Suthar Teerath Kumar

In this comparative study of 12 pigs (six Songlei black [SL] and six Duroc × Landrace × Yorkshire [DLY]), small RNA sequencing was performed on longissimus dorsi muscle samples to identify miRNAs associated with meat quality traits. A total of 343 known and 191 novel miRNAs were identified, including 21 differentially expressed miRNAs (DE-miRNAs) between breeds. Enrichment analysis showed that their target genes were enriched in the PI3K-Akt, MAPK, and calcium signaling pathways. Integration of miRNA and transcriptome datasets identified a regulatory network comprising five key miRNAs (ssc-miR-10383, ssc-miR-127, ssc-miR-370, ssc-miR-874, and a novel miRNA, novel_494) and 32 target genes annotated to autophagy, AMPK, mTOR, and FoxO signaling pathways. All five miRNAs were negatively correlated with IMF content (r = −0.77 to −0.95) and positively correlated with shear force (r = 0.62 to 0.76). This study provides the first miRNA expression profile of the longissimus dorsi muscle in SL and DLY pigs. These findings suggest that coordinated miRNA regulation may contribute to breed-specific differences in fat deposition and meat tenderness, providing candidate biomarkers for improving pork quality.

Deoxynivalenol (DON) is a common mycotoxin linked to ovarian oxidative stress, toxicity, and reduced reproductive performance. Fermented Chinese chive is known for its antioxidant properties and potential reproductive benefits, but their individual and combined effects on ovarian function remain unclear in post-pubertal mice. In this study, a 21-day oral gavage model in female Kunming mice was used to evaluate the effects of DON (2 mg/kg/day), fermented Chinese chive extract (LEEK; 0.2 mL/day), and their combined exposure (LKDON) on ovarian physiology, oocyte quality, and ovarian transcriptomic responses. The results showed that DON exposure significantly reduced the zygote cleavage rate, increased intracellular reactive oxygen species levels, and disrupted oocyte mitochondrial membrane potential. While histological examination revealed disturbed follicular architecture. Transcriptomic hub gene analysis showed that DON exposure down-regulate the key associated with innate immune responses and motile cilia/axonemal structure, including Rsph4a, Drc1, Zmynd10, Hydin, and Tmem212. In contrast, LEEK alone was associated with immunomodulatory upregulated genes, including Il5, Cd27, and Crp. Interestingly, LKDON and DON comparison revealed upregulation of a motile cilia/axoneme gene network (Dnah5, Dnah11, Tekt1, Zmynd10, Cfap44, and Spag6l), rather than a global reversal of DON-induced changes. Overall, finding suggest that DON disrupts ovarian immune and structural pathways, while fermented Chinese chive provides partial protection by modulating specific biological processes. Further studies are needed to confirm the underlying mechanisms.

The study analyzed ten reproductive traits in three major commercial breeds—Yorkshire, Landrace, and Duroc—raised under uniform management. Genetic parameters were estimated using a repeatability animal model in ASReml, genome-wide association studies (GWAS) were performed with 46,358 post-QC SNPs using GCTA, and genomic prediction was evaluated with GBLUP. Heritability estimates were low to moderate, with gestation length (GL) highest (0.33–0.41). GWAS identified significant loci across breeds: in Yorkshire, 37 genome-wide significant SNPs across 17 SSCs for seven traits; in Landrace, 16 SNPs for TNB and one for NBW; and in Duroc, 31 SNPs across 12 SSCs (predominantly for TNB). Among these SNPs, CNC10042060, CNC10160995, and CNCB10003799 were consistently associated with TNB in both Yorkshire and Duroc pigs. Additionally, five SNPs, CNC10012965, CNC10042060, CNC10120451, CNCB10003799, and CNCB10007759, showed significant associations with NBW in Yorkshire and Landrace pigs. Candidate genes mapped within ±1 Mb of significant SNPs were enriched for biologically plausible pathways. Genomic prediction accuracies ranged from low to high depending on trait and breed, such as reaching 0.68 for GL in 39 Yorkshire and 0.59 in Landrace. These results delineate shared and breed-specific genetic architectures, provide actionable markers and candidate genes, and can accelerate genetic gains in commercial breeding programs.

Heterosis or hybrid vigor is a well-recognized biological phenomenon, where crossbred progeny exhibit superior growth performance, stress tolerance, and productivity compared to their purebred parents. However, the molecular mechanisms underlying heterosis for meat quality traits in pigs remain poorly understood. In this study, we compared the longissimus dorsi muscle transcriptomes of Songliao Black Pig (SBP), Large White × Landrace pig (LWLDP), and their crossbred progeny (BXW) to uncover genetic mechanisms contributing to hybrid vigor in meat quality. Results identified 4290 differentially expressed genes (DEGs) in SBP vs. BXW and 3820 in LWLDP vs. BXW. Among these, 1358 genes displayed overdominant expression in BXW, indicating potential heterotic activation. Functional enrichment analysis identified key pathways involved in lipid metabolism, energy homeostasis, and muscle growth, including mTOR, AMPK, insulin, PI3K-Akt, MAPK, and calcium signaling. Over dominantly expressed genes such as FASN, CPT1A, PPARG, ACACA, PPARA, SREBF1, FABP4, DGAT1, PPARGC1A, LIPC, ACSL5, PLCG2, and members of the COX family were closely associated with intramuscular fat deposition, oxidative metabolism, and tenderness. Phenotypically, BXW exhibited improved meat color, moderate fat deposition, and lower shear force compared with parental breeds, clearly aligning with transcriptomic findings. These transcriptomic findings offer valuable insights into precision breeding strategies targeting superior meat quality through genomic selection and crossbreeding programs.

Pork is one of the most widely consumed meats worldwide, with tenderness and intramuscular fat (IMF) content serving as key determinants of consumer acceptance. The rising demand for high-quality pork underscores the need to better understand the molecular mechanisms regulating IMF deposition and meat tenderness. In this study, we systematically examined the tenderness and IMF in the Longissimus dorsi (LD) muscle of 104 eight-month-old Songliao black pigs and Leixiang pigs raised under identical conditions. In addition, three pigs from each breed were randomly selected for multi-omics analyses, including Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq), transcriptomics, and proteomics to elucidate the molecular networks underlying IMF deposition and tenderness. We identified a total of 2635 differentially accessible chromatin (DARs) regions associated with 2006 functional genes and 351 regulatory transcription factors, predominantly enriched in adipocyte differentiation and muscle metabolism pathways. Transcriptome analysis revealed 624 differentially expressed genes (DEGs) involved in lipid metabolism and tissue structure maintenance. While proteomic profiling detected 153 differentially expressed proteins (DEPs) enriched in fatty acid degradation/metabolism, PPAR signaling, energy metabolism, and thermogenesis pathways. Further, combined integrated multi-omics analysis identified nine candidate genes (MBP, DCLK1, COL3A1, ART3, COL14A1, PDK4, VCAN, LIPE, and GPX1) and transcription factor–target interaction networks predicted key regulatory factors including MEF2A/C/D, PR, GR, AR-HALLSITE, NF1-HALLSITE, AP4, TCF21, MYOG, ATOH1, TCF12, BHLHA15, MYF5, ASCL1, and SIX2, which were potentially involved in the regulation of meat tenderness and IMF deposition. These findings provide novel insights into the molecular determinants of IMF and tenderness, offering valuable targets for improving meat quality through genetic breeding strategies.

Early testicular development is vital for adult male fertility but remains highly vulnerable to stress during the suckling stage. Fermented Chinese chive (Allium tuberosum) is known for its antioxidant and immunomodulatory properties, yet its role in testicular development remains unclear. In this study, Songliao Black piglets received 3‰ fermented Chinese chive (LK group) mixed with starter feed and compared to a control (OD group). Testicular samples at weaning (28 days) underwent transcriptomic and metabolomic analyses. Although no significant differences were observed in gross testicular morphology, the LK group significantly increased individual (13.85%) and litter (15.11%) weaning weights (p < 0.05), with elevated serum triglycerides, total cholesterol, and a 32.2% rise in IgG levels (p < 0.05). Integrated analysis identified 76 shared pathways, including ferroptosis, insulin resistance, PI3K-Akt, MAPK, and cAMP signaling. Upregulated genes in the LK group were mainly related to energy metabolism, antioxidant defense, immune regulation, steroidogenesis, and neuroendocrine signaling, suggesting improved metabolic activity, reduced oxidative stress, and accelerated reproductive maturation. Molecular docking indicated that kaempferol and isorhamnetin from Chinese chive bind strongly to proteins involved in testicular development. Overall, fermented Chinese chive supplementation enhances early testicular development in suckling piglets via integrated modulation of metabolic, immune, and signaling pathways, providing a nutritional strategy to optimize reproductive potential in breeding boars.

Meat quality is a complex trait that exhibits significant variation across pig breeds, and the regulatory mechanisms governing pork meat quality are not fully elucidated. We compared the transcriptomics and metabolomics of the longissimus dorsi (LD) muscle between the Songliao Black Pig (SBP) and Large White × Landrace Pig (LWLDP) to investigate breed-specific differences in meat quality and underlying regulatory pathways. The results showed that SBP meat had a higher marbling score and backfat thickness, a richer color, a lower shear force, and reduced drip loss. Fatty acid (FA) analysis identified 15 significant FAs in the LWLDP, with docosahexaenoic acid (DHA) in the SBP, while amino acid (AA) analysis revealed no breed-based differences. Transcriptome analysis identified 134 upregulated and 362 downregulated genes in the SBP. Protein–protein interaction (PPI) network analysis found 25 key genes, which are associated with muscle development, fat deposition, and overall meat quality, while genes in the insulin signaling pathway, such as PPP1R3B, PPARGC1A, SOCS1, EIF4E, PRKAR2A, PRKAG2, and FASN, play a crucial role in balancing fat metabolism and catabolism. Metabolomic analysis identified 89 upregulated and 10 downregulated metabolites in the SBP, primarily involved in fructose and mannose metabolism, amino acid biosynthesis, nucleotide sugar metabolism, and glucagon signaling pathways. Gene–metabolite association analysis found that the PPP1R3B gene had a strong association with Thr-Leu, Maltol, D-myo-Inositol-4-phosphate, and Fructose-6-phosphate, while MYOG correlated with Mannose-6-phosphate, Fructose-1-phosphate, Mannose-1-phosphate, and Glucose-6-phosphate. In contrast, NR4A3 and PPARGC1A showed a strong negative correlation with most upregulated metabolites. In conclusion, this study identified functional genes, elucidated the mechanisms associated with meat quality traits, and identified gene–metabolite associations involved in energy metabolism, muscle development, and fat deposition, providing valuable insights into the molecular mechanisms that regulate meat quality between pig breeds.

The gut microbiota plays a pivotal role in host metabolism, influencing the production of small metabolites from non-digestible compounds, which can accumulate in tissues and play important role in fatty acids synthesis for improving the meat quality. We investigate the breed-specific differences in longissimus dorsi (LD) muscle fatty acid profile, gut microbiota, and metabolites across the cecum, ileum, and rectum in Chinese Songliao Black pigs (SBP) and commercial Large White × Landrace crossbred pigs (LWLDP) and interactions. Significant correlations highlighting potential microbiota-metabolite interactions that contribute to muscle fatty acid composition. LWLDP pigs exhibited a higher number of significant fatty acids and maintained higher operational taxonomic units (OTUs) in the cecum and rectum, with no differences observed in the ileum between breeds. Firmicutes, Bacteroidetes, Proteobacteria, and Spirochaetes were the predominant phyla across both breeds. Differentially expressed metabolites (DEMs) were more abundant in the cecum and ileum of LWLDP, while rectum showed higher expression in SBP. Integrative analysis identified significant correlations between fatty acids, metabolites, and microbial taxa. DHA was linked to cecal metabolites and rectal microbial families, while saturated and unsaturated fatty acids were associated with different microbes and metabolites. This study demonstrates distinct breed-specific interactions between gut microbiota, metabolites, and fatty acid composition, offering insights into potential microbial interventions to enhance pork quality through fatty acid modulation.