Comparative Transcriptome Analysis of lncRNAs and mRNAs associated with different coat colours in Pashmina fiber
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ABSTRACT:
ORGANISM(S): Capra hircus
PROVIDER: GSE107249 | GEO | 2019/05/15
REPOSITORIES: GEO
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Project description:Comparative Transcriptome Analysis of lncRNAs and mRNAs associated with different coat colours in Pashmina fiber
| PRJNA419413 | ENA
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.
2022-08-18 | GSE135963 | 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.
2011-03-10 | GSE27857 | GEO
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:Identification of genes that regulate fiber cycling in Pashmina goat.
2019-10-15 | GSE117065 | 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
Project description:BackgroundThe fiber yield and quality of cotton are greatly and periodically affected by water deficit. However, the molecular mechanism of the water deficit response in cotton fiber cells has not been fully elucidated.ResultsIn this study, water deficit caused a significant reduction in fiber length, strength, and elongation rate but a dramatic increase in micronaire value. To explore genome-wide transcriptional changes, fibers from cotton plants subjected to water deficit (WD) and normal irrigation (NI) during fiber development were analyzed by transcriptome sequencing. Analysis showed that 3427 mRNAs and 1021 long noncoding RNAs (lncRNAs) from fibers were differentially expressed between WD and NI plants. The maximum number of differentially expressed genes (DEGs) and lncRNAs (DERs) was identified in fibers at the secondary cell wall biosynthesis stage, suggesting that this is a critical period in response to water deficit. Twelve genes in cotton fiber were differentially and persistently expressed at ≥ five time points, suggesting that these genes are involved in both fiber development and the water-deficit response and could potentially be used in breeding to improve cotton resistance to drought stress. A total of 540 DEGs were predicted to be potentially regulated by DERs by analysis of coexpression and genomic colocation, accounting for approximately 15.76% of all DEGs. Four DERs, potentially acting as target mimics for microRNAs (miRNAs), indirectly regulated their corresponding DEGs in response to water deficit.ConclusionsThis work provides a comprehensive transcriptome analysis of fiber cells and a set of protein-coding genes and lncRNAs implicated in the cotton response to water deficit, significantly affecting fiber quality during the fiber development stage.
| S-EPMC8722198 | biostudies-literature
Project description:Soybean cultivars, OX951 & OX736, comparison of seed coat at 3 growth stages, early, mid & late Keywords: time course
2007-01-01 | GSE4276 | GEO
Project description:Coat colour of brushtail possum
| PRJNA1052710 | ENA