Search Results (82)

Optimal dietary calcium (Ca) and phosphorus (P) requirements remain undetermined for Ningxiang pigs, a valuable indigenous Chinese breed. This study conducted a continuous feeding trial with two growth phases (grower: 30–50 kg; finisher: 50–80 kg) using fixed Ca/P ratios to systematically evaluate the effects of Ca/P levels on growth performance and mineral metabolism. A total of 180 pigs per phase were allocated to four Ca/P levels. During the grower phase, a dietary regimen of 0.83% Ca/0.67% P significantly increased the average daily feed intake (ADFI), average daily gain (ADG), and apparent total tract digestibility (ATTD) of energy and P. In the finisher phase, 0.60/0.48% Ca/P showed optimal growth performance, upregulated jejunal mineral transporters (CaSR and SLC34A2), enhanced bone mineralization (metatarsal ash content), and improved intestinal morphology (duodenal and jejunal villus height, jejunal villus surface area). This regimen also selectively enriched Peptostreptococcaceae abundance, indicating improved host–microbe interactions. Based on these findings, stage-specific nutritional strategies were recommended: 0.83% Ca/0.67% P during the grower phase and 0.60% Ca/0.48% P during the finisher phase. These protocols synergistically improve microbial ecology, intestinal function, and bone metabolism, thereby maximizing the growth potential of Ningxiang pigs. Full article

The gut microbiota critically influences lipid metabolism and fat deposition in pigs, processes that underpin pork quality preferences and differentiate the meat traits of Chinese indigenous breeds (fat-type) from those of Western commercial breeds (lean-type). To explore the mechanisms underlying breed-specific fatty acid absorption, we compared the rectal and colonic microbiota and metabolite profiles of Huainan and Large White pigs using 16S rRNA sequencing and untargeted metabolomics. HN pigs exhibited enriched Lactobacillus johnsonii and Lactobacillus amylovorus, along with a significantly higher Firmicutes/Bacteroidetes ratio. Functional predictions further revealed elevated microbial pathways related to glycolysis, pyruvate metabolism, and ABC transporters in HN pigs. Conversely, LW pigs showed increased abundance of potentially pro-inflammatory bacteria and enriched pathways for lipopolysaccharide (LPS) biosynthesis. Metabolites such as 4-ethyl-2-heptylthiazole and picolinic acid were significantly upregulated in HN pigs and served as robust biomarkers (Area Under the Curve, AUC = 1.0),with perfect discrimination observed in both rectal and colonic samples. Integrative analysis identified 52 co-enriched microbial and metabolic pathways in HN pigs, including short-chain fatty acid (SCFA) production, lipid biosynthesis and transport, amino acid metabolism, ABC transporter activity, and the PPAR signaling pathway, supporting a microbiota–metabolite axis that enhances fatty acid absorption and gut immune balance. These findings provide mechanistic insight into breed-specific fat deposition and offer candidate biomarkers for improving pork quality via precision nutrition and breeding. Full article

(1) Objectives: Understanding the genetic basis of muscle development and meat quality traits in divergent pig breeds is crucial for advancing precision breeding strategies. (2) Methods: This study investigated transcriptome differences in the longissimus dorsi muscle between Chinese Congjiang Xiang (CX) and Landrace (LAN) pigs. RNA sequencing was performed on muscle tissues from ten individuals of each breed, generating 874.5 million raw reads with an average mapping rate of 89.3% to the pig reference genome. (3) Results: Transcriptional profiling revealed distinct expression patterns with 785 genes exclusively expressed in CX pigs and 457 genes unique to LAN pigs, while 7099 co-expressed genes were shared by both breeds. Differential expression analysis identified 2459 significantly different genes (|log2FC| ≥ 1, adjusted p-value < 0.05), with 1745 up-regulated and 714 down-regulated in CX pigs. Among the most significantly up-regulated genes in CX pigs were flavor-associated genes (ELOVL5/6, FASN, DGAT2, ALDH1A3, PPAR-γ) with log2FC values ranging from 1.21 to 3.88. GO and KEGG pathway analyses revealed that up-regulated genes in CX pigs were significantly enriched in immune response pathways (adjusted p-value < 0.01), while down-regulated genes were primarily associated with myosin complex formation and PPAR signaling pathway. PPI network analysis identified PPAR-γ as a central hub gene with 16 direct interactions to other flavor-related genes. (4) Conclusions: These findings demonstrate that the superior meat flavor characteristics of indigenous Chinese pigs are driven by enhanced expression of lipid metabolism genes and distinctive immune-related pathways, providing specific molecular targets for breeding programs aimed at improving meat quality while maintaining production efficiency in commercial breeds. Full article

To compare the differences in meat quality between obese-type Chinese pig breeds and lean-type foreign pig breeds, we selected Taoyuan Black (TB) pigs and Duroc pigs at 180 and 210 days of age and analyzed their meat quality, chemical composition, and flavor compounds using an electronic tongue, chromatographic techniques, and two-dimensional gas chromatography-time-of-flight-mass-spectrometry (GC×GC-TOF-MS). A total of 16 main fatty acids, 18 main free amino acids, and 249 flavor compounds were identified. The results showed that TB pigs exhibited redder meat color, higher intramuscular fat, and lower shear force than Duroc pigs (p < 0.05). TB pigs displayed higher levels of flavor nucleotides, free amino acids, and monounsaturated fatty acids (p < 0.05). Furthermore, pigs at 180 days exhibited lower dripping loss and more flavor compounds than those at 210 days (p < 0.05). Electronic tongue analysis revealed higher umami values in TB pigs at 180 days of age. Among the flavor compounds in pork, the four compounds that contributed most significantly to flavor across all species were 2-nonenal, 2-octenal, heptanal, 2,3-butanedione, and 2-pentylfuran. These findings provide fundamental data and insight into pig production. Full article

Chinese native pig breeds exhibit unique advantages over Western pig breeds, but the specific lipid metabolism mechanisms remain unclear. The phenotypic characteristics of Mashen (MS) pigs and Duroc × (Landrace × Yorkshire) (DLY) pigs are studied. The results show that MS pigs exhibit higher intramuscular fat (IMF) content. The area of adipocytes of MS pigs is significantly greater than that in DLY pigs (p < 0.01). Lipidomics analysis reveals distinct profiles in the upper layer of backfat (ULB), leaf lard (LL), greater omentum (GOM), and IMF, with MS pigs showing higher polyunsaturated fatty acids (PUFAs) in ULB, LL, and GOM. Key differential lipids identified in the two pig breeds include the following triglycerides (TGs) and phosphatidylcholines (PC): TG(16:1_18:1_18:3), TG(18:1_18:2_18:3), TG(18:3_18:2_18:2), PC(18:0_18:1), and PC(18:0_18:2). Weighted gene co-expression network analysis (WGCNA) reveals lipid molecules associated with serum biochemical indices. Transcriptomics analysis highlights 1944 differentially expressed genes between the MS-ULB and DLY-ULB. Notably, multiple genes from the cytochrome P450 family (CYP2E1, CYP4A24, CYP2J2), along with PLA2G2D, PLA2G4A, and multiple PCs, are associated with the metabolism of arachidonic acids and linoleic acids. PLA2G2D and PLA2G4A are also involved in the metabolism of α-linolenic acids. This comprehensive analysis provides essential information for breeding strategies and meat quality improvement. Full article

Background: Crossbreeding strategies that combine the growth performance of Western pig breeds with the meat quality traits of Chinese indigenous breeds have garnered considerable interest. Duroc pigs are known for their high growth efficiency but have relatively low intramuscular fat (IMF) content. In contrast, native breeds like the Diannan Small-Eared pig exhibit superior pork quality with higher IMF levels. This study aimed to compare the muscle growth characteristics and molecular mechanisms between Duroc × Landrace × Yorkshire (DLY) and Duroc × Berkshire × Diannan Small-Eared (DBD) pigs. Methods: The longissimus dorsi tissue of 210-day-old DLY and DBD pigs was collected for analysis. HE staining assessed muscle fiber characteristics, IMF content was measured, and ELISA quantified muscle-derived growth and development-related factors. Transcriptome sequencing was conducted, followed by differential gene expression analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) analyses. Functional validation of key genes was performed in C2C12 cells. Results: DBD pigs exhibited significantly larger muscle fiber diameter and higher IMF content compared to DLY pigs. IGF1 and GH levels were elevated in DBD pigs. Transcriptome analysis identified 185 upregulated and 102 downregulated genes, with enrichment in pathways including PI3K-Akt, MAPK, FoxO, and cGMP-PKG signaling. ACSL1 and FABP3 were functionally validated, showing promotion of differentiation and inhibition of proliferation in C2C12 cells. Conclusions: DBD pigs exhibit superior muscle growth traits and higher IMF content compared to DLY pigs. ACSL1 and FABP3 may serve as key regulators of muscle development in pigs. Full article

Liangshan Black pigs are a new Chinese indigenous breed discovered during the Third National Survey of Livestock and Plant Genetic Resources. To uncover genetic diversity, population structure, and potential exotic introgression in this breed, we sampled 191 Liangshan Black pigs from the conservation population and genotyped these individuals using the “Zhongxin-I” porcine chip, then conducted in-depth population genetic analyses in the context of pigs from five introduced breeds. The results revealed that the tested individuals exhibited significant genetic diversity, displayed uneven kinship relationships, and were assigned to nine families according to their clustering patterns in the phylogenetic tree. Further relationship analyses with the five introduced breeds demonstrated that Liangshan Black pigs were clustered separately from the introduced breeds, had larger evolutionary distances with the introduced breeds, and possessed certain genetic components of the introduced breeds, especially those of Duroc. These findings demonstrate that Liangshan Black pigs are generally an indigenous breed independent of the introduced breeds but are slightly affected by the introduced breeds. In summary, the results of our study not only contribute to an in-depth understanding of the population genetic characteristics of Liangshan Black pigs but also provide the necessary data for the implementation of conservation programs. Full article

Meat production traits in pigs are critical economic characteristics, primarily influenced by the formation and development of skeletal muscle. Skeletal muscle development is regulated by a complex transcriptional network, which partly relies on chromatin accessibility for initiation. Ningxiang pigs, a renowned Chinese indigenous breed, are highly valued for their tender meat. However, studies focusing on skeletal muscle development in Ningxiang pigs, particularly from the perspective of chromatin accessibility, have not yet been reported. Based on this, the present study selected several key time points in the skeletal muscle development of Ningxiang pigs to perform Transposase-Accessible Chromatin Sequencing (ATAC-seq) and RNA sequencing (RNA-seq). This was carried out to identify key open chromatin regions and genes during different growth stages, which could influence skeletal muscle development in Ningxiang pigs. We collected longissimus dorsi muscle samples at postnatal days 14 (D14), 28 (D28), 85 (D85), 165 (D165), and 250 (D250). For each age, three individuals were collected for ATAC-seq and RNA-seq. After initial differential analysis among different ages, we identified 6412 differentially accessible chromatin peaks and 1464 differentially expressed genes. To clarify the key candidate transcription factors affecting the development of skeletal muscle in Ningxiang pigs, motif analysis of differential peaks revealed potential cis-regulatory elements with binding sites for transcription factors, including Fosl2 and JunB. Correlation analysis identified 56 overlapping genes and a significant positive correlation (r = 0.73, p = 1 × 10⁻¹⁴) between gene expression and chromatin accessibility. Key candidate genes such as HOXA10, closely related to skeletal muscle development, were specifically examined. These results enhance our understanding of the genetic and epigenetic regulatory mechanisms of porcine skeletal muscle development, providing a robust foundation for future molecular studies. Full article

Pigs are essential agricultural animals, and among the various breeds, the Meishan pig, a native breed of China, is renowned for its high reproductive performance. This breed has been introduced to many countries to enhance local pig breeding programs. However, there have been limited genomic and population genetics studies focusing on Meishan pigs. We created a chromosomal-level genomic assembly using high-depth PacBio sequencing and Illumina sequencing data collected from a Meishan pig. Additionally, we analyzed whole-genome sequencing (WGS) data from Chinese boars and Meishan pigs to identify domestication selection signals within the Meishan breed. The assembled genome of the Meishan pig (MSjxau) was found to be 2.45 Gb in size, with a scaffold length of 139.17 Mb. The quality value was 37.06, and the BUSCO score was 96.2%, indicating good completeness, continuity, and accuracy. We annotated transposable elements, segmental duplication, and genes in the MSjxau genome. By combining these data with 28 publicly available genomes, we provide a high-quality structural variants resource for pigs. Furthermore, we identified 716 selective sweep intervals between Chinese wild pigs and Meishan pigs, where the selected gene PGR may be linked to the high fertility observed in Meishan pigs. Our study offers valuable genomic and variation resources for pig breeding and identifies several genes associated with the domestication of the Meishan pig. This lays the groundwork for further investigation into the genetic mechanisms behind complex traits in pigs. Full article

Chinese local pig breeds have unique meat flavor. In this study, we investigated the meat quality traits and the characteristics of the nutritional flavor substances such as amino acids (AAs), fatty acids (FAs), thiamine (Vitamin B1, VB1), and inosine monophosphate (IMP) in four Shanghai local pig breeds (MMS, SW, PD, and SHW) and the commercial crossbred Duroc × Landrace × Yorkshire (DLY) breed. The results showed that the intramuscular fat (IMF) and protein content in the longissimus dorsi muscle (L) of Shanghai local breeds, especially Shanghai MMS and PD breeds, were significantly higher than those of the DLY breed (p-value < 0.01). The inter-breed differences in amino acid (AA) content were even more significant in the gluteal muscle (G). Total amino acids (TAAs), flavor amino acids (FAAs), and essential amino acids (EAAs) were significantly higher in the G muscle of the four Shanghai local breeds than that in the DLY breed. The results for fatty acids (FAs) revealed that the differences in polyunsaturated fatty acids (PUFAs) were all highly significant (p-value < 0.0001), especially for the MMS breed, where the content of PUFAs in the L and G muscle amounted to (14.86 ± 2.06) g/100 g and (14.64 ± 2.83) g/100 g, respectively, which were significantly higher than those of other breeds. The MMS breed was also found to have the highest IMP content and the lowest thiamine (VB1) content among several pig breeds. Therefore, these differences in meat nutritional flavor substances provide new insights into the characterization of meat flavor in Shanghai local pig breeds. Full article

There is a consensus that indigenous pigs in China are more resistant than modern commercial pigs in terms of disease resistance. Generally, the immune response is an important part of anti-disease capability; however, the related mechanism in pigs is largely puzzling. Here, the public transcriptome data of peripheral blood mononuclear cells (PBMCs) from Dapulian (Chinese local breed) and Landrace (Commercial breed) pigs after stimulation with polyinosinic-polycytidylic acid (poly I:C, a conventional reagent used for simulation of the viral infection) were reanalyzed, and the immune response mechanism in different pig breeds was investigated from a transcriptomic perspective. Of note, through comparative analyses of Dapulian and Landrace pigs, the candidate genes involved in swine broad-spectrum resistance were identified, such as TIMD4, RNF128 and VCAM1. In addition, after differential gene expression, target gene identification and functional enrichment analyses, a potential regulatory network of miRNA genes associated with immune response was obtained in Dapulian pigs, including five miRNAs and 12 genes (such as ssc-miR-181a, ssc-miR-486, IL1R1 and NFKB2). This work provides new insights into the immune response regulation of antiviral responses in indigenous and modern commercial pigs. Full article

Despite identifying genes regulating the coat colour in Western pig breeds, the genetic basis of the coat colour in Chinese indigenous pigs is still not understood due to the diversity of indigenous breeds and their genetic differences from exotic pigs. In this study, 215 Wuzhishan pigs with three coat colour patterns (white, black, and black-back/white-belly) were used to conduct a genome-wide association analysis. We found that genes responsible for the coat colour in the Wuzhishan breed are located on chromosome 8. Ninety-seven genome-wide significant SNPs are related to the animal’s coat colour. Using a haplotype-sharing analysis, we narrowed the potential candidate region to a 10.1 Mb interval encompassing only one gene, RAPGEF2, which participates in the regulation of melanogenesis. Two additional candidate genes, PDGFRA and KIT, are located within 1 Mb of the genome-wide significant SNPs. Gene ontology analysis and literature mining suggest that these candidate genes are associated with the animal’s coat colour. mRNA expression results revealed that RAPGEF2 and PDGFRA had significantly higher expressions in black pigs than in white pigs and higher expressions in black skin than in white skin from the same black-back/white-belly pigs. These results suggest that RAPGEF2 and PDGFRA are potential candidate genes regulating the coat colour in Wuzhishan pigs. Interestingly, mutations of KIT (a gene duplication and a G to A substitution at the splicing site in intron 17) were detected in white Wuzhishan pigs but not in black-back/white-belly or black pigs, suggesting a close genetic relationship between white Wuzhishan pigs and Western white pig breeds. In summary, these results indicate that the expression of RAPGEF2 and PDGFRA may cause the coat colour variation by influencing the deposition of melanin, while the mutation of KIT causes the white coat colour. Our results may provide a theoretical basis for the breeding of white coat colour Wuzhishan pigs, and shed light on the complex genetic background of coat colour variations in indigenous Chinese pig breeds. Full article

The quality of pork meat directly influences the price and consumption. The genetic improvement of pigs has mainly focused on high productive efficiency, which has resulted in poor meat quality. Crossbreeds containing commercial and indigenous breeds could improve the meat quality, but identifying breed composition was difficult because of the lack of an ancestry reference panel. Therefore, we first constructed an abundant reference panel and convenient pipeline to identify ancestry/breed composition. The ancestry reference panel consisted of 517 reliable individuals, including three commercial breeds (Duroc, Landrace, and Yorkshire) and 38 indigenous Chinese breeds. The nature of the reference panel showed that the European domestic breed (EUD) and Asian domestic breed (ASD) were distinctly divided into two clusters. The evaluation of ancestry identification revealed that the reference panel performed well in identifying EUD and ASD ancestry proportions for commercial breeds, indigenous breeds, and crossbreeds. In addition, the ancestry reference panel also performed excellently in identifying breed composition for 3 commercial and 38 indigenous breeds. Specifically, the reference panel showed the outstanding identification of breed composition for crossbred individuals. These results suggested that the ancestry reference panel and convenient pipeline played a good role in identifying breed composition for pigs. Full article

[Background/Objectives] Mycoplasma hyopneumoniae (M. hyopneumoniae) is widespread in the global swine industry, leading to significant economic losses, and is particularly severe in native Chinese pig breeds. The Ningxiang pig, a well-known native breed in China, is susceptible to M. hyopneumoniae, exhibiting high morbidity and mortality rates. This study was designed to evaluate the clinical effectiveness of the M. hyopneumoniae live vaccine (strain 168). [Methods] The vaccine was delivered to 7-day-old piglets in the farrowing room through intrapulmonary administration, and its efficacy was compared with that of the M. hyopneumoniae inactivated vaccine (strain J). Four experimental groups were designed: Group 1 (inactivated vaccine + inactivated vaccine), Group 2 (live vaccine + inactivated vaccine), Group 3 (live vaccine), and Group 4 (control), which was not vaccinated. The production performance of each group was measured, and the lung lesion scores and pneumonia lesion reduction rates were evaluated at slaughter. Nasal swabs and serum samples were collected on days 0, 14, 28, 56, 84, 112, and 140 to assess SIgA, IgG antibody levels, and the M. hyopneumoniae pathogen. [Results] The results showed that Group 3 had the best production performance and clinical outcomes, with the lowest average lung lesion score, of 4.43 ± 2.44, which was significantly different from the other groups (*** p < 0.001). [Conclusions] This study provided scientific evidence to support vaccination strategies for preventing and controlling the M. hyopneumoniae in native pig populations. Full article

The Ningxiang pig, one of the well-known Chinese native pig breeds, has the advantages of tender meat, high intramuscular fat (IMF) content, and roughage tolerance, compared to the commercial lean pig breeds. The genetic basis for complex traits in Ningxiang pigs has been previously studied through other genetic markers, such as Single Nucleotide Polymorphism (SNP), while the characteristics of copy number variation (CNV) and the selection signal have not been investigated yet. In this study, GGP 50 k genotyping data of 2242 Ningxiang pigs (NX) and 1137 Duroc pigs (Duroc) were involved in CNV atlas construction and selection signals identification. Annotations of genes and quantitative trait locus (QTLs) were performed on the target candidate regions, as follows: (1) 162 CNVs were detected in Ningxiang pigs, while 326 CNVs were detected in Duroc pigs, and there are 21 copy number variation regions (CNVRs) shared between them; (2) The CNVRs of Duroc are more abundant, with 192 CNVRs, accounting for 1.61% of the entire genome, while those of Ningxiang pigs only have 98 CNVRs, accounting for 0.49%; (3) The QTLs annotated on CNVs and selected regions of Ningxiang pigs were mainly associated with meat quality and fertility. In contrast, the Duroc QTLs’ notes relate primarily to the carcass and immunity, and explain why they have a higher slaughter rate and immunity; (4) There is a presence of high-frequency acquired CNVs, specifically in Ningxiang pigs, with 24 genes significantly enriched in the sensory receptor-related pathway in this region; (5) Based on the CNVs atlas, candidate genes such as 3 inositol 1,4,5-triphosphate receptor, type 3 (ITPR3), forkhead box protein K2 (FOXK2), G-protein coupled estrogen receptor 1 (GPER1), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), triosephosphate isomerase 1 (TPI1), and other candidate genes related to fat deposition and differentiation were screened. In general, this study improved our knowledge about copy number variation and selection signal information of Ningxiang pigs, which can not only further explain the genetic differences between Chinese native and Western commercial pig breeds, but also provide new materials for the analysis of the genetic basis of complex traits. Full article