Project description:We performed gene expression profiling on chicken livers at five important embryonic developmental stages (E7, E12, E14, E17 and E21), which were selected from chicken lines with significant differences in abdominal fat content. Each developmental stage had its unique gene expression pattern and stage-specific differentially expressed genes (DEGs). Furthermore, the three rapid growth periods (E12, E14 and E17) had similar expression patterns. Between the two broiler lines, E17 had the largest number of significantly differentially expressed genes (979), specifically enriched in fatty acid metabolism and biosynthesis, PPAR signaling and glycolysis pathways. Therefore, genome-wide gene expression recapitulated the developmental pattern of chicken embryos, and found the important molecular pathways for hepatic lipid metabolism.
2018-06-04 | GSE101182 | GEO
Project description:genes involved in fatty acid biosynthesis in chicken according to genetic background, sex and diet
Project description:Copy number variation profiles comparing control female Dehong chiken blood DNA with 11 different chicken breeds(Silkie, Tibetan Chicken, Gallus gallus spadiceus, Bearded Chicken, Jinhu Chicken, Anak Chicken, Beijing Fatty Chicken, Langshan Chicken, Qingyuan partridge Chicken, Shek-Ki Chicken, Wenchang Chicken) blood DNA. Each test breeds had one male and one female sample, totally 22 test DNA samples.Goal is to get the golbal copy number variation profile between chicken breeds.
Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.
Project description:In plants, fatty acids are de novo synthesized predominantly in plastids fromacetyl-CoA. Although fatty acid biosynthesis has been biochemically well-studied, little isknown about the regulatory mechanisms of the pathway. Here, we show that overexpressionof the Arabidopsis (Arabidopsis thaliana) LEAFY COTYLEDON1 (LEC1) gene causesglobally increased expression of fatty acid biosynthetic genes, which are involved in keyreactions of condensation, chain elongation and desaturation of fatty acid biosynthesis. Inthe plastidial fatty acid synthetic pathway, over 58% of known enzyme-coding genes areupregulated in LEC1-overexpressing transgenic plants, including those encoding threesubunits of acetyl-CoA carboxylase, a key enzyme controlling the fatty acid biosynthesisflux. Moreover, genes involved in glycolysis and lipid accumulation are also upregulated.Consistent with these results, levels of major fatty acid species and lipids were substantiallyincreased in the transgenic plants. Genetic analysis indicates that the LEC1 function ispartially dependent on ABSCISIC ACID INSENSITIVE3, FUSCA3 and WRINKLED1 in theregulation of fatty acid biosynthesis. Moreover, a similar phenotype was observed intransgenic Arabidopsis plants overexpressing two LEC1-like genes of Brassica napus.These results suggest that LEC1 and LEC1-like genes act as key regulators to coordinate theexpression of fatty acid biosynthetic genes, thereby representing a promising target forgenetic improvement of oil-production plants.
2008-08-31 | GSE12137 | GEO
Project description:RNA-Seq Analysis of Bivalves for Identifying Genes Involved in Polyunsaturated Fatty Acid Biosynthesis
Project description:we compared the phosphoproteomes of SY and F6 follicles in laying hens and identified several genes involved in chicken follicle selection.
Project description:The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as "dwarf", namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.
Project description:Pre-incubation formaldehyde (FA) fumigation of hatching eggs is widely implemented for microbial control, yet its epigenetic consequences in embryonic tissues remain unclear. Here, we profiled the methylome of chicken embryo liver and skeletal muscle following commercial-dose FA fumigation using whole-genome bisulfite sequencing (WGBS). We generated 16 WGBS libraries (per tissue: control n=4; FA n=4), producing ~1.80 billion clean reads with mapping rates of 88.1–89.9% and bisulfite conversion efficiencies of ~99.4–99.7%. Although global methylation patterns were largely maintained, FA exposure induced widespread locus-specific remodeling dominated by CpG hypomethylation in both tissues. We identified 10,496 DMRs in liver and 10,487 DMRs in muscle, with hypomethylated DMRs comprising 83.4% and 91.2%, respectively. Functional enrichment analyses revealed a tissue-specific adaptive logic. In liver, CG-DMR–associated genes were significantly enriched in Focal adhesion, Tight junction, and core signaling pathways (MAPK, Wnt, Insulin signaling). Notably, hypermethylated genes were enriched for Glycine, serine and threonine metabolism, whereas hypomethylated genes were enriched for Protein processing in endoplasmic reticulum and Autophagy. In the CHG context, hypomethylation preferentially involved ether lipid metabolism, glycerolipid metabolism, and cell–cell adhesion pathways (Adherens junction, Focal adhesion), while CHH-context hypermethylation enriched MAPK and tight junctions. In muscle, CG-DMRs were enriched for “housekeeping” stress-response pathways (Autophagy, Ubiquitin-mediated proteolysis), while a distinct metabolic signature emerged: hypermethylated genes were enriched for PPAR signaling and Biosynthesis of amino acids, whereas hypomethylated genes enriched for Fatty acid metabolism. A decisive metabolic switch was evident in the CHH context, where promoters of Biosynthesis of amino acids were hypermethylated, while catabolic energy pathways (Fatty acid degradation, Valine, leucine and isoleucine degradation, TCA cycle) were hypomethylated. Collectively, these data demonstrate that commercial-dose FA fumigation leaves tissue- and context-specific epigenetic imprints in embryonic liver and skeletal muscle, characterized by CpG-dominant hypomethylation coupled with pathway-level reprogramming of adhesion/signaling and lipid homeostasis in liver, and energy-flux rewiring in muscle.
Project description:Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates and these included genes required for the pentose cycle, and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.