A central challenge in functional genomics is understanding the difference between correlative transcriptomic observations and definitive causal understanding of gene function in vivo. Poultry skeletal muscle, a system of significant agricultural and biological importance, demonstrates this challenge. While transcriptomic studies have cataloged extensive RNA expression dynamics during muscle development and in growth-related myopathies like wooden breast, establishing causative roles for these molecules is lacking. This review synthesizes how advanced genetic tools are now enabling a shift from correlation to causation in avian muscle biology. We detail how viral vectors (e.g., adenovirus, lentivirus, and RCAS) and CRISPR/Cas9 systems have provided direct in vivo validation of the functional roles of specific mRNAs, miRNAs, lncRNAs, and circRNAs in regulating myogenesis, hypertrophy, and atrophy. We contrast this success in fundamental biology with the study of myopathies, which remains largely descriptive. Here, a wealth of transcriptomic data has identified dysregulated pathways, including ECM remodeling, metabolism, and inflammation, but functional validation for most candidates is absent. We argue that the critical next step is to apply this established functional genomics toolkit to disease models. By defining causal mechanisms, this research will not only address a major agricultural issue but also provide a model for using genetic tools to dissect complex traits in a post-genomic era.

Streptococcus agalactiae ATCC 27956 is a highly contagious Gram-positive bacterium that causes mastitis, has a high infectivity for mammary epithelial cells, and becomes challenging to treat. However, the molecular interactions between it and mammary epithelial cells remain poorly understood. This study analyzed differential gene expression in mammary epithelial cells with varying levels of S. agalactiae infection using UID-Dual transcriptome sequencing and bioinformatics tools. This study identified 211 differentially expressed mRNAs (DEmRNAs) and 452 differentially expressed lncRNAs (DElncRNAs) in host cells, primarily enriched in anti-inflammatory responses, immune responses, and cancer-related processes. Additionally, 854 pathogen differentially expressed mRNAs (pDEmRNAs) were identified, mainly enriched in protein metabolism, gene expression, and biosynthesis processes. Mammary epithelial cells activate pathways, such as the ERK1/2 pathway, to produce reactive oxygen species (ROS) to eliminate bacteria. The bacteria disrupt the host’s innate immune mechanisms by interfering with the alternative splicing processes of mammary epithelial cells. Specifically, the bacterial genes of tsf, prfB, and infC can interfere with lncRNAs targeting RUNX1 and BCL2L11 in mammary epithelial cells, affecting the alternative splicing of target genes and altering normal molecular regulation.

The impacts of omnivorous feeding on intestinal morphology and microbial community structure remain a critical area of research in poultry science, uncovering potential biological mechanisms regulating growth and development. This study investigated how feeding regimes modulate antioxidant enzyme activities, intestinal morphological structure, gut microbiota, and the relationship between gut microbiota and meat quality. We conducted a comprehensive analysis integrating antioxidant enzyme activities, intestinal histomorphology, and 16S rRNA gene sequencing. Correlation analyses were performed to identify key microbial taxa influencing meat quality. Omnivorous feeding significantly altered the activities of certain antioxidant enzymes in the serum and selected intestinal tissues of both White Recessive Rock and Xinghua chickens. Omnivorous feeding significantly reduced the VH/CD ratio in specific intestinal segments. Microbial analysis revealed that omnivorous feeding modulated the relative abundances of Bacillus, Enterococcus, Escherichia-Shigella, and Romboutsia. These shifts promoted metabolic functions, including carbohydrate, amino acid, and energy metabolism. Crucially, correlation analysis identified Faecalibacterium, Bacillus, Romboutsia, Streptococcus, and unclassified UCG_010 as key genera significantly associated with meat quality traits. The findings suggest that omnivorous feeding shows the potential to improve poultry health and meat quality.

Domestic chicken is an ideal model to study the relationship between lipid metabolism and environmental stress. However, the lipid composition of chicken embryonic brain under hypoxic conditions has not been systematically elucidated. We employed targeted lipidomics to comprehensively describe the alterations in the brain lipid profiles of embryonic day 18 TBCs and DLCs under hypoxia (13% O₂, HTBC18, and HDLC18) and normoxia (21% O₂, NTBC18, and NDLC18). Totally 1288 lipid species from 18 lipid classes were identified and screened for 47 (three up-regulated and 44 down-regulated) and 55 (10 up-regulated and 45 down-regulated) SDLs in HTBC18 compared to NTBC18 and HDLC18 compared to NDLC18, respectively. The five SDLs were shared between HTBC18 vs. NTBC18 and HDLC18 vs. NDLC18, including PI (16:0_20:3), PE (18:1_20:4), PC (20:0_22:5), PS (16:1_18:0) and PS (16:0_20:3), which were identified as candidate hypoxia-responsive lipids. Furthermore, the analysis of SDLs’ metabolic pathways revealed that glycerophospholipid metabolism was the most crucial. The present results provide insights into the dynamic composition of lipid in chicken embryo brains under hypoxic conditions.

Mastitis severely hinders dairy farming, with Streptococcus agalactiae (S. agalactiae) serving as a major causative pathogen. Prolonged antibiotic administration promotes the emergence of multidrug-resistant strains, thereby compromising mastitis control. Consequently, novel natural antibacterial agents are urgently needed. In this study, bacteriostatic assays identified the MIC of rosmarinic acid (RA) against S. agalactiae as 8 mg/mL. At the MIC, RA reduced the adhesion capacity of S. agalactiae by 16.6% and inhibited biofilm formation by 25.09%. RA also disrupted bacterial membrane architecture and markedly downregulated the expression of virulence factors. A mouse model of mastitis treated with varying doses of RA (25, 50, and 100 mg/kg) indicated that RA attenuated pathological damage to the mammary duct architecture and ameliorated inflammatory responses in S. agalactiae-infected mice. ELISA revealed that RA significantly reduced pro-inflammatory mediators, including IL-1α, IL-1β, IL-6, and TNF-α. RT-qPCR results indicated that mRNA expression levels of TLR2, NF-κB, AKT, and PI3K were substantially reduced following RA treatment, whereas apoptosis-related genes p53, RUNX1, and Bim exhibited distinct expression patterns. Western blotting analysis further indicated that RA modulated the phosphorylation of Bim, RUNX1, and p53 in mastitis tissues, suppressed the TLR2/NF-κB inflammatory signaling pathway, and regulated the PI3K/AKT cascade. By targeting multiple pathways, RA suppressed S. agalactiae proliferation and attenuated mammary gland inflammation, highlighting its potential as a green therapeutic agent for sustainable animal husbandry.