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: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:This project aimed to characterise the immune response of cattle to buffalo fly infestation using cattle serum samples. The cattle were phenotyped into two groups, high buffalo fly burden and low buffalo fly burden cattle, following exposure to buffalo flies. The SWATH analysis was sued to measure the relative abundance of proteins in serum samples of the two groups at different time points.
Project description:While cold stress has been shown to seriously impact cattle industry, there are only a few reports investigating the effect of cold stress on cattle. Whether severe cold stress results in alterations in gene expression and affects molecular genetic mechanisms remains unknown. We used microarrays to analyze the alterations in gene expression in peripheral blood samples in response to cold exposure and identified differentially regulated genes. This study was performed on 30 healthy Sanhe heifers with similar genetic backgrounds, weight, and age. In order to induce cold stress, the cattle were transferred outdoor and were exposed to a temperature of -32°C for 3 hours followed by housing in cowshed at 5°C for 15 hours. Blood samples with EDTA were collected from each animal before and after the cold exposure. After total RNA was isolated from blood cells, six RNA samples (three derived before and three after the cold exposure), were collected from three animals randomly selected from the 30 healthy heifers for gene expression profiling in response to severe cold stress.
Project description:In the present study, a oligonucleotide microarray platform is used to compare expression profiles of beef cattle muscle in animals treated with either Dexamethazone (Dex) or Dexamethazone plus 17β-estradiol (Estr) administered at sub-therapeutic dosage, against untreated controls. Seventeen male beef cattle 15-18 months old, around 450 kg mean body weight were randomly allocated in three groups: 6 were untreated (group Ctrl), 5 were administered with dexamethazone via feed 0.75mg/head for 43 days (group D); the last 6 animals were administered via feed for 43 days with Dex (0.75mg/head) and intramuscularly (i.m.) for three times with 17β-oestradiol, 20mg/head, (group DE). Three additional control animals, matching in sex and age, collected in a previous experiment were included in the Ctrl group to increase sample size and to control for biological variation. For each sample, total RNA was extracted from a specific anterior limb muscle (biceps branchii). Data analysis demonstrates that the expression profiles were strongly affected by Dex treatment with hundreds of genes up-regulated with relevant fold-change, whereas the myostatin gene was significantly down-regulated. On the contrary, the administration of Dex-Estr reveals a weaker effect on gene expression.
Project description:Compensatory growth is a naturally occurring accelerated growth phenomenon observed in cattle upon re-alimentation following a prior period of dietary restriction (Hornick et al., 2000). It is incorporated into man production systems as a method to reduce feed costs and consequently is economically important for animal production systems. The goal of our research project is to identify biomarkers for cattle with a superior ability to display compensatory growth. Transcriptional profiling studies of liver and muscle tissues in cattle have shown large numbers of differentially expressed genes in animals undergoing dietary restriction and subsequent compensatory growth when compared to a continuously-fed ad libitum control group of cattle (Connor et al., 2010; Keogh et al., 2016a,b). Given the identification of differential expression at the transcript level, the intended project aims to evaluate potential differences in protein abundance between animals that are diet restricted and subsequently undergo compensatory growth compared to a continuously-fed ad libitum control group of cattle. Differences in genes that are apparent at both the protein and the transcript level are more likely to be transferable across breed type (Snelling et al., 2013) and consequently have more utility for incorporation within genomic selection breeding programs for cattle evaluations.
Project description:The cattle industry is the largest of the agricultural commodities in the United States and generated over $101 billion in farm cash receipts during 2016; 28% of all US farm cash receipts. Although the sequence of the bovine reference genome has been publicly available since 2009, annotation of functional genome elements is largely incomplete, resulting in limitations for exploiting the genome to phenome relationship. This project generate high-quality detailed transcript and miRNA status datasets from a comprehensive set of bovine tissues, developmental stages, and cells through a set of rationally selected assays.