Coat colour in fallow deer
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB38970 | ENA |
REPOSITORIES: ENA
Similar Datasets
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Project description:Seed coat colour is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds, such as seed dormancy, longevity, oil content, protein content and fibre content. In Brassica napus, inheritance of seed coat colour is related to maternal effects and pollen effects (xenia effects). In this research, we isolated a mutation of yellow seeded B. napus controlled by a single Mendelian locus with pollen effect. Microcopy of transverse sections of the mature seed shows pigment is deposited only in the epidermal cells, the first cell layer of seed coat. By Illumina Hiseq 2000 sequencing technology, a total of 12 G clean data, 116x coverage of coding sequences of B. napus, was achieved from 26-day old brown and yellow seeds. It was assembled into 172,238 independent transcripts and 55,637 unigenes by Trinity. A total of 150 orthologous genes of Arabidopsis transparent testa (TT) genes were mapped in silico to 19 chromosomes of B. napus. Only 49 of the TT orthologous genes are transcripted in seeds. However transcription of all the orthologs was independent of the embryonal control of seed coat colour. Of all the Trinity-assembled unigenes, only 55 genes were found to be differentially expressed between the brown seeds and yellow mutant. Among them 50 were up-regulated and 5 were down-regulated in the yellow seeds as compared to the brown counterpart. By KEGG classification, 14 metabolic pathways were enriched significantly. Of these, 5 pathways: phenylpropanoid biosynthesis, cyanoamino acid metabolism, plant hormone signal transduction, metabolic pathways and biosynthesis of secondary metabolites, were related with seed coat pigmentation. Free amino acid quantification showed that Ala and Phe were produced at higher levels in the embryo of yellow seeds as compared to brown seeds. This increase was not observed in the seed coat. Moreover, the excess amount of free Ala was exactly twice that of Phe in the 26-day embryo of yellow seeds. Pigment indispensable substrate chalcone is synthesized from two molecules of Ala and one molecule of Phe. The correlation between accumulation of Ala and Phe and disappearance of pigment in the yellow seeded mutant indicate that embryonal control of seed coat colour is related with Phe and Ala metabolism in the embryo of B. napus.
2018-05-19 | GSE69137 | GEO
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.
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2011-09-15 | GSE30346 | GEO
Project description:Purpose: The goal of this study is to compare (RNA-seq) transcriptomes of in vitro cultured human bone marrow-derived mesenchymal stem cells (hMSCs) and fallow deer antler-derived skeletal progenitors (FD RM Cells) under multiple conditions to identify candidate proliferation and mineralization genes responsible for fast antler regeneration Methods: hMSCs and FD RM Cells were cultured in vitro under 1) serum-free (0% serum) or serum (10% serum) conditions for 2.5 days or 2) Control (0 ng/mL BMP-2 and 0 nM dexamethasone) and osteogenic (100 ng/mL BMP-2 and 100 nM dexamethasone) media for 24 days. mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads were analyzed at the transcript isoform level STARS followed by Cufflinks. Validation for genes of interest was performed using immunofluorescence staining. Results: Comparison of human and fallow deer skeletal progenitor datasets yielded proliferation and mineralization gene candidates Conclusions: Our study represents the first detailed analysis of human and fallow deer transcriptomes of skeletal progenitor cells under proliferation and mineralization conditions, with biologic replicates, generated by RNA-seq technology. Our in vitro comparative approach circumvent some of the logistical and technical challenges in identifying candidate proliferation and mineralization genes responsible for rapid deer antler regeneration. We conclude that in vitro comparison of RNA-seq based transcriptomes identified candidate proliferaiton and mineralization genes to advance bone biology and holds promise to rapidly regenerate large bone volumes for regenerative medicine. The comparative approach utilized here can be adapted for almost any tissue to study a specific phenomenon of interest.
2018-11-16 | GSE89796 | 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:Transcriptional profiling during Arabidopsis seed coat development at 3 key developmental timepoints by using 2 mutant lines and their wild types. The data provides a globe view of seed coat development in arabidopsis can be used for identification of new gene candidates for seed coat development.
2011-03-10 | GSE27857 | GEO
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).
2018-04-01 | GSE98180 | GEO
Project description:Transcriptional profiling during Arabidopsis seed coat development at 3 key developmental timepoints by using 2 mutant lines and their wild types. The data provides a globe view of seed coat development in arabidopsis can be used for identification of new gene candidates for seed coat development. 3 seed coat development stages, 4 lines (2 wild type + 2 mutants) of arabidopsis were sampled. 4 biological replicates.
2011-03-10 | E-GEOD-27857 | biostudies-arrayexpress