Bos taurus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA316693 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:The incidence of sub-fertility is higher in crossbred bulls compared to zebu bulls. In the present study, we analysed the metabolomic profile of seminal plasma from crossbred and zebu bulls and uncovered differentially expressed metabolites between these two breeds. Using a high-throughput LC-MS/MS-based approach, we identified 990 and 1,002 metabolites in crossbred and zebu bull seminal plasma respectively. After excluding the exogenous metabolites, we found that 50 and 68 putative metabolites were unique to crossbred and zebu bull seminal plasma, respectively, whilst 87 metabolites were common to both. After data normalisation, 63 metabolites were found to be dysregulated between crossbred and zebu bull seminal plasma. Observed pathways included Linoleic acid metabolism (observed metabolite was phosphatidylcholine) in crossbred bull seminal plasma whereas inositol phosphate metabolism (observed metabolites were phosphatidylinositol-3,4,5-trisphosphate/inositol 1,3,4,5,6-pentakisphosphate/myo-inositol hexakisphosphate) was observed in zebu bull seminal plasma. Abundance of Tetradecanoyl-CoA was significantly higher, whilst abundance of Taurine was significantly lower in crossbred bull seminal plasma. In conclusion, the present study established the seminal plasma metabolomic profile in crossbred and zebu bulls and suggest that increased lipid peroxidation coupled with low concentrations of antioxidants in seminal plasma might be associated with high incidence of sub-fertility in crossbred bulls.
2021-12-22 | MTBLS1642 | MetaboLights
Project description:Discovery of novel and differentially expressed microRNAs between fetal and adult backfat in cattle
| PRJNA210714 | ENA
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: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:Tropical theileriosis in a cattle disease of global economic importance, caused by the tick-borne protozoan parasite Theileria annulata. Conventional control strategies are failing to contain the disease and an attractive alternative is the use of pre-existing genetic resistance or tolerance. However, tropical theileriosis tolerant cattle are less productive than some susceptible breeds. To combine resistance and production traits requires an understanding of the mechanisms involved in resistance. Therefore, we have compared the response of monocytes derived from tolerant (Sahiwals, Bos indicus) and susceptible (Holstein-Friesians, B. taurus) cattle to in vitro infection with T. annulata. Over 150 genes exhibited breed-specific differential expression during the course of infection and nearly one third were differentially expressed in resting cells, implying that there are inherent differences between monocytes from the breeds. Fifty sequences currently only match ESTs or are unique to the library used to generate the microarray. The differential expression of a selection of genes was validated by quantitative RT-PCR, e.g. CD9, prion protein and signal-regulatory protein alpha. A large proportion of the differentially expressed genes encode proteins expressed on the plasma membrane or in the extracellular space and cell adhesion was one of the major Gene Ontology biological processes identified. We therefore hypothesise that the breed-specific tolerance of Sahiwal cattle compared to Holstein-Friesians is due to the interaction of infected cells with other immune cells, which influences the immune response generated against T. annulata infection. The BoMP microarray is available from the ARK-Genomics facility (www.ark-genomics.org).
2007-04-26 | E-MAXD-25 | biostudies-arrayexpress
Project description:We hypothesized that the relative abundances of host cell transcripts in lymph nodes of animals with malignant catarrhal fever (MCF), compared to healthy controls, may be used to identify pathways that may help to explain the pathogenesis of MCF. Therefore, an abundance of host cell gene expression patterns in lymph nodes of animals with MCF and healthy controls were analyzed by microarray. Indeed, a vast number of genes related to inflammatory processes, lymphocyte activation, cell proliferation and apoptosis were detected at different abundances. However, the IL-2 transcript was eminent among the transcripts, which were, compared to healthy controls, less abundant in animals with MCF. Compared to healthy cattle, bovines with MCF appear to mimic an IL-2 knockout phenotype that has been described in mice. This supports the hypothesis that immunopathogenic events are linked to the pathogenesis of MCF. IL-2-deficiency may play an important role in the process. Keywords: disease state analysis
2009-08-01 | GSE13852 | GEO
Project description:Wandong cattle are an autochthonous Chinese breed used extensively for beef production. The breed tolerates extreme weather conditions and raw feed and are resistant to tick-borne diseases. However, the genetic basis of testis development and sperm production as well as breeding management is not well established in local cattle. In this study, we performed total RNA-Seq and comprehensively analyzed the circ-RNA expression profiling of the testes samples of six bulls at 3 years and 3 months of developmental age. In total, 17 013 circ-RNAs were identified, of which 681 circRNAs (P-adjust < 0.05) were differentially expressed (DE). Among these DE circ-RNAs, 579 were upregulated and 103 were downregulated in calf and bull testes. The Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the identified target genes were classified into three broad functional categories, including biological process, cellular component, and molecular function, and were enriched in the lysine degradation, cell cycle, and cell adhesion molecule pathways.
2021-09-05 | GSE183347 | GEO
Project description:Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype*weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.
2020-01-07 | GSE140460 | GEO
Project description:Comparison of Mycobacterium bovis-infected cattle versus control non-infected cattle using the BOTL-5 microarray
| PRJNA102213 | ENA