Background: There have been many studies on the relationship between circRNAs and fat deposition. Although the liver is a central organ for fat metabolism, there are few reports on the relationship between circRNAs in the liver and fat deposition. Methods: In this study, we systematically analyzed circular RNAs in the liver of Ningxiang pigs, at four time points after birth (30 days, 90 days, 150 days and 210 days). Results: A total of 3705 circRNAs were coexpressed in four time periods were found, and KEGG analysis showed that the significantly upregulated pathways were mainly enriched in lipid metabolism and amino acid metabolism, while significantly downregulated pathways were mainly related to signal transduction, such as ECM–receptor interaction, MAPK signaling pathway, etc. Short time-series expression miner (STEM) analysis showed multiple model spectra that were significantly enriched over time in the liver. By constructing a competing endogenous RNA (ceRNA) regulatory network, 9187 pairs of networks related to the change in development time were screened. Conclusions: The expression profiles of circRNAs in Ningxiang pig liver were revealed at different development periods, and it was determined that there is differential coexpression. Through enrichment analysis of these circRNAs, it was revealed that host genes were involved in metabolism-related signaling pathways and fatty acid anabolism. Through STEM analysis, many circRNAs involved in fat metabolism, transport, and deposition pathways were screened, and the first circRNA–miRNA–mRNA regulation network map in Ningxiang pig liver was constructed. The highly expressed circRNAs related to fat deposition were verified and were consistent with RNA-Seq results.

Although age-related changes in the gut microbiome of pigs have been extensively studied, the dynamic patterns of fecal microbiota and SCFAs during the gestation-to-weaning period in sows remain poorly characterized. We aim to characterize the changes in fecal microbiota and SCFAs from pregnancy to weaning, and to investigate their associations with maternal weight gain during gestation. We systematically collected 100 fecal samples at four time points (day 30 of pregnancy (T1), 1–2 days before delivery (T2), day 10 after delivery (T3), and day 21 of weaning stage (T3)), and measured the body weight of sows at T1 (132 kg ± 10.8) and T2 (205 kg ± 12.1). The primary nutrient components of the diets during the gestation and lactation periods are summarized. All fecal samples were subjected to 16S rRNA gene sequencing. We found that a high proportion of crude fiber (bran) is a key feature of the gestation diet, which may affect enterotype shifts and gut microbial composition. Sows fed a high-fiber diet showed significant enrichment of gut microbiota, including genera such as Prevotellaceae_UCG-003, Prevotellaceae_NK3B31_group, and Prevotella_9 during the gestational period (LDA score > 2). Moreover, Eubacterium_coprostanoligenes_group (average relative abundance: 5.5%) and Lachnospiraceae_NK4A136_group (average relative abundance: 2.5%) were the dominant bacteria during the lactation stage. Fecal propionate and butyrate levels were lowest in late gestation, and propionate negatively and acetate positively correlated with body weight change (p < 0.05). Additionally, certain Prevotella taxa were associated with arachidonic acid metabolism and acetate production (p < 0.05). Our study identified key microbial communities across four stages from gestation to weaning and revealed that dietary patterns can shape the sow gut microbiota. Furthermore, we observed significant correlations between SCFAs and body weight change during pregnancy. These findings provide a scientific basis and theoretical support for future strategies aimed at modulating gut microbiota and targeting SCFAs to improve maternal health and productivity throughout the gestation-to-weaning period.

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.

Skeletal muscles, accounting for 40% of mammalian body mass, exhibit pronounced heterogeneity due to their distinct anatomical locations. Animal husbandry has focused excessively on longissimus dorsi (LDM) development while neglecting other muscles. In this study, we integrated Bulk RNA Sequencing (bulk RNA-seq) and Liquid Chromatography–Mass Spectrometry (LC-MS) analyses of Soleus (SOL), Gastrocnemius (GAS), and Psoas major muscles (PMM) across three key stages in Duroc pigs. We identified nine critical genes (S100A1, MBOAT2, CA3, GYG2, ACTN3, ENO3, SLC3A2, SLC16A10, and GAPDH) and eight metabolites potentially involved in regulating both skeletal muscle development and fiber-type transformation. The heterogeneity between SOL and GAS was low at birth but increased gradually during development. In contrast, PMM exhibited higher heterogeneity than SOL and GAS from birth. Notably, expression levels of MYH7, MYH1, and MYH4 displayed stage-specific and muscle type-dependent variations. Moreover, we observed a developmental shift from the MAPK signaling pathway (1–21 d) to the regulation of the actin cytoskeleton (21–120 d). Pairwise comparisons between the SOL, GAS, and PMM revealed that the signaling pathways were enriched in muscle fiber-type switching. Collectively, through the integration of bulk RNA-seq and LC-MS data, this study provides novel molecular breeding strategies for the genetic improvement of meat-producing animals.

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.

To unravel the genetic basis of economically critical reproductive traits in swine, we genotyped 839 sows from three commercial breeds (Duroc, Landrace, Yorkshire) using the Porcine Breeding Chip_plus 50K SNP array, and analyzed three key traits: total number born (TNB), number born alive (NBA), and number of healthy piglets (NHP). We integrated principal component analysis (PCA) for population structure, runs of homozygosity (ROH) detection, genome-wide association studies (GWAS), and GO/KEGG enrichment analysis. Phenotypically, Yorkshire sows exhibited superior and persistent reproductive capacity across parities 1–7 (peak TNB: 14.17 ± 2.82 at parity 4 based on N ≥ 3 data), Duroc sows had limited data with only parity 1 available (TNB: 9.44 ± 2.13), and Landrace sows showed moderate to high performance across parities 1–4 and 7, with peak TNB at parity 4 (17.08 ± 4.61). ROH analysis further revealed that short ROH fragments (1–5 Mb) were the most abundant category across breeds, while the majority of detected ROH were under 10 Mb in length. GWAS identified significant SNPs concentrated on chromosomes 1 and 2, and annotated candidate genes including AMH (ovarian reserve), IZUMO4 (embryo implantation), ACSBG2 (steroid synthesis), RFX2 (follicular maturation), and DOT1L (embryonic development). GO/KEGG enrichment highlighted pathways such as “histone methyltransferase activity” and “fatty acid biosynthesis”, which are critical for reproductive processes. This study clarifies breed-specific reproductive patterns and identifies key genetic loci/genes for porcine reproductive traits, providing molecular markers and a theoretical basis for improving swine reproductive performance via molecular breeding.