Project description:Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle. Ruminal wall samples from two randomly chosen animals per group were obtained, totaling four samples. The animals were born, raised and maintained at the Wye Angus farm. This herd, which has been closed for almost 75 years and yielded genetically similar progenies, constitutes an excellent resource to perform transcriptomic analysis. The genetic resemblance among individuals permits us to better control the cause of variation between experimental clusters and individuals. The randomly chosen pairs of animals were part of larger sets of steers that received a particular treatment. All animals received the same diet until weaning. The grain group received conventional diet consisting of corn silage, shelled corn, soy bean and trace minerals. The grass fed steers consumed normally grazed alfalfa; during wintertime, bailage was utilized. The alfalfa has been harvested from land without any fertilizers, pesticides or other chemicals. The steers ate no animal, agricultural or industrial byproducts and never receive any type of grain. Then, the calves were randomly assigned to one diet and exclusively received that regimen until termination. Grain–fed animals reached the market weight around the age of 14 month-old, however, grass-fed steers required approximately 200 additional days to achieve the same weight. Immediately after termination at the Old Line Custom Meat Company (Baltimore, MD) a small piece of ruminal wall was excised, cleaned and preserved at -80°C for posterior processing.

Project description:Hanwoo cattle are a Korean breed renowned for their cultural significance and high-quality beef, characterized by low cholesterol and high unsaturated fat ratio. Growth is divided into a growing phase focused on development and a fattening phase 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 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 and roles during their growth. In this 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. Weighted gene co-expression network analysis identified and organized as three modules: turquoise, blue, and yellow. The turquoise module, linked to immune response, showed 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. The growth stages of Hanwoo steers were explored in our investigation utilizing rumen transcriptome data. The rumen plays critical role in their development, particularly during the growing and fattening phases. 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.

Project description:The rumen plays an essential role in ruminant digestion, absorption, metabolism, and health. The rumen undergoes substantial changes in size and function from birth to adulthood. The molecular mechanisms underlying these changes are not fully understood. This study was aimed to identify the transcription factors and signaling pathways mediating these changes in cattle. We used 6 neonatal bull calves and 6 adult steers, all Angus-crossbred, in this study. We found that the ratios of the emptied rumen, reticulum, omasum, and abomasum to total body weight in adult steers were 4.8 (P < 0.01), 3.1 (P < 0.01), 6.0 (P < 0.01), and 0.8 (P = 0.9) times those in neonatal calves, respectively. Histological examinations showed a 7.4-, 2.0-, 3.0-, 2.9-, and 4.6-fold increase (P < 0.01 for all) in the length of the rumen papillae and the thickness of the rumen epithelium, tunica mucosa and submucosa, tunica muscularis, and tunica serosa, respectively, from neonatal calves to adult steers. Papilla density was lower in adult steers than in neonatal calves (P < 0.05). The size of the rumen epithelial cells was not different between neonatal calves and adult steers (P = 0.57). RNA sequencing identified 2,906 genes differentially expressed (adjusted P < 0.05 and |log2fold change| ≥ 1) in the rumen between neonatal calves and adult steers, of which 1,586 were downregulated and 1,320 upregulated in adult steers. Bioinformatic analyses indicated organ development and morphogenesis, neuronal differentiation, blood vessel development, Ras signaling, and Wnt signaling were among the functional terms enriched in genes downregulated in adult steers, while fatty acid metabolism, ketogenesis, immune responses, PPAR signaling, and Rap1 signaling were among those enriched in genes upregulated in adult steers. Bioinformatic analyses also indicated that SRF, IRF4, SPI1, ETS1, and PURA were the major transcription factors mediating gene upregulation and that TCF4, MESP1, TCF3, ID4, and SNAI2 were the major transcription factors mediating gene downregulation in the rumen from neonatal calves to adult steers. Taken together, these results suggest that the rumen grows by increasing the number, not by the size, of individual cells from birth to adulthood, that the absorptive, metabolic, immune, and motility functions of the rumen are attained or enhanced during the postnatal life, and that the changes in rumen size and function from birth to adulthood are mediated by many transcription factors including SRF and TCF4 and many signaling pathways including the PPAR and Wnt signaling pathways.

Project description:Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle.

			Action	DRS
	SRR23823218_1.fastq.gz	Fastqsanger.gz
	SRR23823219_1.fastq.gz	Fastqsanger.gz
	SRR23823220_1.fastq.gz	Fastqsanger.gz
	SRR23823221_1.fastq.gz	Fastqsanger.gz
	SRR23823222_1.fastq.gz	Fastqsanger.gz

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