Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1308631 | ENA |
REPOSITORIES: ENA
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Project description:While genetic markers related to meat production traits have been identified in many other breeds of cattle, research on weight in Hanwoo cattle (Korean native cattle) has been relatively limited. In this study, we performed expression quantitative trait loci (eQTL) analysis and differential gene expression analysis to detect candidate genes influencing the weight characteristics of 32 castrated Hanwoo cattle across 22 tissues and identify variants that affect gene expression levels. In total, we identified a total of 2,465 differentially expressed genes, among which we discovered key genes such as UBD, RGS2, FASN, and SCD that have functions related to adipogenesis, body weight, obesity, and lipid metabolism. Gene-set enrichment analysis revealed that candidate genes in adipose tissue are involved in metabolic pathways related to Obesity-related traits, adipose metabolism, and lipid metabolism. Additionally, we found that decreased expression of TRIM31 contributes to weight gain which can be explained by the associated candidate cis-eQTL genotypes for TRIM31 and their effect on differential gene expression between the lower and higher weight groups. Our findings revealed candidate genes associated with the weight of Hanwoo cattle and perhaps can provide comprehensive insights into the association of weight with various tissues beyond adipose tissue and muscle, indicating the potential for expanding the focus of livestock trait research.
2024-03-21 | E-MTAB-13398 | biostudies-arrayexpress
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.
2024-06-02 | GSE267733 | GEO
Project description:Korean native cattle (Hanwoo) Genome sequencing
| PRJNA343986 | ENA
Project description:Transcriptomes from Longissimus dorsi samples of Korean Native Cattle (Hanwoo)
| PRJNA102877 | ENA
Project description:Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes. A customized bovine Combimatrix microarray containing 10,199 genes were constructed, and transcripome of longissimus dorsi muscle was compared between Korean cattle bulls (3 bulls) and steers (3 high-marbled and 3 low-marbled steers) by using the microarray hybridzation.
2013-06-30 | E-GEOD-35085 | biostudies-arrayexpress
Project description:Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes.
2013-06-30 | GSE35085 | GEO
Project description:MicroRNAs (miRNAs) regulate gene expression. The aim of this study was to identify circulating miRNAs that are involved with meat yield and connect exosomes and longissimus dorsi (LD) muscle in Korean cattle steer. Thus, we performed analyses of the carcass characteristics, exosome extraction, bovine miRNA array, mature miRNA qPCR, bioinformatics, and qPCR. Our analysis of the carcass characteristics relative to the yield grade (YG) showed that the yield index (YI) and rib eye area were the highest, whereas the backfat thickness was the lowest for YG A cattle among the three YGs. We performed a miRNA microarray and a Venn diagram analysis to sort the circulating miRNAs that connect exosomes and LD muscle. Mature miRNA qPCR showed that miR-15a (r = 0.84), miR-26b (r = 0.91), and miR-29c (r = 0.92) had positive relationships with exosomes and LD muscle. In YG A cattle, miR-26b was considered to be a circulating miRNA connecting exosomes and LD muscle because the expression pattern of miR-26b was similar in the microarray and miRNA qPCR for miR-26b-targeted genes, where the expression levels of DIAPH3 and YOD1 were lower than those in YG C cattle. Our results suggest that circulating miR-26b may participate in cell maintenance by regulating DIAPH3 and YOD1 in the LD muscle of Korean cattle. 29 or 30 month Korean cattle steers were classified by yield grade(YG) A, B, and C. miRNA expression patterns for exosome and LD muscle were compared among YGs.
2016-03-01 | E-GEOD-73389 | biostudies-arrayexpress
Project description:The coat color of mammals is determined by the melanogenesis pathway, which is responsible for maintaining the balance between black-brown eumelanin and yellow-reddish phaeomelanin. It is also believed that the color of the bovine nose is regulated in a similar manner; however, the molecular mechanism underlying pigment deposition in the black nose has yet to be elucidated. The aim of the present study was to identify melanogenesis-associated genes that are differentially expressed in the black vs. yellow nose of native Korean cows. Experiment, Yellow nose vs. Black nose HanWoo
2013-12-26 | E-GEOD-53657 | biostudies-arrayexpress
Project description:*Background: Adipocytes mainly function as energy storage and endocrine cells. The amount and distribution of fat are important factor that influence the meat quality in the beef industry. Fat depot can be found around internal organ (ometal), beneath the skin (subcutaneous), and between muscles (intramuscular). Different adipose depot showed the biological and genetic difference depending on their location. This inter-depot variation might be influenced by the inherent genetic programing for development of adipose depots. In this study, we used RNA-seq data to investigate the difference in transcriptome of various adipose depots in Hanwoo. *Results: Using RNA-seq, we identified 5797, 2156, and 5455 DEGs in the comparison between OI, OS, and IS respectively (FDR<0.01) and found 853, 48, and 979 DEGs specific to subcutaneous, intramuscular and omental fat respectively. DEGs in intramuscular fat were highly enriched the metabolism related pathways compared to other fat depots. DEGs specific to the omental fat is significantly enriched in PPAR signaling pathway and cell-junction related pathway. In subcutaneous fat, cytokine-cytokine receptor interaction with chemokines (CXC and CC subfamily) was the most significantly enriched the pathways. Interestingly, melanogenesis pathway was associated with the subcutaneous depot. Even though the adipose tissues shared the same pathways for adipocyte differentiation, the regulation of genes were different based on the depot. *Conclusions: We comparatively analyzed the transcripome profile from different adipose tissues using NGS and identified DEGs between adipose depot and specific to depot in Hanwoo animals. The functional annotation analysis of DEGs found that transcriptome profile difference in various adipose tissue of intramuscular, subcutaneous, and ometal fat. whole mRNA sequencing profiles of nine Korean native cattle (nine profiles of omental fat tissue, nine profiles of intramuscular fat tissue, nine profiles of subcutaneous fat tissue and eight profiles of muscle tissue)
2013-07-25 | E-GEOD-39618 | biostudies-arrayexpress