Tibetan pigs are indigenous to the Qinghai–Tibet Plateau and have been the subject of extensive genomic research primarily focused on their adaptation to high altitudes. However, genetic modifications associated with their response to low-altitude acclimation have not been thoroughly explored. To investigate the genetic basis underlying the low-altitude acclimation of Tibetan pigs, we generated and analyzed genotyping data of Tibetan pigs that inhabit high-altitude regions (average altitude 4000 m) and Tibetan pigs that have inhabited nearby low-altitude regions (average altitude 500 m) for approximately 20 generations. We found that the highland and lowland Tibetan pigs have distinguishable genotype and phenotype variations. We identified 46 and 126 potentially selected SNPs associated with 29 and 56 candidate genes in highland and lowland Tibetan pigs, respectively. Candidate genes in the highland Tibetan pigs were involved in immune response (NFYC and STAT1) and radiation (NABP1), whereas candidate genes in the lowland Tibetan pigs were related to reproduction (ESR2, DMRTA1, and ZNF366), growth and development (NTRK3, FGF18, and MAP1B), and blood pressure regulation (CARTPT). These findings will help to understand the mechanisms of environmental adaptation in Tibetan pigs and offer valuable information into the genetic improvement of Tibetan pigs pertaining to low-altitude acclimation and economic traits.

Characterizing the transcriptomic profiles of gastrointestinal tract tissues in high-altitude pigs is crucial for understanding the molecular mechanisms underlying their metabolic adaptation to high-altitude environments. Here, we generated RNA-seq data from five gastrointestinal tract tissues (i.e., stomach, jejunum, cecum, colon, rectum) and the triceps brachii muscle of six 300-day-old castrated male Tibetan pigs (inhabiting high-altitude regions) and six Black pigs (inhabiting low-altitude regions). Pigs were group-housed and fasted for 24 h before sampling. We identified transcriptional differences between these two pig populations, revealing that genes upregulated in the gastrointestinal tract tissues and triceps brachii muscle of Tibetan pigs, compared to Black pigs, are primarily associated with immune response and metabolic processes, including lipid metabolism. Consistently, a comparative analysis demonstrated that the fatty acid content was higher in the triceps brachii muscles of Tibetan pigs than in those of Black pigs. Additionally, we identified 18 genes, including HDC , SETD9 , HUS1 , and RPSA , whose expression in gastrointestinal tract tissues was significantly correlated with the metabolite abundance (amino acid and fatty acid, etc.) in the triceps brachii muscles. This study may contribute to the understanding of high-altitude adaptation mechanisms in Tibetan pigs and provides valuable insights for further genetic improvement of pig breeds.

Pork is a major source of animal protein for humans, and as living standards have improved, consumer demand has shifted from quantity to quality. Amino acid and fatty acid compositions determine the nutritional value and flavor of pork. However, the genetic mechanisms underlying variation in these parameters have not been fully elucidated. In this study, we quantified 17 amino acids and 42 fatty acids in the longissimus dorsi muscle from three crossbred pig populations, namely Yorkshire × Tibetan (YT), Yorkshire × Neijiang (YN), and Duroc × Tibetan (DT). YT and YN pigs exhibited higher amino acid concentrations, while DT pigs showed elevated fatty acid levels. Subsequently, whole-genome resequencing of 73 pigs identified 24,125,658 high-quality SNPs, among which 146 were significantly associated with fatty acid traits, leading to the identification of 19 candidate genes linked to palmitic acid (i.e., GALNT2, RET, RHOU, PHYHIPL, FAM13C, BICC1 , and TAF5L ), oleic acid (i.e., ABCB10, LRP1B, ZNF37A, RHOBTB1, HNRNPF, TMEM26, URB2, FXYD4, PGBD5, LOC110256649 , and LOC110256821 ), and total fatty acids (i.e., UBE2E2 ). Functional annotation revealed that these candidate genes participate primarily in pathways related to lipid metabolism, glucose homeostasis, and energy balance. The identified SNPs and candidate genes provide valuable insights into the genetic architecture of the fatty acid composition in pork and may serve as molecular targets for improving meat quality through breeding.

Tibetan pigs exhibit remarkable adaptability to hypoxic high-altitude conditions. However, metatranscriptomics has not been used to investigate the transcriptional activity and functional responses of the gastrointestinal microbiota as part of their adaptation to high altitude. We collected 57 samples of the contents of the stomach, jejunum, cecum, colon, and rectum of six high-altitude Tibetan pigs (n = 6, elevation 3750 m) and six low-altitude black pigs (n = 6, elevation 500 m) for metatranscriptomic analysis. We identified 79 differentially abundant bacterial genera and 69 differentially abundant bacterial species. In particular, Lactobacillus crispatus and Lactobacillus delbrueckii were significantly more abundant in the gastrointestinal microbiota of the high-altitude Tibetan pigs than in that of the low-altitude black pigs. Functional analysis revealed differences in transcripts associated with energy, carbohydrate, and amino acid metabolism. The microbial correlation network of Tibetan pigs contained more nodes and edges than that of black pigs. Consistent with this, within the CAZyme database, the CBM32 family of carbohydrate-binding modules and GH27 glycosidases were significantly enriched in the Tibetan pig samples, suggesting that these enzymes may play a crucial role in energy acquisition and carbon source metabolism in these pigs. These findings provide insights into the gastrointestinal microbial characteristics of Tibetan pigs and black pigs. In summary, these changes may enhance the stability of the gut ecosystem of Tibetan pigs and improve their energy utilization in nutrient-deficient high-altitude environments. These findings suggest that the gut microbiota may contribute to metabolic regulation in Tibetan pigs at high altitude and provide important clues regarding the gastrointestinal adaptations of high-altitude animals.