Rumen microorganism of Simmental crossbred cattle
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA685990 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Rumen microorganism of Simmental crossbred cattle Raw sequence reads
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Project description:The intramuscular fat (IMF) content of different beef cattle breeds varies greatly, which plays an important role in taste and nutritional value. However, the molecular mechanism of fat metabolism and deposition in beef cattle is still not very clear. In this study, the meat quality traits of Angus cattle and Chinese Simmental cattle were compared, the transcriptome of the longissimus dorsi muscle (LD) between Angus cattle and Chinese Simmental cattle was then analyzed to identify key genes related to fat metabolism and adipogenesis by high-throughput RNA-seq technology. In the current study conducted a comprehensive analysis on the transcriptome of the longissimus dorsi muscle (LD) of Angus and Simmental cattle, and identified differentially expressed genes related to lipid metabolism，which may have a great impact on on the formation of IMF.
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Project description:To understand the etiology behind higher incidence of infertility in crossbred bulls, we performed transcriptomic analysis of testicular samples derived from crossbred males and compared with testicular transcriptomic profile of Zebu cattle
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Project description:Investigation of whole genome gene expression level changes in rumen epithelium of dairy cattle at different stages of rumen development and on different diets.
2009-11-01 | GSE18382 | GEO
Project description:Bovine tropical theileriosis is a major haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints for of the livestock development programmes in India and southern Asia. Indigenous cattle (Bos indicus) are less affected by this disease than exotic and crossbred cattle. Genetic basis of resistance to tropical theileriosis in indigenous cattle is not well studied. Recent studies gives an idea that differentially genes expressed in exotic and indigenous breeds play an important role in breed specific resistance to tropical theileriosis. The present study was designed to visualize the global gene expression profiling in PBMCs derived from indigenous (Tharparkar) and crossbred cattle with in vitro infection of T. annulata. T. annulata Parbhani strain, originally isolated from Maharashtra (India) and maintained as cryopreserved stabilates of ground-up tick tissue sporozoite (GUTS) of infected H. anatolicum anatolicum was used as infective material. Two separate microarray experiments were carried out using separately each for crossbred and Tharparkar cattle. The crossbred cattle showed 1082 differentially expressed genes (DEGs). Out of total DEGs, 597 genes were downregulated and 485 were upregulated. Their fold change varies from 2283.93 to -4816.02. Tharparkar cattle showed 875 differentially expressed genes. Out of total DEGs in Tharparkar cattle, 451 genes were downregulated and 424 genes were upregulated. Their fold change varies from 94.93 to -19.20. A subset of genes was validated by quantitative RT-PCR and results correlated well with data obtained from the microarrays indicating that the microarray results gave an accurate report of transcript level. Functional annotation study of differentially expressed genes has confirmed their involvement in various pathways including response to oxidative stress, immune system regulation, cell proliferation, cytoskeletal changes, kinases activity and apoptosis. Gene network analysis of these differentially expressed genes provided an effective way to understand the interaction among them. It is therefore, hypothesised that the dissimilar susceptibility to tropical theileriosis exhibited by indigenous and crossbred cattle is due to breed-specific differences in the interaction of infected cells with other immune cells, which ultimately influences the immune response generated against T. annulata infection. Global gene expression profiling in PBMCs derived from indigenous (Tharparkar) and crossbred cattle were studied after in vitro infection of T. annulata Parbhani strain at 2h time period. Two separate microarray experiments were carried out using Bovine (V2) Gene Expression Microarray, 4x44K (Agilent). Two biological replicate samples were profiled per condition (i.e. replicates samples each in crossbred and Tharparkar cattle).
2016-07-01 | E-GEOD-81419 | biostudies-arrayexpress
Project description:Background: Transcriptomic variation among cattle breeds and their crossbreds may help to better understanding of consequences of crossbreeding and heterosis. In this study the differences in biological functions and pathways of three crossbreds including 50 and 75 percent Holstein were compared with their purebred parents, Holstein and Taleshi (an indigenous breed) cattle. Results: Five populations and their ten comparisons were studied by bioinformatics tools for transcriptome analysis. We pooled blood RNA of at least 8 animals of each population prior to RNA sequencing. The obtained results showed that total expressed transcripts in all populations were 72,812 with 22,627 annotated genes. Functional analysis of differentially expressed genes (DEGs) showed that the genetics information processing and metabolism were the most highly-impacted pathways. Among all significantly enriched pathways, eukaryotic translation initiation factor-2 signaling had the highest activation z-score (5.3) in crossbred compared to purebred cattle. The majority of upstream regulators of genes including transcription regulators and cytokines were differentially expressed among populations in which their activation z-score in purebred was more than crossbred cattle. Conclusions: Crossing of Holstein with Taleshi breed resulted in higher activity of pathways related to genetic information processing and lower activity of pathways related to immunity and inflammatory responses. To the best of our knowledge, this is the first study where the differences in pathways and functions were studied using high throughput sequencing of blood in a cattle crossbreeding program. The analysis revealed that the most important differences between studied genotypes, especially between purebred and crossbred cattle, were related to immune functions and metabolism.
2016-09-29 | GSE79677 | GEO
Project description:Bovine tropical theileriosis is a major haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints for of the livestock development programmes in India and southern Asia. Indigenous cattle (Bos indicus) are less affected by this disease than exotic and crossbred cattle. Genetic basis of resistance to tropical theileriosis in indigenous cattle is not well studied. Recent studies gives an idea that differentially genes expressed in exotic and indigenous breeds play an important role in breed specific resistance to tropical theileriosis. The present study was designed to visualize the global gene expression profiling in PBMCs derived from indigenous (Tharparkar) and crossbred cattle with in vitro infection of T. annulata. T. annulata Parbhani strain, originally isolated from Maharashtra (India) and maintained as cryopreserved stabilates of ground-up tick tissue sporozoite (GUTS) of infected H. anatolicum anatolicum was used as infective material. Two separate microarray experiments were carried out using separately each for crossbred and Tharparkar cattle. The crossbred cattle showed 1082 differentially expressed genes (DEGs). Out of total DEGs, 597 genes were downregulated and 485 were upregulated. Their fold change varies from 2283.93 to -4816.02. Tharparkar cattle showed 875 differentially expressed genes. Out of total DEGs in Tharparkar cattle, 451 genes were downregulated and 424 genes were upregulated. Their fold change varies from 94.93 to -19.20. A subset of genes was validated by quantitative RT-PCR and results correlated well with data obtained from the microarrays indicating that the microarray results gave an accurate report of transcript level. Functional annotation study of differentially expressed genes has confirmed their involvement in various pathways including response to oxidative stress, immune system regulation, cell proliferation, cytoskeletal changes, kinases activity and apoptosis. Gene network analysis of these differentially expressed genes provided an effective way to understand the interaction among them. It is therefore, hypothesised that the dissimilar susceptibility to tropical theileriosis exhibited by indigenous and crossbred cattle is due to breed-specific differences in the interaction of infected cells with other immune cells, which ultimately influences the immune response generated against T. annulata infection.
2016-07-01 | GSE81419 | GEO
Project description:Creatine pyruvate (CrPyr) is a new multifunctional nutrient that can provide both pyruvate and creatine. It has been shown to relieve the heat stress of beef cattle by improving antioxidant activity and rumen microbial protein synthesis, but the mechanism of CrPyr influencing rumen fermentation remains unclear. This study aimed to use metaproteomics technologies to investigate the bacterial protein function in rumen fluid samples taken from heat-stressed beef cattle treated with or without 60 g/d CrPyr.
2021-03-31 | PXD025118 |