Age is an important physiological factor that affects the metabolism and immune function of beef cattle. While there have been many studies using the blood transcriptome to study the effects of age on gene expression, few have been reported on beef cattle. To this end, we used the blood transcriptomes of Japanese black cattle at different ages as the study subjects and screened 1055, 345, and 1058 differential expressed genes (DEGs) in the calf vs. adult, adult vs. old, and calf vs. old comparison groups, respectively. The weighted co-expression network consisted of 1731 genes. Finally, blue, brown, and yellow age-specific modules were obtained, in which genes were enriched in signaling pathways related to growth and development and immune metabolic dysfunction, respectively. Protein-protein interaction (PPI) analysis showed gene interactions in each specific module, and 20 of the highest connectivity genes were chosen as potential hub genes. Finally, we identified 495, 244, and 1007 genes by exon-wide selection signature (EWSS) analysis of different comparison groups. Combining the results of hub genes, we found that VWF, PARVB, PRKCA, and TGFB1I1 could be used as candidate genes for growth and development stages of beef cattle. CORO2B and SDK1 could be used as candidate marker genes associated with aging. In conclusion, by comparing the blood transcriptome of calves, adult cattle, and old cattle, the candidate genes related to immunity and metabolism affected by age were identified, and the gene co-expression network of different age stages was constructed. It provides a data basis for exploring the growth, development, and aging of beef cattle.

Negative energy balance (NEB) during the perinatal period leads to metabolic and immunological disorders in dairy cows, resulting in systemic responses and inflammation. The innate immune system is crucial for the host’s protection and inflammatory response. However, systematic research is still lacking on how NEB affects the innate immune system to alter the ’host defense capability and inflammatory response. In this investigation, raw transcriptome data of adipose, blood, endometrial, hypothalamus, and liver tissues were downloaded from a public database, cleaned, aligned, quantified, and batch-corrected. The innate immune gene list was retrieved from innateDB, followed by the expression matrix of innate immune genes in various tissues for differential expression analysis, principle component analysis (PCA), and gene set enrichment analysis (GSEA). Under the effect of NEB, adipose tissue had the most differentially expressed genes, which were predominantly up-regulated, whereas blood GSEA had the most enriched biological processes, which were predominantly down-regulated. The gene sets shared by different tissues, which are predominantly involved in biological processes associated with defense responses and inflammation, were dramatically down-regulated in endometrial tissues and highly up-regulated in other tissues. Under the impact of NEB, LBP, PTX3, S100A12, and LCN2 play essential roles in metabolism and immunological control. In conclusion, NEB can downregulate the defensive response of innate immune genes in endometrial, upregulate the immune and inflammatory response of other tissues, activate the host defense response, and increase the systemic inflammatory response. The analysis of the effects of NEB on innate immune genes from the multiple tissues analysis provides new insights into the crosstalk between metabolism and immunity and also provides potential molecular targets for disease diagnosis and disease resistance breeding in dairy cows.

Maternal parity is an important physiological factor influencing beef cow reproductive performance. However, there are few studies on the influence of different calving periods on early growth and postpartum diseases. Here, we conducted blood transcriptomic analysis on cows of different parities for gene discovery. We used Short Time Series Expression Miner (STEM) analysis to determine gene expression levels in cows of various parities and divided multiple parities into three main periods (nulliparous, primiparous, and multiparous) for subsequent analysis. Furthermore, the top 15,000 genes with the lowest median absolute deviation (MAD) were used to build a co-expression network using weighted correlation network analysis (WGCNA), and six independent modules were identified. Combing with Exon Wide Selection Signature (EWSS) and protein-protein interaction (PPI) analysis revealed that TPCN2, KIF22, MICAL3, RUNX2, PDE4A, TESK2, GPM6A, POLR1A, and KLHL6 involved in early growth and postpartum diseases. The GO and KEGG enrichment showed that the Parathyroid hormone synthesis, secretion, and action pathway and stem cell differentiation function-related pathways were enriched. Collectively, our study revealed candidate genes and gene networks regulating the early growth and postpartum diseases and provided new insights into the potential mechanism of reproduction advantages of different parity selection.

Optimizing calcium metabolism is crucial for skeletal development and overall productivity in growing ruminants. Twenty-four Sunite lambs were randomly assigned to four groups and fed 0, 0.6, 1.2, or 2.4 g/(d·head) of γ-PGA for 60 days. Growth performance, serum parameters, duodenal morphology and calcium transporter expression, bone microarchitecture, and duodenal microbiota were analyzed. Supplementation with 1.2 g/(d·head) of γ-PGA (the M group) yielded optimal results, significantly improving final body weight and size. It enhanced duodenal health, evidenced by increased villus height, crypt depth, and microvilli density. Crucially, this dose significantly upregulated the expression of key duodenal calcium transporters (TRPV5/6, CaBPD9k, PMCA, VDR, claudin-12) and altered systemic calcium-regulating hormones (elevated calcitriol, PTH, FGF23). Bone micro-CT analysis revealed changes in trabecular architecture indicative of active remodeling. 16S rRNA sequencing and weighted OTU co-expression network analysis (WOCNA) revealed that γ-PGA reshaped the duodenal microbiota and identified core microbial modules strongly associated with host phenotypes. Genera such as [Eubacterium]_ruminantium_group, Fusicatenibacter, and Prevotella emerged as central hubs. In conclusion, dietary γ-PGA at 1.2 g/(d·head) enhances calcium absorption and bone metabolism in lambs through a coordinated modulation of intestinal integrity and calcium transport, systemic endocrine responses, and the duodenal microbial community, with specific microbiota identified as potential key mediators associated with these effects.

The Bactrian camel (Camelus bactrianus), with its unique physiological adaptations and immune characteristics, represents a highly valuable model for innate immunity research. However, a systematic dissection of its innate immune gene repertoire and the key functional drivers within its immune response remains limited. This study integrated CRISPR-Cas9 knockout screening with time-resolved transcriptomic profiling to systematically unveil the immune regulatory mechanisms in camel dermal fibroblasts challenged with the viral mimic poly(I:C) and the bacterial mimic LPS. The CRISPR screen successfully identified 59 key genes conferring a survival advantage under lethal pathogenic challenge. The gene sets required for resisting viral versus bacterial mimics were entirely distinct, revealing divergent genetic underpinnings. Transcriptomic analysis further delineated a dynamic reprogramming of gene expression, uncovering a shared core immune response program alongside significant stimulus-specific regulation. Integrative analysis pinpointed pivotal genes, such as HSP90AA1 in the antiviral process and CSF1 in the antibacterial process, which played critical roles at both the functional screening and transcriptional regulatory levels. These key genes exhibited dynamic and evolving co-expression networks across different time points, indicating their temporally specific regulatory roles throughout the immune response. By combining functional genomics and transcriptomics, this study provides the first systematic mapping of the innate immune landscape and its dynamic regulation in the Bactrian camel, not only deepening the understanding of camelid immunobiology but also offering a new framework and insights for evolutionary studies of immune adaptation mechanisms in mammals.