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Whole-transcript Expression data from skin of different coat color in Chinese Merion (Junken type)

ABSTRACT: 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).

ORGANISM(S): Ovis aries

PROVIDER: GSE98180 | GEO | 2018/04/01

REPOSITORIES: GEO

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Project description:Plumage color plays a prominent role in reproductive isolation and thus understanding the genetic basis of pigmentation patterns can provide critical insight into speciation. Subspecies of the dark-eyed junco (Junco hyemalis) show marked differences in melanic plumage coloration known to have evolved rapidly since the Last Glacial Maximum just 18,000 years ago. To understand this rapid radiation we studied the pigment composition and the genetic basis of coloration in two divergent subspecies, the slate-colored and Oregon juncos. We used HPLC and light microscopy to investigate pigment deposition patterns in feathers from four body areas. RNA-seq data generated under common garden experimental conditions were then used to compare the relative roles of differential gene expression in growing feathers and sequence divergence in loci expressed during feather development. Junco feathers were found to differ in eumelanin and pheomelanin content and distribution, producing a range of black, gray and brown colors. Transcriptomic data revealed marked regulatory differences among subspecies and among body-parts within subspecies in known melanin-pathway genes (including PMEL, TYR, TYRP1, OCA2, MLANA), but also in several novel or poorly known loci (EDAR, VPS33B, HPS1). Within subspecies, lighter feathers expressed less melanin synthesis genes, more ASIP, and showed differential expression of Wnt signaling genes. Feathers from different body regions also showed differential expression of Hox genes. The two subspecies differed in expression of ASIP and three other genes (MFSD12, KCNJ13, HAND2) previously associated with color development. Sequence variation in the expressed genes was not related to color differences between junco subspecies. Our findings suggest that differential expression of a few genes can account for marked differences in plumage color and pattern, a mechanism that can account for the rapid diversification of juncos. Several novel candidate pigmentation genes found in juncos may contribute to the expression of melanic coloration in other vertebrates.

Project description:In the eastern United States the buckeye butterfly, Junonia coenia, shows a seasonal wing color polyphenism where adults emerging in the spring are pale brown, while those emerging in the autumn are dark red. This variation can be artificially induced in laboratory colonies, thus making J. coenia a useful model system to examine the developmental basis of phenotypic plasticity. We used RNA-seq to generate the first set of assembled transcripts for this species while simultaneously quantifying relative gene expression associated with development of alternative seasonal color morphs. The assembled consolidated wing transcriptome was 77.55 Mb. 16,251 contigs of over 1000bp in length were assembled, of which 3,145 were differentially expressed between stages and/or color morphs. Depending on the developmental stage, between 547 and 1420 transcripts were significantly differentially expressed between brown and red wing morphs. These extensive differences in gene expression stand in stark contrast to the much smaller numbers found in previous studies on genetic wing pattern variation, and suggest that environmentally induced phenotypic shifts may arise from very broad systemic processes. Overall gene ontology (GO) analyses revealed that genes associated with structural constituents of ribosomes and oxygen transport were significantly upregulated in the pale brown morph, while genes associated with peptidase activity were very significantly upregulated in the dark red morph. Focused analyses of candidate endocrine and pigmentation pathways revealed a number of notable genes upregulated in the red morph, including several ecdysone-related genes and cinnabar, an ommochrome pigment gene implicated in color pattern variation in other butterflies. Surprisingly, we found numerous melanin-related transcripts, including tan and yellow-family genes, strongly upregulated in the red morph, leading us to speculate that red pigmentation in autumn J. coenia may include red or brown melanins in addition to ommochromes. While we identified several endocrine and pigmentation genes as obvious candidates for color morph differentiation, we speculate that the majority of gene expression differences we observed were due to thermal stress response. The buckeye transcriptome provides a basis for further developmental studies of phenotypic plasticity.

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Whole-transcript Expression data from skin of different coat color in Chinese Merion (Junken type)

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