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PROVIDER: PRJEB59417 | ENA |
REPOSITORIES: ENA
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Project description:The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R and Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping. The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed that the ADP of Ghana has both European and Asian genetic signatures. The ADP also displays considerable variation in the MC1R gene. Black coat colour is the most predominant within the breed, with the dominant black alleles of both Asian and European origin contributing to the majority of alleles in the pool. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. Other colour variants may be due to epistatic interactions with additional coat colour loci, or mutations. The wide variations in coat colour patterns suggest that morphology alone cannot be used to adequately characterise Ghanaian local pigs. PCA analysis of SNP genotyping data revealed a strong location effect on clustering of local Ghanaian pigs. Based on this work, we recommend that further studies be carried out on more local pigs to find out the effect of admixture on important adaptive and economic traits of the ADP and other local Sus breeds in Africa to help develop a sustainable conservation programmes to prevent the decline of this genetic resource.
2017-03-08 | GSE84604 | GEO
Project description:We used single-cell RNA-sequencing (scRNA-seq) of melanocytes isolated from two distict red hair color (RHC) mouse models for comparison with and black hair color, functional MC1R signaling, to reveal a Pheomelanin Gene Signature (PGS) of differentially expressed genes in RHC melanocytes.
2023-10-01 | GSE236918 | GEO
Project description:Lower selection intensity resulted in obvious genetically and phenotypically divergences in China indigenous breeds. Nanyang black pig, a China indigenous breed, was famous for its high lipid deposition and high genetic divergence, which made it an ideal model investigating mechanism of lipid position traits in pig. Here, transcriptome and TMT-based proteome analyses were carried out in longissimus dorsi (LD) tissue of high genetic variation individual Nanyang black pigs. After phenotyping in a big population with multi-production traits indexes, six Nanyang black pigs were selected and divided into relatively high and low lipid deposition groups. Combining analyses of transcriptomic and proteomic data identified 15 candidate genes determining lipid deposition genetic divergence in Nanyang black pig. Among them, FASN, CAT, and SLC25A20 were main causal candidate genes. The other genes could be divided as lipid deposition related gene (BDH2, FASN, CAT, DHCR24, ACACA, GK, SQLE, ACSL4, SCD), PPARA-centered fat metabolism regulatory factors (PPARA, UCP3), transcription or translation regulators (SLC25A20, PDK4, CEBPA), and integrin, structural proteins, signal transduction-related genes (EGFR). The multi-omics data set provided a valuable resource for analyses on lipid deposition-traits in pig, especially in Nanyang black pig.
2021-01-28 | GSE165613 | GEO
Project description:Melanocortins mediate their biological functions via five different melanocortin receptors (MC1R - MC5R). MC1R is expressed in the skin and leukocytes and is thus involved in the regulation of skin pigmentation and inflammatory responses. MC1R is also present in the liver and white adipose tissue, but its functional role in these tissues is unclear. This study aimed at determining the regulatory role of MC1R in fatty acid metabolism. Recessive yellow (Mc1re/e) mice, a model of global MC1R deficiency, and hepatocyte-specific MC1R deficient mice (Mc1r LKO) were fed a chow or Western diet for 12 weeks. The mouse models were characterized for body weight and composition, adipose tissue mass, adipocyte size, glucose metabolism and lipid metabolism. Furthermore, qPCR and RNA sequencing analyses were used to investigate gene expression profiles in the liver and adipose tissue. HepG2 cells and primary mouse hepatocytes were to study the effects of pharmacological MC1R activation. Chow- and Western diet-fed Mc1re/e showed increased liver weight, white adipose tissue mass and plasma triglyceride (TG) concentration compared to wild type mice. This phenotype occurred without significant changes in food intake, body weight, physical activity or glucose metabolism. Mc1r LKO mice displayed a similar phenotype characterized by larger fat depots, increased adipocyte hypertrophy and enhanced accumulation of TGs in the liver and plasma. In terms of gene expression, markers of de novo lipogenesis, inflammation and apoptosis were upregulated in the liver of Mc1r LKO mice, while enzymes regulating lipolysis were downregulated in white adipose tissue of these mice. In cultured hepatocytes, selective activation of MC1R reduced ChREBP expression, which is a central transcription factor for lipogenesis. Hepatocyte-specific loss of MC1R disturbs fatty acid metabolism in the liver and leads to an obesity phenotype characterized by enhanced adipocyte hypertrophy and TG accumulation in the liver and circulation.
2024-08-29 | GSE262618 | GEO
Project description:To investigate the machanism by which MC1R represses the expression of a subset of IFNg reponsvie genes. We then performed ATAC seq and H3K27ac ChIP-seq to identify promoter and enhancer of MC1R-repressed IFNg reponsive genes.
2023-08-09 | GSE225553 | GEO
Project description:The inherent diversity of canines is closely intertwined with the unique color patterns of each dog population. These variations in color patterns are believed to have originated through mutations and selective breeding practices that occurred during and after the domestication of dogs from wolves. To address the significant gaps that persist in comprehending the evolutionary processes that underlie the development of these patterns, we generated and analyzed deep-sequenced genomes of 113 Korean indigenous Jindo dogs that represent five distinct color patterns to identify the associated mutations in CBD103, ASIP, and MC1R. The degree of linkage disequilibrium and estimated allelic ages consistently indicate that the black-and-tan dogs descend from the first major founding population on Jindo island, compatible with the documented literature. We additionally demonstrate that black-and-tan dogs, in contrast to other color variations within the breed, exhibit a closer genetic affinity to ancient wolves from western Eurasia than those from eastern Eurasia. Lastly, population-specific genetic variants with moderate effects were identified, particularly in loci associated with traits underlying body size and behavioral variations, potentially explaining the observed phenotypic diversity based on coat colors. Overall, comparisons of whole genome sequences of each coat color population diverged from the same breed provided an unprecedented glimpse into the properties of evolutionary processes maintaining variation in Korean Jindo dog populations that were previously inaccessible.
2024-04-05 | E-MTAB-13939 | biostudies-arrayexpress
Project description:To investigate the function of MC1R in antitumor immunity, we compared the gene expression between B16F10 WT and B16F10 Mc1r knockdown cells at different conditions. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at three treatments.
2023-08-09 | GSE214859 | GEO
Project description:The Kashmiri population is an ethno-linguistic group that resides in the Kashmir Valley in northern India. A longstanding hypothesis is that this population derives ancestry from Jewish and/or Greek sources. There is historical and archaeological evidence of ancient Greek presence in India and Kashmir. Further, some historical accounts suggest ancient Hebrew ancestry as well. To date, it has not been determined whether signatures of Greek or Jewish admixture can be detected in the Kashmiri population. Using genome-wide genotyping and admixture detection methods, we determined there are no significant or substantial signs of Greek or Jewish admixture in modern-day Kashmiris. The ancestry of Kashmiri Tibetans was also determined, which showed signs of admixture with populations from northern India and west Eurasia. These results contribute to our understanding of the existing population structure in northern India and its surrounding geographical areas.
2016-08-16 | GSE85594 | GEO
Project description:Amplification of the Melanocortin-1 Receptor in Nephrotic Syndrome Renders a Good Target for Podocyte Cytoskeleton Stabilization During the last years, several reports have been presented of beneficial effects of ACTH in patients with nephrotic syndrome. Among the known ACTH receptors, the melanocortin-1 receptor (MC1R) has been suggested as the mediator of the ACTH renoprotective effect with the mechanism of action resulting in stabilization of the actin cytoskeleton in podocytes. To understand how melanocortin receptors are regulated in nephrotic syndrome and how they are involved in restoration of filtration barrier function, melanocortin receptor expression was evaluated in patients and in a rat model of nephrotic syndrome in combination with cell culture analysis. Phosphoproteomic mass spectrometry was applied and identified MC1R pathways confirmed using biochemical analysis. We found that glomerular MC1R expression was increased in nephrotic syndrome, both in humans and in a rat model. A MC1R agonist protected podocytes from protamine sulfate induced stress fiber loss with the top ranked phoshoproteomic MC1R activated pathway beeing actin cytoskeleton signaling. Actin stabilization through the MC1R consisted of ERK1/2 dependent phosphorylation and inactivation of EGFR signaling with stabilization of synaptopodin and stress fibers in podocytes. These results further explain how patients with nephrotic syndrome show responsiveness to ACTH treatment by depressing EGFR signaling through activation of the MC1R receptor and as a consequence restore filtration barrier function by stabilizing the podocyte actin cytoskeleton.
2019-11-12 | PXD009198 | Pride