed at 4 % dry matter of body weight for 98 days. The control diet was formulated with soybean meal as the main CP source, and in the other two experimental diets, CP from soybean was replaced at 25 % (ES25) and 50 % (ES50) by CP from ES. Calculated metabolisable energy intake decreased with ES50 diet, while dry matter intake (DMI) and CP intake (CPI) were the highest in ES25 diet (P < 0.001). Overall, average daily gain (ADG) and feed conversion ratio (FCR) were unaffected by diet treatments. Carcass weight, backfat thickness and dressing percentage were unaffected by soybean CP replacement, while the weights of lung, large intestine and stomach were higher (P < 0.001) when 25 % of soybean CP was replaced by CP from ES. LY pigs had higher (P < 0.001) DMI, CPI and ADG and poorer (P < 0.001) FCR than ML pigs. LY pigs had higher carcass weight (P < 0.001), lower backfat thickness (P < 0.001) and higher organ weight (P < 0.001) than ML pigs, except for small intestine weight, where there was no difference between the LY and ML pigs (P > 0.05). In conclusion, ES can replace up to 50 % of soybean CP in the diet of growing Lao LY and ML pigs without negative effects on performance and carcass traits.