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Cattle traits like average daily weight gain (ADG) greatly impact profitability. Selecting based on ADG considering genetic variability can lead to economic and genetic advancements in cattle breeding. This study aimed to unravel genetic influences on ADG variation in Hanwoo cattle at the skeletal muscle transcriptomic level. RNA sequencing was conducted on longissimus dorsi (LD), semimembranosus (SB), and psoas major (PM) muscles of 14 steers assigned to same feed, grouped by low (≤ 0.71 kg) and high (≥ 0.77 kg) ADG. At P ≤ 0.05 and log2fold > 1.5, the distinct pattern of gene expression was identified with 184, 172, and 210 differentially expressed genes in LD, SB, and PM muscles, respectively. Tissue-specific responses to ADG variation were evident, with myogenesis and differentiation associated JAK-STAT signaling pathway and prolactin signaling pathways enriched in LD and SB muscles, while adipogenesis-related PPAR signaling pathways were enriched in PM muscle. Key hub genes ( AXIN2 , CDKN1A , MYC , PTGS2 , FZD5 , SPP1 ) were upregulated and functionally significant in muscle growth and differentiation. Notably, DPP6 , CDKN1A , and FZD5 emerged as possible candidate genes linked to ADG variation. These findings enhance our understanding of genetic factors behind ADG variation in Hanwoo cattle, illuminating skeletal muscle mechanisms influencing ADG.

Reproduction, especially impregnation, is a critical aspect of dairy cow management that directly influences herd milk productivity. We conducted a noninvasive hair mineral assay to compare the mineral profiles of two dairy cow groups: reproducible and repeat breeder, by investigating the levels of 11 essential minerals (Ca, Mg, Na, K, Fe, Cu, Mn, Zn, Cr, Se, and P) and 6 toxic elements (Hg, Pb, Cd, Al, As, and Ni) in both groups. We also conducted principal component and correlation matrix analyses to compare hair mineral patterns between the groups. Compared to their reproducible counterparts, repeat breeder cows had lower levels of Na, K, and Se. However, Fe, Cd, Al, and As levels were higher in repeat breeders than in their reproducible counterparts. The correlation matrix showed notable correlation patterns for each group. Ca, K, and Na levels were positively correlated in reproducible cows, whereas repeat breeder cows showed positive correlations only between Ca and K levels. Se showed positive correlations with Zn only in the reproducible cow group. Negative correlations were not found in the reproducible group, whereas the repeat breeder group exhibited 7 negative correlations. Despite the limitations of hair mineral analysis, this study provided useful insights into the reproductive potential of dairy cows. These findings aid in easing the prediction of repeat breeder occurrences in herds and are expected to facilitate timely mineral supplementation and other interventions to improve overall herd reproduction in dairy farms.

Background Hanwoo cattle are a Korean breed renowned for their cultural significance and high-quality beef, characterized by low cholesterol and a high unsaturated fat ratio. Their growth is divided into a growing stage focused on development and a fattening stage for marbling. Proper feed management, considering genetic and environmental factors, is vital for maximizing growth potential. The rumen plays a crucial role in digestion and gene expression regulation, with rumen fermentation being central to nutrient absorption and cattle health. In this study, we conduct a transcriptome analysis of the rumen at eight timepoints. Our goal is to identify genetic factors that influence the growth of Hanwoo steers to enhance our understanding of the rumen’s functions during Hanwoo growth. Results In the RNA-sequencing analysis of Hanwoo steer rumen, differential gene expression was examined over eight timepoints, highlighting significant genetic changes, particularly between 12 and 26 months. The results of a weighted gene co-expression network analysis were identified and organized into three modules: turquoise, blue, and yellow. The turquoise module, linked to immune response, showed significantly down-regulation in genes at 30 months. The blue module, associated with steroid metabolism, was notably up-regulated at 26 months. The yellow module’s genes showed a consistent increase in expression with growth. These modules and their functional annotations provide a deeper understanding of the biological processes during Hanwoo growth, highlighting the intricate relationship between gene expression and cattle development. Conclusions The growth stages of Hanwoo steers were explored in our investigation utilizing rumen transcriptome data. The rumen plays a critical role in their development, particularly during the growing and fattening stages. Proper feed management, considering the rumen’s function, is essential for optimal growth. Transcriptome analysis helps identify genes associated with growth and provides insights for cattle breeding and management practices. Understanding the complex connection between gene expression and Hanwoo development is essential for maximizing productivity and health.

This study aims to characterize tissue-specific expression patterns in Hanwoo steers by identifying co-expression modules, functional pathways, and hub genes related to fat and muscle traits using Weighted Gene Co-expression Network analysis (WGCNA). RNA-Seq data were generated from three muscle tissues (longissimus muscle, tenderloin, and rump) and two fat tissues (back fat and abdominal fat) collected from six 30-month-old Hanwoo steers. Quality control of raw sequencing reads was performed using FastQC, and trimmed reads were aligned to the bovine reference genome (ARS-UCD1.3) using HISAT2. We also identified a gene co-expression network via WGCNA using normalized gene expression values. Modules were defined based on topological overlap and correlated with tissue-specific expression patterns. Modules with a significant association (p < 0.05) were used for functional enrichment based on Gene Ontology (GO) and KEGG pathways, as well as Protein–Protein Interaction Network analysis. A total of seven co-expression modules were identified by WGCNA and labeled in distinct colors (yellow, blue, red, brown, turquoise, green, black). Among them, the yellow and blue modules were positively associated with back fat, while the turquoise and green modules showed a negative correlation with abdominal fat. Additionally, the turquoise or green module was positively correlated with longissimus and rump tissues, indicating distinct gene expression patterns between fat and muscle. This study identified key co-expression modules and hub genes associated with muscle and fat metabolism. Notably, ARPC5 (blue module) was involved in lipid metabolism and energy storage, whereas AGPAT5 (turquoise module) was linked to maintaining muscle cell structure and function. These findings reveal biological mechanisms for tissue-specific gene regulation, providing targets for enhancing meat quality in Hanwoo.

Minipigs are widely used as animal models in biomedical research because they have distinctive advantages, including small body size. However, the regulatory roles of long non-coding RNAs (lncRNAs) in shaping their distinct characteristics remain unexplored. In this study, we performed a comparative transcriptomic analysis of five tissues (heart, kidney, liver, lung, and spleen) from three breeds of minipig (ET-type, L-type, and Bama minipigs) and two breeds of pig (Duroc and Landrace). We identified 5,288 lncRNAs and found that their expression patterns distinguished breeds more prominently than protein-coding genes, suggesting the existence of different evolutionary constraints between them. Based on differential expression analyses, we identified tissue-common lncRNAs (tcDELs) that exhibited consistent expression differences between minipigs and pigs, as well as tissue-specific lncRNAs (tsDELs) with unique expression patterns in individual minipig tissues. Expression correlation analysis and functional enrichment of associated protein-coding genes revealed that these lncRNAs are involved in a wide range of biological processes. Notably, tcDELs were linked to pathways related to organ size and gene regulation across tissues, while tsDELs were associated with physiological functions specific to each tissue. These findings demonstrate that lncRNAs may contribute to both tissue-common and tissue-specific traits in minipigs, reinforcing their utility as animal models.

Understanding the genetic regulatory mechanisms of fat accumulation is crucial for improving beef quality. Hanwoo (Korean native cattle) is renowned for its high intramuscular fat (marbling), yet the genetic regulation of adipose gene expression remains insufficiently understood. In this study, we performed expression quantitative trait loci (eQTL) analysis using RNA-Seq data and genotype data from backfat tissue of 75 Hanwoo steers to identify regulatory variants associated with adipose deposition. A total of 25,042 significant cis-eQTL associations (FDR < 0.05) were identified, and 5362 unique top cis-eQTL pairs were retained after gene-wise filtering. Key cis-regulated genes included AGBL1, CACNG1, MYO18B, and DUSP29, which are involved in cytoskeletal organization, muscle development and calcium signaling. Three major cis-regulatory hotspots were located on BTA15 (BTA15:50354741) and BTA21 (BTA21:21526143, and BTA21:21541921). Permutation-based analysis (100,000 iterations) was conducted to control false positives, identifying 12 statistically significant trans-eQTL hotspots (FDR q < 0.05), of which SNP 6:60512276 and SNP 21:17035557 exhibited extensive trans-regulatory activity influencing 429 and 161 genes, respectively. In particular, SNP 21:17035557 acted as a shared cis- and trans-regulatory hub, indicating hierarchical control of adipose gene networks. Functional enrichment analyses revealed significant involvement of cytoskeleton- and calcium-dependent pathways, highlighting the interplay between structural remodeling and metabolic regulation in adipose tissue. These findings provide a comprehensive, system-level view of adipose gene regulation in Hanwoo cattle and highlight candidate molecular targets for genome-assisted and precision breeding. Moreover, this study offers quantitative genomic resources that can support the development of prediction models and decision-support systems for improving carcass traits in Hanwoo breeding programs.

Climate change increases global temperatures, which is lethal to both livestock and humans. Heat stress is known as one of the various livestock stresses, and dairy cows react sensitively to high-temperature stress. We aimed to better understand the effects of heat stress on the health of dairy cows and observing biological changes. Individual cows were divided into normal (21–22 °C, 50–60% humidity) and high temperature (31–32 °C, 80–95% humidity), respectively, for 7-days. We performed metabolomic and transcriptome analyses of the blood and gut microbiomes of feces. In the high-temperature group, nine metabolites including linoleic acid and fructose were downregulated, and 154 upregulated and 72 downregulated DEGs (Differentially Expressed Genes) were identified, and eighteen microbes including Intestinimonas and Pseudoflavonifractor in genus level were significantly different from normal group. Linoleic acid and fructose have confirmed that associated with various stresses, and functional analysis of DEG and microorganisms showing significant differences confirmed that high-temperature stress is related to the inflammatory response, immune system, cellular energy mechanism, and microbial butyrate production. These biological changes were likely to withstand high-temperature stress. Immune and inflammatory responses are known to be induced by heat stress, which has been identified to maintain homeostasis through modulation at metabolome, transcriptome and microbiome levels. In these findings, heat stress condition can trigger alteration of immune system and cellular energy metabolism, which is shown as reduced metabolites, pathway enrichment and differential microbes. As results of this study did not include direct phenotypic data, we believe that additional validation is required in the future. In conclusion, high-temperature stress contributed to the reduction of metabolites, changes in gene expression patterns and composition of gut microbiota, which are thought to support dairy cows in withstanding high-temperature stress via modulating immune-related genes, and cellular energy metabolism to maintain homeostasis.

Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop “Nanchukmacdon” a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes ( UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2 ) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.

Understanding the influence of genetic variations in olfactory receptor (OR) genes on the olfaction-influenced phenotypes such as behaviors, reproduction, and feeding is important in animal biology. However, our understanding of the complexity of the OR subgenome is limited. In this study, we analyzed 1120 typing results of 20 representative OR genes belonging to 13 OR families on 14 pig chromosomes from 56 individuals belonging to seven different breeds using a sequence-based OR typing method. We showed that the presence of copy number variations, conservation of locus-specific diversity, abundance of breed-specific alleles, presence of a loss-of-function allele, and low-level purifying selection in pig OR genes could be common characteristics of OR genes in mammals. The observed nucleotide sequence diversity of pig ORs was higher than that of dogs. To the best of our knowledge, this is the first report on the individual- or population-level characterization of a large number of OR family genes in livestock species.

Background Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because of the lack of accurate identification of related structural variations (SVs) which resulted from the shortage of target breeds, the limitations of sequencing data, and the incompleteness of genome assemblies. The recent generation of a new pig breed with superior meat quality, called Nanchukmacdon, and its chromosome-level genome assembly (the NCMD assembly) has provided new opportunities. Results By applying assembly-based SV calling approaches to various genome assemblies of pigs including Nanchukmacdon, the impact of SVs on meat quality was investigated. Especially, by checking the commonality of SVs with other pig breeds, a total of 13,819 Nanchukmacdon-specific SVs (NSVs) were identified, which have a potential effect on the unique meat quality of Nanchukmacdon. The regulatory potentials of NSVs for the expression of nearby genes were further examined using transcriptome- and epigenome-based analyses in different tissues. Conclusions Whole-genome comparisons based on chromosome-level genome assemblies have led to the discovery of SVs affecting meat quality in pigs, and their regulatory potentials were analyzed. The identified NSVs will provide new insights regarding genetic architectures underlying the meat quality in pigs. Finally, this study confirms the utility of chromosome-level genome assemblies and multi-omics analysis to enhance the understanding of unique phenotypes.