Applying multi-omics data to study the genetic background of bovine respiratory disease infection in feedlot crossbred cattle
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PROVIDER: PRJNA898383 | ENA |
REPOSITORIES: ENA
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Project description:Bovine respiratory disease (BRD) is the most common and costly infectious disease affecting the well-being and productivity of beef cattle in North America. BRD is a complex disease whose development is dependent on environmental factors and host genetics. Due to the polymicrobial nature of BRD, our understanding of the genetic and molecular mechanisms underlying the disease is still limited. This knowledge would augment the development of better genetic/genomic selection strategies and more accurate diagnostic tools to reduce BRD prevalence. Therefore, this study utilized multi-omics data (genomics, transcriptomics, and metabolomics) analyses to study the associations between genome, transcriptome, metabolome, and BRD phenotype of feedlot crossbred cattle. The findings may be useful for the development of genomic selection strategies for BRD susceptibility, and for the development of new diagnostic and therapeutic tools.
2023-01-11 | GSE217317 | GEO
Project description:Bovine respiratory disease (BRD) is the most common and costly infectious disease affecting the wellbeing and productivity of beef cattle in North America. BRD is a complex disease whose development is dependent on environmental factors and host genetics. Due to the polymicrobial nature of BRD, our understanding of the genetic and molecular mechanisms underlying the disease is still limited. This knowledge would augment the development of better genetic/genomic selection strategies and more accurate diagnostic tools to reduce BRD prevalence. Therefore, this study aimed to utilize multi-omics data (genomics, transcriptomics, and metabolomics) analyses to study the genetic and molecular mechanisms of BRD infection. Blood samples of 143 cattle (80 BRD; 63 non-BRD animals) were collected for genotyping, RNA sequencing, and metabolite profiling. Firstly, a genome-wide association study (GWAS) was performed for BRD susceptibility using 207,038 SNPs. Two SNPs (Chr5:25858264 and BovineHD1800016801) were identified as associated (p-value <1 × 10-5) with BRD susceptibility. Secondly, differential gene expression between BRD and non-BRD animals was studied. At the significance threshold used (log2FC>2, logCPM>2, and FDR<0.01), 101 differentially expressed (DE) genes were identified. These DE genes significantly (p-value <0.05) enriched several immune responses related functions such as inflammatory response. Additionally, we performed expression quantitative trait loci (eQTL) analysis and identified 420 cis-eQTLs and 144 trans-eQTLs significantly (FDR <0.05) associated with the expression of DE genes. Interestingly, eQTL results indicated the most significant SNP (Chr5:25858264) identified via GWAS was a cis-eQTL for DE gene GPR84. This analysis also demonstrated that an important SNP (rs209419196) located in the promoter region of the DE gene BPI significantly influenced the expression of this gene. Finally, the abundance of 31 metabolites was significantly (FDR <0.05) different between BRD and non-BRD animals, and 17 of them showed correlations with multiple DE genes, which shed light on the interactions between immune response and metabolism. This study identified associations between genome, transcriptome, metabolome, and BRD phenotype of feedlot crossbred cattle. The findings may be useful for the development of genomic selection strategies for BRD susceptibility, and for the development of new diagnostic and therapeutic tools.
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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
2020-07-08 | GSE153952 | GEO
Project description:Background: The Nguni is an indigenous Bos taurus Sanga breed which is primarily used in extensive commercial and communal farming systems in South Africa. The Nguni is a small framed early maturing breed not preferred for finishing under feedlot systems, as the large framed later maturing types are favoured for high lean meat yield. In this study we aim to investigate differentially expressed genes in Longissimus dorsi muscle of Nguni cattle fed diets differing in energy levels finished under commercial feedlot conditions. Results: Twenty Nguni and twenty Bonsmara were fed either a low (10.9 MJ ME/kg) or a high (12.00 MJ ME/kg) energy diet for 120 days. At slaughter, muscle samples were taken for RNA extraction and RNA-sequencing. A total of 2214 differentially expressed genes (DEG) were observed between the two breeds regardless of diet. For the low energy diets, 2244 DEG in the Nguni and the Bonsmara were significantly expressed, while a higher number of were differentially expression between the Nguni and Bonsmara on high energy diet (3154 DEG). A difference of 288 DEG were identified between the Nguni fed on the low and high energy diets. Most of the fat deposition genes were upregulated in the Bonsmara (ASIP, OXT, SNAI3, FOX01, PPARGC1A), with lower levels in the Nguni. Conclusion: Clear breed differences were found for the number and level of gene expression, while a larger variation in DEG were observed between the two diets within in the Bonsmara breed.
2018-09-07 | GSE119563 | GEO
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:We have used RNA-Seq to examine expression profiles of PBMCs from Crossbred and Thraparkar under heat Stress.
2019-11-02 | GSE136652 | GEO
Project description:Rumen microorganism of Simmental crossbred cattle Raw sequence reads
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Project description:Rumen microorganism of Simmental crossbred cattle Raw sequence reads
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Project description:Oligonucleotide DNA microarrays were used as a platform to compare C. jejuni isolates from feedlot cattle and human clinical cases from Alberta. Comparative genomic hybridization (CGH) analysis was performed on 87 isolates (46 bovine, 41 human) obtained within the same geographical regions and time frame. In addition, We also performed gene association analysis to determine if any genes may be differentially distributed between human and cattle sources or between clusters dominated by either human or cattle isolates (“human enriched” vs “cattle enriched”). Keywords: Comparative Genomic Hybridization; Genomic epidemiology; Gene-association study
2008-10-17 | GSE13228 | 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