Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35221 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| YakSanger.vcf.gz | Vcf | |||
| YakSanger.vcf.gz.tbi | Vcf | |||
| YakWGS.vcf.gz | Vcf | |||
| YakWGS.vcf.gz.tbi | Vcf | |||
| YakMALDI.vcf.gz | Vcf |
Items per page: 5 1 - 5 of 6 |
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Project description:Variation identified in candidate genes for color in domestic yak
2019-11-06 | PRJEB35221 | EVA
Project description:Deciphering the genetics of orange coat color in domestic cats
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Project description:we compared the skin transcriptomes of the black- and white-coated region from the Boer and Macheng Black crossbred goat with black head and white body using the Illumina RNA-Seq method. Six cDNA libraries derived from skin samples of the white coat region (n = 3) and black coat region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for each skin sample of black coat and white coat, respectively, of which 75.39% and 76.05% reads were covered in the genome database. Our study provides insight into the transcriptional regulation of two distinct coat color that might serve as a key resource for understanding coat color pigmentation of goat.
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Project description:We apply developmental and single cell gene expression analysis to fetal skin of domestic cats, together with genetic characterization of Mendelian color variation, to identify when, where, and how, during fetal development, felid color patterns are established. Prior to the appearance of hair follicle placodes, we identify changes in epidermal thickness that represent a signature of color pattern establishment, and that are preceded by a pre-pattern of gene expression in which the secreted Wnt inhibitor encoded by Dickkopf 4 (Dkk4) plays a central role. We also demonstrate that mutations in Dkk4 underlie the Ticked pattern mutation in cats. Our results bring molecular understanding to how the leopard got its spots, suggest that similar mechanisms underlie periodic color pattern and periodic hair follicle spacing, and provide a genomic framework to explore natural selection for diverse pattern types in wild felids.
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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:The Sex-linked orange mutation in domestic cats causes variegated patches of reddish/yellow hair and is a defining signature of random X-inactivation in female tortoiseshell and calico cats. Unlike the situation for most coat color genes, there is no apparent homolog for Sex-linked orange in other mammals. We show that Sex-linked orange is caused by a 5 kb deletion that leads to ectopic and melanocyte-specific expression of the Rho GTPase Activating Protein 36 (Arhgap36) gene. Single cell RNA-seq studies from fetal cat skin reveal that red/yellow hair color is caused by reduced expression of melanogenic genes that are normally activated by the Melanocortin 1 receptor (Mc1r)—cyclic adenosine monophosphate (cAMP)—protein kinase A (PKA) pathway, but Mc1r and its ability to stimulate cAMP accumulation is intact. Instead, we show that expression of Arhgap36 in melanocytes leads to reduced levels of the PKA catalytic subunit (PKAC); thus, Sex-linked orange is genetically and biochemically downstream of Mc1r. Our findings resolve a longstanding comparative genetic puzzle, provide in vivo evidence for the ability of Arhgap36 to inhibit PKA, and reveal a molecular explanation for a charismatic color pattern with a rich genetic history.
2025-05-06 | GSE290420 | GEO
Project description:The Sex-linked orange mutation in domestic cats causes variegated patches of reddish/yellow hair and is a defining signature of random X-inactivation in female tortoiseshell and calico cats. Unlike the situation for most coat color genes, there is no apparent homolog for Sex-linked orange in other mammals. We show that Sex-linked orange is caused by a 5 kb deletion that leads to ectopic and melanocyte-specific expression of the Rho GTPase Activating Protein 36 (Arhgap36) gene. Single cell RNA-seq studies from fetal cat skin reveal that red/yellow hair color is caused by reduced expression of melanogenic genes that are normally activated by the Melanocortin 1 receptor (Mc1r)—cyclic adenosine monophosphate (cAMP)—protein kinase A (PKA) pathway, but Mc1r and its ability to stimulate cAMP accumulation is intact. Instead, we show that expression of Arhgap36 in melanocytes leads to reduced levels of the PKA catalytic subunit (PKAC); thus, Sex-linked orange is genetically and biochemically downstream of Mc1r. Our findings resolve a longstanding comparative genetic puzzle, provide in vivo evidence for the ability of Arhgap36 to inhibit PKA, and reveal a molecular explanation for a charismatic color pattern with a rich genetic history.
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Project description:Molecular and genetic characterization of sex-linked orange coat color in the domestic cat [C96]
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Project description:Molecular and genetic characterization of sex-linked orange coat color in the domestic cat [C4F1]
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Project description:Coat color mainly reflects pigmentation resulting from melanin. Wool color is one of the most visible and heritable traits in sheep. Although several detailed molecular mechanisms involved in coat color have been elucidated, our understanding of differences in gene expression patterns of wool color-related genes in Chinese Merino (Junken type) is limited. We employed the Affymetrix microarray to identify differentially expressed genes. 122 genes were differentially expressed, consisting of 117 upregulated and 5 downregulated genes that were related to black/brown skin. The expression level of the BMP2, BMP4, TYRP1, LEPR, DCT, BMPR1A, and TP45A genes was validated by qRT-PCR, and the results coincided with those of microarray. The expression level of ASIP in the black/brown group was significantly lower than that of the white group, suggesting that this plays a key role in the regulation of wool pigmentation. Some cloned color genes (MITF, MC1R, GPR143, and KIT) showed no significant differences in expression levels between the black/brown- and white-skinned sheep. Functional annotation by using Gene Ontology (GO) showed that the differentially expressed genes enriched specific GO terms, particularly those relating to melanin biosynthesis and metabolic processes. KEGG pathway analysis indicated that the categories of tyrosine metabolism and melanogenesis pathway were enriched with differentially expressed genes. Taken together, the present study has shown that the tyrosine metabolism pathway plays an essential role in regulating wool color. The findings of this study may also be utilized in the elucidation of the molecular mechanisms and relationship between genes and wool color in Chinese Merino (Junken type). We used microarrays to detail the global programme of gene expression and identified distinct different expression genes of skin in different coat color Chinese Merino (Junken type).
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