Search Results (64)

The growth and development of skeletal structures in young animals are important for their overall health and productivity. Deciphering variations in bone growth among pig breeds can optimize breeding strategies and improve animal welfare. This study explored differences in the bone growth and development of different pig breeds at the early growth stages. A total of 120 newborn piglets from Taoyuan black (TB), Xiangcun black (XB), and Duroc piglets, from 30 sows (litter sizes 9–11), were selected to assess their bone growth and development at four different ages (including at 1, 10, 21, and 24 days old). The results showed that the bone length and weight of femur, tibia, rib, and lumbar vertebrae among different pig breeds increased with age. Compared to Duroc piglets, XB and TB piglets exhibited a shorter bone length and lighter bone weight of those four bones at different ages (p < 0.05). XB piglets showed shorter bone length of femur, tibia, and lumbar vertebrae at weaning (21 days old), and a lighter bone weight and lower bone mineral content of those three bones at weaning and three days after weaning (24 days old) compared to TB piglets (p < 0.05). Bone breaking load increased with age, with Duroc piglets exhibiting higher bone breaking load at 10 days old (p < 0.05). Bone mineral density, ash content, and Ca and P deposition varied by breed and age, and TB piglets had a higher bone mineral density at 21 days old compared to XB piglets. In summary, Chinese native piglets have slower bone growth than Duroc piglets, but TB piglets exhibit higher mineral deposition compared to XB piglets. Full article

Fengjing pigs are a Chinese native breed known for their high reproductive ability. Runs of homozygosity (ROHs) have emerged as an effective tool for evaluating inbreeding levels and identifying relevant genes in selection. However, the declining population of Fengjing pigs in recent years has raised concerns about inbreeding. Therefore, this study aimed to investigate the ROH patterns, estimate genomic inbreeding levels, and identify candidate genes associated with economic traits using whole-genome resequencing data from 105 Fengjing pigs. A total of 2448 ROHs were identified, with an average of 23.31 ROHs per individual and an average length of 9.50 Mb. The inbreeding coefficient, based on ROHs, was 0.098. Additionally, three genomic regions with a high frequency of ROHs were identified. These regions contained 64 unique genes, including 14 genes associated with important economic traits. Moreover, six overlapping quantitative trait loci (QTLs) and four candidate genes (HSPG2, CDC42, EPHB2, and GRHL3) were identified on Sus scrofa chromosome (SSC) 6. These QTLs are associated with birth traits (health and reproductive efficiency) and meat development traits (meat quality and growth). This study identified many candidate genes and QTLs that overlapped with ROHs and are associated with economically significant traits. These findings can be used in future breeding, conservation, and utilization of specific Chinese native pig breeds. Full article

Background: Giardia duodenalis is one of the most prevalent protozoan pathogens, commonly infecting a wide range of hosts including humans, livestock, companion animals, and wildlife globally. The Bamaxiang pig (Sus scrofa domesticus), a native livestock variety from China’s Guangxi region, holds significant importance in Bama Yao Autonomous County. This breed not only supports regional meat production systems but also fulfills dual roles as human companions and valuable subjects for biomedical investigations. The aim of present study was to investigate the prevalence of G. duodenalis and assess its genetic characteristics. A total of 311 fresh fecal samples were collected from three farms in Bama Yao Autonomous County. The presence and genetic diversity of G. duodenalis were determined by nested PCR and sequence analysis of the glutamate dehydrogenase (gdh), β-giardin (bg) and triose phosphate isomerase (tpi) genes. Results: The total occurrence rate of G. duodenalis in Bamaxiang Pigs was 17.36% (54/311). Among different age groups, suckling piglets exhibited the highest infection rate at 24.29% (17/70). The infection rates in the sows, fattening pigs, and weaned piglets were 20.88% (19/91), 14.10% (11/78), and 9.72% (7/72), respectively (p < 0.05). Phylogenetic analysis of sequences from three genetic loci identified two G.duodenalis genetic assemblages, namely assemblages A and E. Among them, assemblage A (n = 31) was the predominant genotype across the three farms, followed by the assemblage E (n = 21) and mixed assemblage A/E (n = 2) infections. Conclusions: This study represents the first report demonstrating that G. duodenalis infection is prevalent in Bamaxiang pigs, with variable positivity rates across different growth stages. The zoonotic assemblage A was the predominant assemblage, suggesting a potential risk of transmission to humans through close contact with this specific pig breed. The results provide basic data for controlling infections in Bamaxiang pigs. Full article

Fermented liquid feed (FLF) is a microbiologically fermented, highly nutritious and easily digestible feed. This study investigated the effects of FLF on growth performance, carcass traits, meat quality, antioxidant capacity, and intestinal microbes of Yuedong black pigs. The pigs were divided into a control group and FLF group. Compared with the control, FLF increased (p < 0.05) the ADG and body weight of Yuedong black pigs. FLF increased (p < 0.05) the loin muscle area, and reduced cooking loss and meat color brightness (L*) of longissimus thoracis. Furthermore, FLF reduced (p < 0.05) the contents of bitter amino acids, including histidine and arginine. The expression of MYH4 (a fast glycolytic fiber gene) and TNNI1 (an inhibitor of muscle contraction) was increased (p < 0.05) in longissimus thoracis from the fermentation group. FLF increased (p < 0.05) the lipogenesis-related gene expression of FABP4, CEBPα, and PPARγ and the protein level of FATP4. Moreover, FLF increased (p < 0.05) serum T-AOC and GPx activity. In addition, FLF improved colonic microbial diversity and increased (p < 0.05) the abundance of Fibrobacterota (Phylum)-degrading cellulose and Lachnospiraceae-AC2044-group (genus)-generating butyric acid. In conclusion, FLF has a broad perspective for improving growth performance, meat quality, antioxidant capacity, and intestinal microbiota composition of Yuedong black pigs. Full article

Local adaptation allows animal populations to persist in diverse and changing environments, yet its genomic underpinnings remain poorly characterized in livestock. Chinese indigenous pigs, renowned for their rich phenotypic and ecological diversity, offer a powerful model for investigating environmental adaptation. Here, we integrated whole-genome resequencing data, environmental variables, genotype–environment association (GEA) analyses, and functional annotation to explore the adaptive genomic landscape of 46 native pig breeds across China. Based on 578 individuals and 17.7 million SNPs, we performed genome-wide GEA using latent factor mixed models (LFMMs), identifying 8644 SNPs significantly associated with environmental factors, including 310 linked to precipitation in the wettest quarter (BIO16). Redundancy analysis (RDA) and gradient forest modeling identified BIO16 as a major environmental driver of genomic variation. Functional annotation of BIO16-associated SNPs revealed significant enrichment in regulatory elements and genes highly expressed in the lung, spleen, hypothalamus, and intestine, implicating immune and metabolic pathways in local adaptation. Among the candidate loci, MS4A7 exhibited strong association signals, population differentiation, and tissue-specific regulation, suggesting a role in precipitation-mediated adaptation. This work enhances our understanding of livestock adaptation and informs climate-resilient conservation and breeding strategies. Full article

The Yucatán Black Hairless Pig (YBHP) is a native Mexican breed with cultural and agricultural importance in the Yucatán Peninsula. This study explored the genetic diversity and population structure of YBHP using a genome-wide single-nucleotide polymorphism (SNP) from the porcine GGP 50K chip, comparing it with native and cosmopolitan breeds worldwide. Genetic diversity analyses revealed an observed heterozygosity (HO) of 0.3602 ± 0.032 and an inbreeding coefficient (F_IS) of 0.1517 ± 0.076, indicating moderate diversity and a relatively low level of inbreeding for an endangered native breed. ADMIXTURE analyses revealed a predominant and distinctive ancestry component exclusive to YBHP, along with shared ancestry with European breeds, particularly those of presumed Iberian origin. Principal Component Analysis (PCA) and phylogenetic network clustering supported its genomic singularity while confirming ancestral proximity to traditional European pigs. These findings highlight the dual nature of the YBHP: a genetically distinct native breed shaped by local adaptation yet retaining ancestral signals from Old World lineages. This genomic insight provides a scientific basis for conservation planning, supports the breed’s recognition as a unique genetic resource, and promotes its sustainable use in regional production systems. 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

Researchers focused on assessing differences in gene diversity within and between populations, whether cosmopolitan or local. However, the identification of patterns of variation in non-random heterozygous genomic stretches, known as Heterozygosity-Rich regions (HRRs), has not yet been determined in European local pig breeds. A total of 23 pig breeds (20 local and 3 cosmopolitan) were assessed and compared in terms of heterozygosity-rich regions. The breeds with the highest number of HRRs were Large White, Lithuanian Old type, and Landrace, followed by Lithuanian Native, Mora Romagnola, and Duroc. The breeds with the lowest number were Alentejana, Iberian, and Majorcan Black. No shared HRR islands were found in all breeds, but gene enrichment analysis performed in the most common HRRs revealed several biologically important genes that cluster together and play significant roles, primarily related to the immune system. Permutation analysis indicated that some local breeds serve as true reservoirs of genetic diversity, displaying distinct and unique characteristics in terms of heterozygosity. This study suggests the importance of investigating heterozygosity to develop a comprehensive picture of pig breeds, regardless of the production system, country of origin, or population size. 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

[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

The Hezuo pig, an important native Tibetan breed in China, exhibits differences in adult body weight, with females typically heavier than males. The underlying mechanisms for this disparity remain unclear. DNA methylation changes are known to influence animal growth and development and regulate Hezuo pig growth by altering gene expression related to these processes, thus differentially affecting adult body weight between genders. This study conducted DNA methylation analysis and expression profiling using pituitary tissues from male and female Hezuo pigs at 3 and 8 months old (M3M, M3F, M8M, and M8F). In total 346, 795, 371, and 839 differentially methylated genes (DMGs) were identified in the M3M vs. M3F, M3F vs. M8F, M3M vs. M8M, and M8M vs. M8F groups, respectively. The comparative analysis of differentially methylated regions (DMRs) genes and DEGs (differentially expressed regions) revealed that key genes involved in growth, hormone secretion, and the hypothalamic-pituitary-gonadal axis are primarily enriched in signaling pathways such as PI3K-Akt, Hippo, and adrenergic. Further analysis combining methylation and transcriptomics identified five candidate methylated genes (CCL2, MYL2, GST, CTSH, and MCH) linked to adult body weight in Hezuo pigs. Additionally, the correlation analysis suggested that these genes influence growth and development in boars and sows by regulating the secretion and synthesis of related hormones, leading to heavier weights in females. In conclusion, variations in adult body weight between male and female pigs may stem from the impact of DNA methylation on gene expression related to growth and development. These findings offer new insights into the regulatory mechanisms of DNA methylation during weight gain in Hezuo pigs. Full article

The objectives of this study were to determine the apparent ileal digestibility and standardized ileal digestibility (SID) of crude protein (CP) and amino acids (AA) in feed ingredients, compare the ileal digestibility of CP and AA between commercial crossbred pigs and mini-Jeju Island native pigs (JINP), and develop models for estimating SID of CP and AA for commercial pigs using mini-JINP data. The study involved five crossbred commercial pigs (31.5 ± 1.6 kg of body weight and 11 weeks of age; Landrace × Yorkshire) and five mini-JINP (31.0 ± 3.2 kg body weight and 20 weeks of age). The pigs were surgically equipped with a T-cannula at the end of ileum. Each pig breed was assigned to 5 dietary treatments in a 5 × 10 incomplete Latin square design with 10 periods. Four experimental diets were formulated to contain each of soybean meal, corn gluten feed, copra meal, and sesame expellers as the sole source of nitrogen. A nitrogen-free diet was also prepared to determine basal endogenous losses of CP and AA. No interaction between breed and feed ingredient was observed for the digestibility of CP and all indispensable AA. The SID of CP and all indispensable AA, except Arg, His, and Lys, did not differ between the two breeds of pigs. Prediction equations were developed for SID of CP and AA of commercial pigs using the SID values of mini-JINP: SID of CP (%) = (1.02 × SID of CP in mini-JINP) − 5.20 with r² = 0.97 and p < 0.05; SID of Lys (%) = (1.12 × SID of Lys in mini-JINP) − 9.10 with r² = 0.98 and p < 0.05; and SID of Met (%) = (1.08 × SID of Met in mini-JINP) − 4.27 with r² = 0.96 and p < 0.05. The digestibility for most AA in feedstuffs for commercial pigs can be estimated using data from mini-JINP. Full article

The meat of local livestock breeds often has unique qualities and flavors. In this study, three Shanghai native pig breeds (MSZ, SWT, and SHB) exhibited better meat quality traits than globalized commercial pig breeds (DLY). Subsequently, metabolomic and lipidomic differences in the longissimus dorsi (L) and gluteus (T) muscles of the Shanghai native pig breeds and DLY pig breed were compared using liquid chromatography–mass spectrometry (LC–MS). The results demonstrated that the metabolites mainly consisted of (28.16%) lipids and lipid-like molecules, and (25.87%) organic acids and their derivatives were the two most dominant groups. Hundreds of differential expression metabolites were identified in every compared group, respectively. One-way ANOVA was applied to test the significance between multiple groups. Among the 20 most abundant differential metabolites, L-carnitine was significantly different in the muscles of the four pig breeds (p-value = 7.322 × 10⁻¹¹). It was significantly higher in the L and T muscles of the two indigenous black pig breeds (MSZ and SWT) than in the DLY pigs (p-value < 0.001). Similarly, lipidomic analysis revealed the PA (18:0/18:2) was significantly more abundant in the muscle of these two black breeds than that in the DLY breed (p-value < 0.001). These specific metabolites and lipids might influence the meat quality and taste properties and lead to customer preferences. Therefore, this study provided insights into the characterization of meat metabolites and lipids in Shanghai native pig breeds. Full article