With the rising cost of animal feed protein, finding affordable and effective substitutes is crucial. Walnut kernel cake, a polyphenol-, fiber-, protein- and fat-rich byproduct of walnut oil extraction, has been underexplored as a potential protein replacement in pig feed. In this study, we found that feeding large Diqing Tibetan pigs walnut kernel cake promoted adipose deposition and improved pork quality during pig growth. Transcriptome analysis revealed the upregulation of genes ANGPTL8, CCNP, ETV4, and TRIB3, associated with adipose deposition. Pathway analysis highlighted enrichment in adipose deposition-related pathways, including PPAR, insulin, PI3K-Akt, Wnt, and MAPK signaling. Further analysis identified DEGs (differentially expressed genes) positively correlated with adipose-related traits, such as PER2 and PTGES. Single-cell transcriptome data pointed to the specific expression of CD248 and PTGES in adipocyte progenitor/stem cells (APSCs), pivotal for adipocyte differentiation and adipose deposition regulation. This study demonstrates walnut kernel cake’s potential to substitute soybean cake in pig feed, providing high-quality protein and promoting adipose deposition. It offers insights into feed protein replacement, human functional food, fat metabolism, and related diseases, with marker genes and pathways supporting pig breeding and pork quality improvement.

The Jianshui yellow–brown duck is a unique country-specific waterfowl species in Yunnan Province, well known for its tender meat. However, there is a lack of comprehensive systematic research on the molecular genetic characteristics, especially germplasm resources and economic traits, of the Jianshui yellow–brown ducks. This study investigated the molecular genetic characteristics of Jianshui yellow–brown ducks, compared their selection signals with those of ancestral mallard and meat-type Pekin ducks, and identified genes specific to their meat-use performance. Furthermore, this study also evaluated the breeding potential for its meat performance. In this study, phylogenetic trees, PCA and Admixture analysis were used to investigate the population genetic structure among local duck breeds in China; population genetic differentiation index (Fst), nucleotide diversity and Tajima’s D were used to detect selected loci and genes in the population of Jianshui yellow–brown ducks; and transcriptome technology was used to screen for differentially expressed genes in the liver, sebum and breast muscle tissues, and finally, the results of the genome selection signals and transcriptome data were integrated to excavate functional genes affecting the meat performance of the Jianshui yellow–brown ducks. The results of the genetic structure of the population showed that Jianshui yellow–brown ducks were clustered into a separate group. Selection signal analysis indicated significant selection pressure on certain genes related to meat characteristics (ELOVL2, ELOVL3, GDF10, VSTM2A, PHOSPHO1, and IGF2BP1) in both Jianshui yellow–brown ducks and mallards. Transcriptomic data analysis suggested that ELOVL3, PHOSPHO1, and GDF10 are vital candidate genes influencing meat production and quality in Jianshui yellow–brown ducks. A comparison of selection signals between Jianshui yellow–brown ducks and Pekin ducks revealed only 21 selected genes in the Jianshui yellow–brown duck population, and no significant genes were related to meat traits. Moreover, whole-genome resequencing data suggested that the Jianshui yellow–brown duck represents a unique category with distinct genetic mechanisms. Through selection signaling and transcriptomic approaches, we successfully screened and identified important candidate genes affecting meat traits in Jianshui yellow–brown ducks. Furthermore, the Jianshui yellow–brown duck has good potential for improved meat performance, highlighting the need for further improvement.

Tibetan pigs, which have long inhabited the Qinghai-Tibet Plateau at elevations exceeding 3000 m, serve as an ideal model for studying adaptation to extreme high-altitude environments. The multifunctionality of the liver (hematopoiesis, metabolism, detoxification) plays a crucial role in the adaptation of Tibetan pigs to hypoxic and cold environments, yet the specific mechanisms remain unclear. This study employed single-nucleus RNA sequencing to profile and conduct bioinformatic analyses on the liver tissues of Diqing Tibetan pigs across 5 developmental stages (embryonic day 25, embryonic day 55, day of birth, development to 30 days, and development to 90 days). The goal was to identify and investigate key cell types and the regulatory mechanisms of core gene expression that facilitate adaptation to hypoxia and cold. In the fetal liver, various subpopulations of erythrocytes were detected. Analysis of these subpopulations allowed for the construction of a cellular development trajectory from proliferative erythrocytes to division erythrocytes to denucleating erythrocytes, revealing that key transcription factors (JUNB and MAFF) and functional genes (HBP1 and PPP2CB) play significant roles in erythrocyte enucleation. Furthermore, the presence of hematopoietic stem cells in the postnatal liver was observed, with identification of subpopulations exhibiting myeloid differentiation tendencies. These cells continuously support hematopoiesis and facilitate new blood vessel formation, thereby increasing red blood cell counts to aid in the adaptation of Diqing Tibetan pigs to hypoxic conditions. Additionally, a class of hepatocytes capable of converting metabolic energy into heat through uncoupling processes was identified, which assists in the adaptation to the cold environments of the plateau. In summary, our study provides new scientific perspectives on the adaptation mechanisms of high-altitude animals to extreme environments.

Meat yield, determined by muscle growth and development, is an important economic trait for the swine industry and a focus of research in animal genetics and breeding. PDZ and LIM domain 5 (PDLIM5) are cytoskeleton-related proteins that play key roles in various tissues and cells. These proteins have multiple isoforms, primarily categorized as short (PDLIM5-short) and long (PDLIM5-long) types, distinguished by the absence and presence of an LIM domain, respectively. However, the expression patterns of swine PDLIM5 isoforms and their regulation during porcine skeletal muscle development remain largely unexplored. We observed that PDLIM5-long was expressed at very low levels in pig muscles and that PDLIM5-short and total PDLIM5 were highly expressed in the muscles of slow-growing pigs, suggesting that PDLIM5-short, the dominant transcript in pigs, is associated with a slow rate of muscle growth. PDLIM5-short suppressed myoblast proliferation and myogenic differentiation in vitro. We also identified two single nucleotide polymorphisms (−258 A > T and −191 T > G) in the 5′ flanking region of PDLIM5, which influenced the activity of the promoter and were associated with muscle growth rate in pigs. In summary, we demonstrated that PDLIM5-short negatively regulates myoblast proliferation and differentiation, providing a theoretical basis for improving pig breeding programs.

With the rising cost of animal feed protein, finding affordable and effective substitutes is crucial. Walnut kernel cake, a polyphenols, fiber, protein and fat-rich byproduct of walnut oil extraction, has been underexplored as a potential protein replacement in pig feed. In this study, we found that feeding large Diqing Tibetan pigs walnut kernel cake promoted adipose deposition and improved pork quality during pig growth. Transcriptome analysis revealed the upregulation of genes ANGPTL8, CCNP, ETV4, and TRIB3, associated with adipose deposition. Pathway analysis highlighted enrichment in adipose-deposition-related pathways, including PPAR, Insulin, PI3K-Akt, Wnt, and MAPK signaling. Further analysis identified DEGs (differentially expressed genes) positively correlated with adipose-related traits, such as PER2 and PTGES. Single-cell transcriptome data pointed to the specific expression of CD248 and PTGES in adipocyte progenitor/stem cells (APSCs), pivotal for adipocyte differentiation and adipose deposition regulation. This study demonstrates walnut kernel cake's potential to substitute soybean cake in pig feed, providing high-quality protein and promoting adipose deposition. It offers insights into feed protein replacement, human functional food, fat metabolism, and related diseases, with marker genes and pathways supporting pig breeding and pork quality improvement.

This study investigated the metabolite dynamic changes and transformation pathways in Diqing Tibetan pig (DTP) hams during fermentation (0, 30, 90, 180, 360, 540 d) by widely targeted metabolomics. A total of 873 metabolites in 17 subclasses were detected, with significant changes in 448 metabolites. Additionally, 65 key metabolites were found to be involved in the top 10 pathways, with the top pathways for metabolite markers in mature hams including protein metabolism (2-oxocarboxylic acid metabolism, tryptophan metabolism and amino acid biosynthesis) and lipid metabolism (unsaturated fatty acid biosynthesis and linoleic acid metabolism). Overall, the unique DTP ham taste, flavor, and nutritional value may be contributed to by the significant accumulation of essential amino acids, MSG-like amino acids, free fatty acids (arachidonic acid, docosahexaenoic acid, and eicosapentaenoic acid), citric acid, oxaloacetic acid, succinic acid, and vitamin B. This study facilitates a comprehensive understanding of metabolic profiling and the transformation pathways of DTP hams during fermentation, providing novel insights into the biochemical mechanisms underlying traditional Tibetan pig hams, bridging traditional knowledge with modern omics technologies.