Background: A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. We performed a large-scale gene expression analysis and generated a high-resolution atlas of the transcriptome in beef cattle. Results: Our transcriptome atlas was generated from 135 bovine tissues in adult beef cattle, covering 51 tissue types of major organ systems (e.g., muscular system, digestive system, immune system, reproductive system). Approximately 94.76% of sequencing reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We detected a total of 60,488 transcripts, and 32% of them were not reported before. We identified 2654 housekeeping genes (HKGs) and 477 tissue-specific genes (TSGs) across tissues. Using weighted gene co-expression network analysis, we obtained 24 modules with 237 hub genes (HUBGs). Functional enrichment analysis showed that HKGs mainly maintain the basic biological activities of cells, while TSGs were involved in tissue differentiation and specific physiological processes. HKGs in bovine tissues were more conserved in terms of expression pattern as compared to TSGs and HUBGs among multiple species. Finally, we obtained a subset of tissue-specific differentially expressed genes (DEGs) between beef and dairy cattle and several functional pathways, which may be involved in production and health traits. Conclusions: We generated a large-scale gene expression atlas across the major tissues in beef cattle, providing valuable information for enhancing genome assembly and annotation. HKGs, TSGs, and HUBGs further contribute to better understanding the biology and evolution of multiple tissues in cattle. DEGs between beef and dairy cattle also fill in the knowledge gaps about differential transcriptome regulation of bovine tissues underlying economically important traits.

Background: Beef cuts in different regions of the carcass have different meat quality due to their distinct physiological function. The objective of this study was to characterize the region-specific expression differences using comparative transcriptomics analysis among five representative beef cuts (tenderloin, longissimus lumborum, rump, neck, chuck). Results: We obtained 15,701 expressed genes in 30 muscle samples across five regions from carcass meat. We identified a total of 80 region-specific genes (RSGs), ranging from three (identified in the rump cut) to thirty (identified in the longissimus lumborum cut), and detected 25 transcription factors (TFs) for RSGs. Using a co-expression network analysis, we detected seven region-specific modules, including three positively correlated modules and four negatively correlated modules. We finally obtained 91 candidate genes related to meat quality, and the functional enrichment analyses showed that these genes were mainly involved in muscle fiber structure (e.g., TNNI1, TNNT1), fatty acids (e.g., SCD, LPL), amino acids (ALDH2, IVD, ACADS), ion channel binding (PHPT1, SNTA1, SUMO1, CNBP), protein processing (e.g., CDC37, GAPDH, NRBP1), as well as energy production and conversion (e.g., ATP8, COX8B, NDUFB6). Moreover, four candidate genes (ALDH2, CANX, IVD, PHPT1) were validated using RT-qPCR analyses which further supported our RNA-seq results. Conclusions: Our results provide valuable insights into understanding the transcriptome regulation of meat quality in different beef cuts, and these findings may further help to improve the selection for health-beneficial meat in beef cattle.

Beef is an important dietary source of quality animal proteins and amino acids in human nutrition. The fatty acid composition is one of the indispensable indicators affecting nutritional value of beef. However, a comprehensive understanding of the expression changes underlying fatty acid composition in representative beef cuts is needed in cattle. This study aimed to characterize the dynamics of fatty acid composition using comparative transcriptomic analysis in five different type of beef cuts. We identified 7545 differentially expressed genes (DEGs) among 10 pair-wise comparisons. Co-expression gene network analysis identified two modules, which were significantly correlated with 2 and 20 fatty acid composition, respectively. We also identified 38 candidate genes, and functional enrichment showed that these genes were involved in fatty acid biosynthetic process and degradation, PPAR, and AMPK signaling pathway. Moreover, we observed a cluster of DEGs (e.g., SCD, LPL, FABP3, and PPARD) which were involved in the regulation of lipid metabolism and adipocyte differentiation. Our results provide some valuable insights into understanding the transcriptome regulation of candidate genes on fatty acid composition of beef cuts, and our findings may facilitate the designs of genetic selection program for beneficial fatty acid composition in beef cattle.

Body weight is a polygenic trait with intricate inheritance patterns. Functional genomics enriched with multi-layer annotations offers essential resources for exploring the genetic architecture of complex traits. In this study, we conducted an extensive characterization of regulatory variants associated with body weight-related traits in cattle using multi-omics analysis. First, we identified seven candidate genes by integrating selective sweep analysis and multiple genome-wide association study (GWAS) strategies using imputed whole-genome sequencing data from a population of 1577 individuals. Subsequently, we uncovered 3340 eGenes (genes whose expression levels are associated with genetic variants) across 227 muscle samples. Transcriptome-wide association studies (TWASs) further revealed a total of 532 distinct candidate genes associated with body weight-related traits. Colocalization analyses unveiled 44 genes shared between expression quantitative trait loci (eQTLs) and GWAS signals. Moreover, a comprehensive analysis by integrating GWAS, selective sweep, eQTL, TWAS, epigenomic profiling, and molecular validation highlighted a positively selected genomic region on Bos taurus autosome 6 (BTA6). This locus harbors pleiotropic genes (LAP3, MED28, and NCAPG) and a prioritized functional variant involved in the complex regulation of body weight. Additionally, convergent evolution analysis and phenome-wide association studies underscored the conservation of this locus across species. Our study provides a comprehensive understanding of the genetic regulation of body weight through multi-omics analysis in cattle. Our findings contribute to unraveling the genetic mechanisms governing weight-related traits and shed valuable light on the genetic improvement of farm animals.

Fatty acid composition is a complex trait governed by a polygenic architecture. Although numerous genetic variants associated with fatty acids have been id