Project description:Circular RNAs (circRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of circRNAs across cattle muscle development has never been investigated. Here, we examine the expression of circRNA in cattle skeletal muscle at embryonic stage and adult stage, exhibiting the first report of circRNA in the cattle muscle development of a large animal. 12,981 circRNAs are identified and annotated in Qinchuan cattle muscle tissues, including 530 circular intronic RNAs (ciRNAs). We discovered that one parental gene could generate multiple circRNA isoforms with only one or two circRNA isoforms being expressed at higher levels, and several host genes produced different alternative circularization numbers between different muscle development stages. The most circRNA candidates contained two to seven exons, and the genomic distance of the back-splicing site was generally no more than 50 kb. The flanking intron length of most circRNAs was not more than 105 nt and the mean length of upstream or downstream flanking intron was about 11,000 nt. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these circRNAs, including several highly abundant circRNAs, and a subset of differently expressed circRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results display that an abundant circRNAs are dynamically expressed in a spatio-temporal manner in cattle muscle, indicating important and diverse functions during mammalian muscle development.
Project description:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research. The custom aCGH chips that interrogated the whole genome CNVs were build for 90 cattles from diverse breeds, with Hereford L1 Dominette 01449 as refference sample.
Project description:The transcriptome signature of peripheral blood mononuclear cells (PBMCs) of Ladakhi cattle adapted to high altitude vis a vis Sahiwal cattle adapted to the arid/semi-arid region at mean sea level was established using bovine expression microarray chips. The transcriptome analysis of PBMCs from these cattle types living at two distinct altitudes, resulted in identification of several hundred differentially expressed genes, biological processes, molecular functions and pathways.
Project description:Bovine Viral Diarrhea Virus (BVDV) is an endemic virus of North American cattle populations with significant economic and animal health impacts. While BVDV infection has a myriad of clinical manifestations, a unique and problematic outcome is the establishment of a persistently infected (PI) animal following in-utero viral infection. While it is well established that PI animals serve as a constant reservoir of BVDV, the mechanism for the maintained infection remains unknown despite multiple theories. The purpose of this study was to use transcriptome analysis to further define long term immune status of adult PI cattle and offer insight into the potential mechanistic establishment of persistent BVDV infection, in utero. Peripheral blood mononuclear cells were collected from PI beef cattle (N=6) and uninfected controls (N=6) for targeted RNAseq analysis conducted using 54 genes of interest and followed by pathway enrichment analysis. Analysis revealed 29 differentially expressed genes (FDR < 0.05, fold change > 2) representing 14 significant KEGG pathways between PI and control animals (FDR < 0.05). Transcriptome changes indicate chronic upregulation of interferon gamma (IFNG) with unexpected expression of related genes, suggesting a maintained stimulation of the PI immune system resulting in virus-mediated dysregulation of immune function.
Project description:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.
Project description:Black cattle is a new breed of beef cattle developed by combining modern biotechnologies such as somatic cell cloning and conventional breeding methods. To provide new ideas for improving meat quality and generating new breeds of cattle, the important candidate genes affecting fat deposition in two kinds of cattle were identified. Eighteen months Black cattles and Luxi cattles were randomly assigned into two environmental. The longissimus dorsi muscle were collected on Black cattle and Luxi cattle,for analyses including fatty acid determinationrs, high-throughput sequencing metagenomics, qRT-PCR expression profile and western blot.The ratio of unsaturated fatty acids to saturated fatty acids was 1.37:1 and 1.24:1 in the muscle tissues of Black cattle and Luxi cattle, respectively. The results of RNA-Seq analysis revealed 1,415 DEGs(fold change ≥ ± 2, P<0.05) between the longissimus dorsi of Black cattle and yellow cattle. A total of 939 genes were upregulated, and the other 476 genes were downregulated. With GO enrichment analysis, it was found that the identified DEGs were significantly enriched in biological regulation, regulation of the Wnt signaling pathway, negative regulation of the Wnt signaling pathway, cAMP metabolic process, fat cell differentiation, and brown fat cell differentiation, among other functions. Regulation of lipolysis in adipocytes, AMPK signaling pathway, adipocytokine signaling pathway and PPAR signaling pathway in the KEGG pathway database were significantly enriched. PPI network analysis showed that the downregulated genes FABP4, ADIPOQ, PLIN1, PLIN2 and LIPE were closely linked to other DEGs and were the key sites of multiple metabolic pathways. Combined with qRT-PCR and protein expression profile analysis, the expression level of fat acid metabolism related genes (FABP4, ADIPOQ) in black cattle was high and the difference was significant. Changes in the expression of fatty acid metabolism-related genes in Black cattle and Luxi cattle were analyzed and important candidate marker genes (such as ADIPOQ and FABP4) that affect fat deposition were identified in order to provide a genetic basis for the efficient breeding of production performance, establish a molecular marker database for local cattle breeds and support the cultivation of new breeds.
Project description:Background: African animal trypanosomiasis (AAT) caused by tsetse fly-transmitted protozoa of the genus Trypanosoma is a major constraint on livestock and agricultural production in Africa and is among the top ten global cattle diseases impacting on the poor. Here we show that a functional genomics approach can be used to identify temporal changes in host peripheral blood mononuclear cell (PBMC) gene expression due to disease progression. We also show that major gene expression differences exist between cattle from trypanotolerant and trypanosusceptible breeds. Using bovine long oligonucleotide microarrays and real time quantitative reverse transcription PCR (qRT-PCR) validation we analysed PBMC gene expression in naïve trypanotolerant and trypanosusceptible cattle experimentally challenged with Trypanosoma congolense across a 34-day infection time course. Results: Trypanotolerant N’Dama cattle displayed a rapid and distinct transcriptional response to infection, with a ten-fold higher number of genes differentially expressed at day 14 post infection compared to trypanosusceptible Boran cattle. These analyses identified coordinated temporal gene expression changes for both breeds in responses to trypanosome infection. In addition, a panel of genes were identified that showed pronounced differences in gene expression between the two breeds, which may underlie the phenomena of trypanotolerance and trypanosusceptibility. Gene ontology (GO) analysis demonstrate that the products of these genes may contribute to increased mitochondrial mRNA translational efficiency, a more pronounced B cell response, an elevated activation status and a heightened response to stress in trypanotolerant cattle. Conclusions: This study has revealed an extensive and diverse range of cellular processes that are altered temporally in response to trypanosome infection in African cattle. Results indicate that the trypanotolerant N’Dama cattle respond more rapidly and with a greater magnitude to infection compared to the trypanosusceptible Boran cattle. Specifically, a subset of the genes analyzed by qRT-PCR, which display significant breed differences, could collectively contribute to the trypanotolerance trait in N’Dama.
Project description:Long non-coding RNAs (lncRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of lncRNAs across Guangxi native cattle and swamp buffalo muscle development has never been investigated. Here, we examine the expression of lncRNA in cattle and buffalo muscle at adult stage(12 months), exhibiting the first report of lncRNA in the Guangxi native cattle and swamp buffalo muscle development of a large animal. 16,236 lncRNA candidates were obtained from buffalo skeletal muscle samples, of which a number of lncRNAs were highly abundant, and 2,161 lncRNAs were differentially expressed between buffalo and cattle. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these lncRNAs, including several highly abundant lncRNAs, and a subset of differently expressed lncRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results indicate that abundant lncRNA is differentially expressed in bovine muscle, indicating important and diverse functions in mammalian muscle development.