Comparative Transcriptome Analysis of Mink (Neovison vison) Skin Reveals the Key Genes Involved in the Melanogenesis of Black and White Coat Colour

Song, Xuguang; Xu, Chao; Liu, Zongyue; Yue, Zhengkai; Liu, Linling; Yang, Tao; Cong, Bin; Yang, Fenghuan

doi:10.1038/s41598-017-12754-0

Cited by 37 publications

(35 citation statements)

References 64 publications

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“…The steel panda allele is caused by an inversion that disrupts the upstream regulatory region of Kitl, which also leads to diluted pigmentation [49,51]. In both goats and mink, KITLG expression is lower in lighter-colored animals as compared to more darkly pigmented animals [52,53]. In this work, expression levels of KITLG were not evaluated due to challenges in obtaining skin samples from healthy pet dogs; however, based on the work done in other species, the CNV likely alters expression levels of KITLG in the hair follicle.…”

Section: Discussionmentioning

confidence: 99%

Pigment Intensity in Dogs is Associated with a Copy Number Variant Upstream of KITLG

Weich

Affolter

York

et al. 2020

Genes

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Dogs exhibit a wide variety of coat color types, and many genes have been identified that control pigment production, appearance, and distribution. Some breeds, such as the Nova Scotia Duck Tolling Retriever (NSDTR), exhibit variation in pheomelanin pigment intensity that is not explained by known genetic variants. A genome-wide association study comparing light red to dark red in the NSDTR identified a significantly associated region on canine chromosome 15 (CFA 15:23 Mb–38 Mb). Coverage analysis of whole genome sequence data from eight dogs identified a 6 kb copy number variant (CNV) 152 kb upstream of KITLG. Genotyping with digital droplet PCR (ddPCR) confirmed a significant association between an increased copy number with the dark-red coat color in NSDTR (p = 6.1 × 10−7). The copy number of the CNV was also significantly associated with coat color variation in both eumelanin and pheomelanin-based Poodles (p = 1.5 × 10−8, 4.0 × 10−9) and across other breeds. Moreover, the copy number correlated with pigment intensity along the hair shaft in both pheomelanin and eumelanin coats. KITLG plays an important role in melanogenesis, and variants upstream of KITLG have been associated with coat color variation in mice as well as hair color in humans consistent with its role in the domestic dog.

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Section: Discussionmentioning

confidence: 99%

Pigment Intensity in Dogs is Associated with a Copy Number Variant Upstream of KITLG

Weich

Affolter

York

et al. 2020

Genes

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“…Similar to tyrp1, expression of lef1 is associated with the production of pheomelanin, a pigment 373 associated with lighter color phenotypes (Song et al 2017;Stuckert et al 2019). We see early expression 374 of lef1 which rapidly drops off until there is functionally no expression by the end of development when 375 melanic coloration becomes most obvious in tadpoles.…”

Section: Wnt Signaling Pathway: 288mentioning

confidence: 81%

The genomics of mimicry: gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system

Stuckert

Chouteau

McClure

et al. 2019

Preprint

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9Evolutionary biologists have long investigated the ecological contexts, evolutionary forces, and 10 proximate mechanisms that produce the diversity of animal coloration we see in the natural world. In 11 aposematic species, color and pattern is directly tied to survival and thus understanding the origin of the 12 phenotype has been a focus of both theoretical and empirical inquiry. In order to better understand this 13 diversity, we examined gene expression in skin tissue during development in four different color morphs 14 of the aposematic mimic poison frog, Ranitomeya imitator. We identified a suite of candidate color-15 related genes a priori and identified the pattern of expression in these genes over time, differences in 16 expression of these genes between the mimetic morphs, and genetic variants that differ between color 17 morphs. We identified several candidate color genes that are differentially expressed over time or 18 across populations, as well as a number of color genes with fixed genetic variants between color 19 morphs. Many of the color genes we discovered in our dataset are involved in the canonical Wnt 20 signaling pathway, including several fixed SNPs between color morphs. Further, many genes in this 21 pathway were differentially expressed at different points in development (e.g., lef1, tyr, tyrp1). 22 Importantly, Wnt signaling pathway genes are overrepresented relative to expression in Xenopus 23 tropicalis. Taken together, this provides evidence that the Wnt signaling pathway is contributing to color 24 pattern production in R. imitator, and is an excellent candidate for producing some of the differences in 25

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“…When studying the expression of target genes in skin tissue from other species, such as Angora rabbits [27], mink [28], mice [29], and even humans [30], ACTB or GAPDH are generally used as the HKGs. The selection of HKGs from neighboring species has been widely recognized and accepted.…”

Section: The Hkgs Of Skin Tissue In Goats and Other Speciesmentioning

confidence: 99%

Transcriptome-based Selection and Validation of Optimal House-keeping Genes for Skin Research in Goats (Capra hircus)

Zhang

Deng

et al. 2020

Preprint

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Background: In Quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression data is dependent on optimal amplification of house-keeping genes (HKGs). The RNA-seq technology offers a novel approach to detect new HKGs with improved stability. Goat (Capra hircus) is an economically important livestock species, and plays an indispensable role in the world animal fiber and meat industry. Unfortunately, uniform and reliable HKGs be used in skin research of goats have not been identified. Therefore, this study seeks to identify a set of stable HKGs for the skin tissue of C. hircus using the new high-throughput sequencing technology.Results: Based on the transcriptome dataset of 39 goat skin tissues, 8 genes (SRP68, NCBP3, RRAGA, EIF4H, CTBP2, PTPRA, CNBP, and EEF2) with relatively stable expression levels were identified and selected as new candidate HKGs. The classical HKGs including SDHA and YWHAZ from a previous study, and 2 conventional genes (ACTB and GAPDH) were also considered. Four different experimental materials: (1) different development stages, (2) hair follicle cycle stages, (3) breeds and (4) sampling sites were provided for determination and validation. Four algorithms (geNorm, NormFinder, BestKeeper, and ΔCt method) and a comprehensive algorithm (ComprFinder, developed in-house) were used to assess the stability of each HKG. It was observed that NCBP3+SDHA+PTPRA was more stably expressed than previously used genes, in all conditions analyzed. This combination was effective at normalizing target gene expression. Moreover, a new algorithm, ComprFinder, was developed and released for comprehensive analysis.Conclusion: This study presents the first data of candidate HKGs selection for skin tissues of C. hircus based on an RNA-seq dataset. We propose the use of the NCBP3+SDHA+PTPRA combination as the triplet HKGs in skin molecular biology in C. hircus and other closely related species in order to standardize analyses across studies. In addition, we also encourage researchers who are performing candidate HKG evaluations and have the needs of a comprehensive analysis to adopt our new algorithm, ComprFinder.

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Comparative Transcriptome Analysis of Mink (Neovison vison) Skin Reveals the Key Genes Involved in the Melanogenesis of Black and White Coat Colour

Cited by 37 publications

References 64 publications

Pigment Intensity in Dogs is Associated with a Copy Number Variant Upstream of KITLG

Pigment Intensity in Dogs is Associated with a Copy Number Variant Upstream of KITLG

The genomics of mimicry: gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system

Transcriptome-based Selection and Validation of Optimal House-keeping Genes for Skin Research in Goats (Capra hircus)

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