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

Investigating the impact of pigmentation variation of breast muscle on growth traits, melanin deposition, and gene expression in Xuefeng black-bone chickens

The blackness traits, considered an important economic factor in the black-bone chicken industry, still exhibits a common phenomenon of significant difference in blackness of breast muscle. To improve this phenomenon, this study compared growth traits, blackness traits, and transcriptome of breast muscles between the High Blackness Group (H group) and Low Blackness Group (L group) in the Xuefeng black-bone chickens. The results are as follows: 1) There was no significant difference in growth traits between the H group and the L group (P > 0.05). 2) The skin/breast muscle L values in the H group were significantly lower than those in the L group, while the breast muscle melanin content exhibited the opposite trend (P < 0.05). 3) A significant negative correlation was observed between breast muscle melanin content and skin/breast muscle L value (P < 0.05), and skin L value exhibiting a significant positive correlation with breast muscle L value (P < 0.05). 4) The breast muscle transcriptome comparison between the H group and L group revealed 831 and 405 DEGs in female and male chickens, respectively. This included 37 shared DEGs significantly enriched in melanosome, pigment granule, and the melanogenesis pathway. Seven candidate genes (DCT, PMEL, MLANA, TYRP1, OCA2, EDNRB2, and CALML4) may play a crucial role in the melanin production of breast muscle in Xuefeng black-bone chicken. The findings could accelerate the breeding process for achieving desired levels of breast muscle blackness and contribute to the exploration of the mechanisms underlying melanin production in black-bone chickens.

Ssc-mir-221-3p regulates melanin production in Xiang pigs melanocytes by targeting the TYRP1 gene

BACKGROUND

MicroRNAs (miRNAs) are small endogenous non-coding RNAs that regulate gene expression by down-regulating it. Several studies have suggested that miRNAs plays a crucial role in mammalian skin color production. The TYRP1 gene, a member of the tyrosine family, is an important candidate gene that affects melanogenesis. This study aimed to identify genes and miRNAs that affect melanin production in Xiang pigs by transcriptome sequencing, and to validate their targeted regulatory relationships.

RESULTS

17 miRNAs and 1,230 genes were significantly differentially expressed (P < 0.05) in the black and white skin tissues of Jianbai Xiang pigs. miRNA-221-3p was identified as a candidate miRNA for melanin formation and its target gene, TYRP1, was selected. The TYRP1 gene is a member of the TYR gene family, which evolved from the TYR gene through chromosome segmental duplication. The function of the gene was highly conserved throughout the evolutionary process. overexpression of TYRP1 gene significantly increased the expression of TYR, TYRP1, and DCT genes P < 0.01, which led to an increase in the relative content of melanin. Silencing of TYRP1 through the use of TYRP1-siRNA significantly reduced the expression of TYR, TYRP1, and DCT genes in Jianbai Xiang pig melanocytes P < 0.01, which in turn decreased the relative melanin content. The targeted binding relationship between ssc-miR-221-3p and TYRP1 gene was validated. After transfection of porcine melanocytes with ssc-miR-221-3p mimic, the expression of ssc-miR-221-3p was significantly up-regulated (P < 0.01). Furthermore, the mRNA and protein levels of TYR, TYRP1, and DCT genes were significantly down-regulated (P < 0.01), and melanin content in cells was significantly reduced (P < 0.01).

CONCLUSION

The TYRP1 gene affects melanogenesis in melanocytes of Jianbai Xiang pigs, and ssc-miR-221-3p targets the TYRP1 gene to regulate melanogenesis in melanocytes of Jianbai Xiang pigs.

Genome-Wide Association Study Identifies Candidate Genes for Stripe Pattern Feather Color of Rhode Island Red Chicks

Feather colors of chickens are not only characteristics of breeds but also as phenotypic markers in chicken breeding. Pure-bred Rhode Island Red (RIR) chicks have a stripe pattern and a non-stripe pattern on the back. The stripe pattern of RIR is generally shown as four longitudinal black stripes on the back and is more likely to appear in females. In this study, we performed a genome-wide association study (GWAS) to identify candidate genes controlling the stripe pattern of RIR chicks, and then, based on physical location and biological functions, quantitative RT-PCR analysis was used to validate the differential expression of candidate genes between stripe pattern and non-stripe pattern back skin tissue. The GWAS showed that a major signal contains 768 significant single nucleotide polymorphisms (SNPs) and 87 significant small insertions-deletions (INDELs) spanning 41.78 to 43.05 Mb (~1.27 Mb) on GGA1, corresponding to 16 genes associated with stripe pattern phenotype. Among these 16 genes, KITLG and TMTC3 could be considered candidate genes as they showed different expressions between back skin tissues of stripe pattern and non-stripe pattern chicks in value (p = 0.062) and the significant level (p < 0.05), respectively. This study provided novel insight into the mechanisms underlying feather pigmentation and stripe formation in RIR chicks.

Genetic and phenotypic parameters for feed efficiency and component traits in American mink

Feed cost is the largest expense of mink production systems, and therefore, improvement of feed efficiency (FE) through selection for high feed efficient mink is a practical way to increase the mink industry's sustainability. In this study, we estimated the heritability, phenotypic and genetic correlations for different FE measures and component traits, including harvest weight (HW), harvest length (HL), final body length (FBL), final body weight (FBW), average daily gain (ADG), daily feed intake (DFI), feed conversion ratio (FCR), residual feed intake (RFI), residual gain (RG), residual intake and gain (RIG), and Kleiber ratio (KR), using data from 2,288 American mink (for HW and HL), and 1,038-1,906 American mink (for other traits). Significance (P < 0.05) of fixed effects (farm, sex, and color-type), a covariate (age of animal), and random effects (additive genetic, maternal, and common litter) were evaluated through univariate models implemented in ASReml-R version 4. Genetic parameters were estimated via fitting a set of bivariate models using ASReml-R version 4. Estimates of heritabilities (±SE) were 0.28±0.06, 0.23±0.06, 0.28±0.10, 0.27±0.11, 0.25±0.09, 0.26±0.09, 0.20±0.09, 0.23±0.09, 0.21±0.10, 0.25±0.10, and 0.26±0.10 for HW, HL, FBL, FBW, ADG, DFI, FCR, RFI, RG, RIG, and KR, respectively. RIG had favorable genetic correlations with DFI (-0.62±0.24) and ADG (0.58±0.21), and non-significant (P > 0.05) genetic correlations with FBW (0.14±0.31) and FBL (-0.15±0.31). These results revealed that RIG might be superior trait as it guarantees reduced feed intake with faster-growing mink yet with no negative impacts on body weight and length. In addition, the strong positive genetic correlations (±SE) between KR with component traits (0.88±0.11 with FBW; 0.68±0.17 with FBL; and 0.97±0.02 with ADG) suggested KR as an applicable indirect measure of FE for improvement of component traits as it did not require the individual feed intake to be measured. Overall, our results confirmed the possibility of including FE traits in mink breeding programs to effectively select feed-efficient animals.

Canine coat pigmentation genetics: a review

Our understanding of canine coat colour genetics and the associated health implications is developing rapidly. To date, there are 15 genes with known roles in canine coat colour phenotypes. Many coat phenotypes result from complex and/or epistatic genetic interactions among variants within and between loci, some of which remain unidentified. Some genes involved in canine pigmentation have been linked to aural, visual and neurological impairments. Consequently, coat pigmentation in the domestic dog retains considerable ethical and economic interest. In this paper we discuss coat colour phenotypes in the domestic dog, the genes and variants responsible for these phenotypes and any proven coat colour-associated health effects.

MiR-19 3b regulated the formation of coat colors by targeting WNT10A and GNAI2 in Cashmere goats

MiRNAs as a series of small noncoding RNAs that play a crucial part in regulating coat color and hair follicle development. In the previous Solexa sequencing experiments, there were many miRNAs expressed differentially in alpacas with different coat color, including miR-193b.But the mechanism of miR-193b in mammalian pigmentation is still unknown. In this study, bioinformatics analysis showed that WNT10A and GNAI2 might be the target genes of miR-193b. qRT-PCR showed the expression of miR-193b in white Cashmere goats' skins was obviously lower than that in browns, and the expression of WNT10A and GNAI2 were similar with miR-193b. The protein levels of WNT10A and GNAI2 indicated the same findings. Furthermore, the expression of WNT10A and GNAI2 in keratinocytes were analyzed from mRNA and protein levels, the results manifested that the group of overexpression of miR-193b in HaCaT cells increased the expressions of target genes, and miR-193b inhibition group reduced expressions. Luciferase report assays confirmed that the targeting relationship between miR-193b and target genes (WNT10A and GNAI2), the results showed that miR-193b was positively correlated with target genes. These experimental data showed that miR-193b might participate in adjustment of coat color in skin tissue of Cashmere goat by targeting WNT10A and GNAI2.

Five genetic variants explain over 70% of hair coat pheomelanin intensity variation in purebred and mixed breed domestic dogs

In mammals, the pigment molecule pheomelanin confers red and yellow color to hair, and the intensity of this coloration is caused by variation in the amount of pheomelanin. Domestic dogs exhibit a wide range of pheomelanin intensity, ranging from the white coat of the Samoyed to the deep red coat of the Irish Setter. While several genetic variants have been associated with specific coat intensity phenotypes in certain dog breeds, they do not explain the majority of phenotypic variation across breeds. In order to gain further insight into the extent of multigenicity and epistatic interactions underlying coat pheomelanin intensity in dogs, we leveraged a large dataset obtained via a direct-to-consumer canine genetic testing service. This consisted of genome-wide single nucleotide polymorphism (SNP) genotype data and owner-provided photos for 3,057 pheomelanic mixed breed and purebred dogs from 63 breeds and varieties spanning the full range of canine coat pheomelanin intensity. We first performed a genome-wide association study (GWAS) on 2,149 of these dogs to search for additional genetic variants that underlie intensity variation. GWAS identified five loci significantly associated with intensity, of which two (CFA15 29.8 Mb and CFA20 55.8 Mb) replicate previous findings and three (CFA2 74.7 Mb, CFA18 12.9 Mb, CFA21 10.9 Mb) have not previously been reported. In order to assess the combined predictive power of these loci across dog breeds, we used our GWAS data set to fit a linear model, which explained over 70% of variation in coat pheomelanin intensity in an independent validation dataset of 908 dogs. These results introduce three novel pheomelanin intensity loci, and further demonstrate the multigenic nature of coat pheomelanin intensity determination in domestic dogs.

Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries)

Background

Minxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation.

Methods

Skin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds.

Results

Small-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds.

Genetic and phenotypic parameters for body weights, harvest length, and growth curve parameters in American mink

Understanding the genetics underlying growth curve is important for selection of animals with better growth potential, but little is known about the genetics of growth curve parameters in mink. This study estimated the genetic parameters for body weights (BWs), harvest length (HL), and growth parameters derived from the Richards model. For this purpose, individual BW of 1,088 mink measured seven times in 3-wk intervals (weeks 13 to 31 of life) were used for growth curve modeling using the Richards model. The BW traits included BW at week 13 (BW13), 16 (BW16), 19 (BW19), 22 (BW22), 25 (BW25), 28 (BW28), and 31 (BW31). Univariate analyses indicated that sex and birth-year had significant effects (P < 0.05) on BW, HL, asymptotic weight (α), growth rate at mature (k), shape parameter (m), weight at the inflection point (WIP), and age at the inflection point (AIP). In contrast, the color type had only significant effect (P < 0.05) on BW31 and HL. Estimated heritabilities (±SE) were ranged from 0.36 ± 0.13 (BW13) to 0.46 ± 0.10 (BW22) for BW and were 0.51 ± 0.09, 0.29 ± 0.09, 0.30 ± 0.09, 0.33 ± 0.1, 0.44 ± 0.10, and 0.47 ± 0.10 for HL, α, k, m, WIP, and AIP, respectively. The parameter α had non-significant (P > 0.05) genetic correlations (±SE) with k (-0.21 ± 0.23) and m (-0.10 ± 0.22), suggesting that changing shape parameters (k and m) will not influence asymptotic weight (α). Strong significant (P < 0.05) phenotypic (from 0.46 ± 0.03 to 0.60 ± 0.03) and genetic (0.70±0.13 to 0.88±0.09) correlations were observed between HL and different BW measures. The α, AIP, and WIP parameters had significant (P < 0.05) genetic correlations with HL indicated that selection for higher α, AIP, and WIP values would increase HL. Parameters k and m had nonsignificant (P > 0.05) genetic correlations with HL, indicating the change of the curve shape could not influence HL. Overall, the results suggest that growth curve parameters are heritable and can respond to genetic or genomic selection for optimizing the performance in mink.

High Genetic Diversity of an Invasive Alien Species: Comparison between Fur-Farmed and Feral American Mink (Neovison vison) in China

Simple Summary

The American mink (Neovison vison) is one of the best-known and most widespread invasive species in China and worldwide. To investigate the genetic characteristics and increase comprehension of the invasiveness process for this species, we compared the genetic characteristics of farmed and feral populations in northeastern China using mitochondrial DNA sequences and microsatellite loci. We found a relatively high diversity among the feral populations that was as high as that of the farmed mink. This demonstrated that high genetic diversity promotes the invasiveness and rapid evolution in the wild.

Abstract

Genetic characteristics play an important role in alien species for achieving high adaptation and rapid evolution in a new environment. The American mink (Neovison vison) is one of the best-known and most widespread invasive species that has successfully invaded the Eurasian mainland over quite a short period, including most parts of northeastern China. However, genetic information on farmed and feral American mink populations introduced in China is completely lacking. In this study, we combined mitochondrial DNA sequences and polymorphic microsatellites to examine the genetic divergence and genetic diversity of farmed and feral American mink populations. Our results suggest that there is admixture of individuals of different genetic characteristics between farmed and feral populations of mink. Furthermore, the genetic diversity of both farmed and feral American mink populations was high, and no bottleneck or population expansion was detected in most of the populations. These findings not only highlight the genetic characteristics of American mink in northeastern China but also contribute to the general understanding of the invasiveness of farmed species.

Genetics and Evolution of Mammalian Coat Pigmentation

The diversity of mammalian coat colors, and their potential adaptive significance, have long fascinated scientists as well as the general public. The recent decades have seen substantial improvement in our understanding of their genetic bases and evolutionary relevance, revealing novel insights into the complex interplay of forces that influence these phenotypes. At the same time, many aspects remain poorly known, hampering a comprehensive understanding of these phenomena. Here we review the current state of this field and indicate topics that should be the focus of additional research. We devote particular attention to two aspects of mammalian pigmentation, melanism and pattern formation, highlighting recent advances and outstanding challenges, and proposing novel syntheses of available information. For both specific areas, and for pigmentation in general, we attempt to lay out recommendations for establishing novel model systems and integrated research programs that target the genetics and evolution of these phenotypes throughout the Mammalia.

Molecular Plasticity in Animal Pigmentation: Emerging Processes Underlying Color Changes

Animal coloration has been rigorously studied and has provided morphological implications for fitness with influences over social behavior, predator–prey interactions, and sexual selection. In vertebrates, its study has developed our understanding across diverse fields ranging from behavior to molecular biology. In the search for underlying molecular mechanisms, many have taken advantage of pedigree-based and genome-wide association screens to reveal the genetic architecture responsible for pattern variation that occurs in early development. However, genetic differences do not provide a full picture of the dynamic changes in coloration that are most prevalent across vertebrates at the molecular level. Changes in coloration that occur in adulthood via phenotypic plasticity rely on various social, visual, and dietary cues independent of genetic variation. Here, I will review the contributions of pigment cell biology to animal color changes and recent studies describing their molecular underpinnings and function. In this regard, conserved epigenetic processes such as DNA methylation play a role in lending plasticity to gene regulation as it relates to chromatophore function. Lastly, I will present African cichlids as emerging models for the study of pigmentation and molecular plasticity for animal color changes. I posit that these processes, in a dialog with environmental stimuli, are important regulators of variation and the selective advantages that accompany a change in coloration for vertebrate animals.

Transcriptome-based selection and validation of optimal house-keeping genes for skin research in goats (Capra hircus)

BACKGROUND

In quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression results are dependent on optimal amplification of house-keeping genes (HKGs). 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 for skin research have not been identified in goat. Therefore, this study seeks to identify a set of stable HKGs for the skin tissue of C. hircus using high-throughput sequencing technology.

RESULTS

Based on the transcriptome dataset of 39 goat skin tissue samples, 8 genes (SRP68, NCBP3, RRAGA, EIF4H, CTBP2, PTPRA, CNBP, and EEF2) with relatively stable expression levels were identified and selected as new candidate HKGs. Commonly used HKGs including SDHA and YWHAZ from a previous study, and 2 conventional genes (ACTB and GAPDH) were also examined. Four different experimental variables: (1) different development stages, (2) hair follicle cycle stages, (3) breeds, and (4) sampling sites were used 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 shown that NCBP3 + SDHA + PTPRA were more stably expressed than previously used genes in all conditions analysis, and that this combination was effective at normalizing target gene expression. Moreover, a new algorithm for comprehensive analysis, ComprFinder, was developed and released.

CONCLUSION

This study presents the first list of candidate HKGs for C. hircus skin tissues based on an RNA-seq dataset. We propose that the NCBP3 + SDHA + PTPRA combination could be regarded as a triplet set of HKGs in skin molecular biology experiments in C. hircus and other closely related species. In addition, we also encourage researchers who perform candidate HKG evaluations and who require comprehensive analysis to adopt our new algorithm, ComprFinder.

KIT is involved in melanocyte proliferation, apoptosis and melanogenesis in the Rex Rabbit

BACKGROUND

Melanocytes play an extremely important role in the process of skin and coat colors in mammals which is regulated by melanin-related genes. Previous studies have demonstrated that KIT is implicated in the process of determining the color of the coat in Rex rabbits. However, the effect of KIT on the proliferation and apoptosis of melanocytes and melanogenesis has not been clarified.

METHODS

The mRNA and protein expression levels of KIT were quantified in different coat colored rabbits by qRT-PCR and a Wes assay. To identify whether KIT functions by regulating of melanogenesis, KIT overexpression and knockdown was conducted in melanocytes, and KIT mRNA expression and melanin-related genes TYR, MITF, PMEL and DCT were quantified by qRT-PCR. To further confirm whether KIT influences melanogenesis in melanocytes, melanin content was quantified using NaOH lysis after overexpression and knockdown of KIT. Melanocyte proliferation was estimated using a CCK-8 assay at 0, 24, 48 and 72 h after transfection, and the rate of apoptosis of melanocytes was measured by fluorescence-activated cell sorting.

RESULTS

KITmRNA and protein expression levels were significantly different in the skin of Rex rabbits with different color coats (P < 0.05), the greatest levels observed in those with black skin. The mRNA expression levels of KIT significantly affected the mRNA expression of the pigmentation-related genes TYR, MITF, PMEL and DCT (P < 0.01). Melanin content was evidently regulated by the change in expression patterns of KIT (P < 0.01). In addition, KIT clearly promoted melanocyte proliferation, but inhibited apoptosis.

CONCLUSIONS

Our results reveal that KIT is a critical gene in the regulation of melanogenesis, controlling proliferation and apoptosis in melanocytes, providing additional evidence for the mechanism of pigmentation of animal fur.

Transcriptome Comparison Reveals Key Components of Nuptial Plumage Coloration in Crested Ibis

Nuptial plumage coloration is critical in the mating choice of the crested ibis. This species has a characteristic nuptial plumage that develops from the application of a black sticky substance, secreted by a patch of skin in the throat and neck region. We aimed to identify the genes regulating its coloring, by comparing skin transcriptomes between ibises during the breeding and nonbreeding seasons. In breeding season skins, key eumelanin synthesis genes, TYR, DCT, and TYRP1 were upregulated. Tyrosine metabolism, which is closely related to melanin synthesis, was also upregulated, as were transporter proteins belonging to multiple SLC families, which might act during melanosome transportation to keratinocytes. These results indicate that eumelanin is likely an important component of the black substance. In addition, we observed upregulation in lipid metabolism in breeding season skins. We suggest that the lipids contribute to an oil base, which imbues the black substance with water insolubility and enhances its adhesion to feather surfaces. In nonbreeding season skins, we observed upregulation in cell adhesion molecules, which play critical roles in cell interactions. A number of molecules involved in innervation and angiogenesis were upregulated, indicating an ongoing expansion of nerves and blood vessels in sampled skins. Feather β keratin, a basic component of avian feather filament, was also upregulated. These results are consistent with feather regeneration in the black skin of nonbreeding season ibises. Our results provide the first molecular evidence indicating that eumelanin is the key component of ibis coloration.

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

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.

Transcriptome profiling analysis reveals key genes of different coat color in sheep skin

Background

To investigate the molecular mechanisms determining the coat color of native breed sheep in Xinjiang.

Methods

Bashibai sheep, Yemule white sheep and Tulufan black sheep were selected. Illumina HiSeq X Ten sequencing technology was used to detect the genes responsible for the white, light brown, black and cyan gray coat colors in sheep. Sequence analysis and functional gene annotation analysis were performed to analyze the results. The signal pathways and differentially expressed genes related to sheep hair color production regulation were screened and finally verified by real-time polymerase chain reaction.

Results

Functional annotation by Kyoto Encyclopedia of Genes and Genomes analysis revealed significant differences in enrichment of immunity-related pathways as well as melanogenesis synthetic and tyrosine metabolism pathways. Our results showed that the DCT, TYR, TYRP1, PMEL, SLC45A2 and MLANA six genes may be associated with the regulation of coat color development and provide a theoretical basis for selecting natural coat colors of sheep.

MiR-27a regulates WNT3A and KITLG expression in Cashmere goats with different coat colors

MicroRNAs(miRNAs) regulate and control gene expression at the post-transcriptional level by base pairing with its target gene 3'UTR, resulting in degradation of the target mRNA or inhibition of its translation. The previous high-throughput sequencing results indicated that miR-27a was involved in coat color regulation. However, the mechanism of action is not still illuminated. In this research, using western blotting and real-time quantitative polymerase chain reaction(qRT-PCR), the expression of miR-27a, WNT3A and KITLG were examined in the skin of Cashmere goats with white and brown, and human embryonic kidney 293 T cells (HEK-293T cells) which over-express miR-27a. Targeting relationship between miR-27a and WNT3A or KITLG was examined by the luciferase reporter gene system. The qRT-PCR detection showed that miR-27a was more highly expressed in white Cashmere goats skin than that in brown Cashmere goats skin. Furthermore, WNT3A and KITLG mRNA and protein expression were down-regulated by miR-27a in vitro and in vivo. A dual-luciferase reporter gene indicated that miR-27a negatively correlates with WNT3A or KITLG. In a word, our research demonstrated that the expression of miR-27a was evidently differential in the white and brown Cashmere goats skin and WNT3A or KITLG was negatively regulated by miR-27a.

Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus

Background

Color and pattern phenotypes have clear implications for survival and reproduction in many species. However, the mechanisms that produce this coloration are still poorly characterized, especially at the genomic level. Here we have taken a transcriptomics-based approach to elucidate the underlying genetic mechanisms affecting color and pattern in a highly polytypic poison frog. We sequenced RNA from the skin from four different color morphs during the final stage of metamorphosis and assembled a de novo transcriptome. We then investigated differential gene expression, with an emphasis on examining candidate color genes from other taxa.

Results

Overall, we found differential expression of a suite of genes that control melanogenesis, melanocyte differentiation, and melanocyte proliferation (e.g., tyrp1, lef1, leo1, and mitf) as well as several differentially expressed genes involved in purine synthesis and iridophore development (e.g., arfgap1, arfgap2, airc, and gart).

Conclusions

Our results provide evidence that several gene networks known to affect color and pattern in vertebrates play a role in color and pattern variation in this species of poison frog.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1410-7) contains supplementary material, which is available to authorized users.

Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs

Coat color is one of the most important characteristics for distinguishing Chinese indigenous pig breeds. In Wuzhishan pigs, the animals have black on the back and white on the abdomen. However, the molecular genetic basis of this phenotype is unclear. In this study, we used high-throughput RNA sequencing to compare expression profiles of coding and non-coding RNAs from white and black skin samples obtained from individual Wuzhishan pigs. The expression profiling revealed that 194 lncRNAs (long non-coding RNAs), 189 mRNAs (messenger RNAs), and 162 miRNAs (microRNAs) had significantly different levels of expression (|log₂ fold change| > 1, p-value < 0.05) in white and black skin. Compared to RNA levels in black skin, white skin had higher levels of expression of 185 lncRNAs, 181 mRNAs, and 23 miRNAs and lower levels of expression of 9 lncRNAs, 8 mRNAs, and 139 miRNAs. Functional analysis suggested that the differentially expressed transcripts are involved in biological processes such as melanin biosynthesis, pigmentation and tyrosine metabolism. Several key genes involved in melanogenesis, including MLANA, PMEL, TYR, TYRP1, DTC, TRPM1 and CAMK2A, had significantly different levels of expression in the two skin tissues. Potential lncRNA–miRNA–gene interactions were also examined. A total of 15 lncRNAs, 11 miRNAs and 7 genes formed 23 lncRNA–miRNA–gene pairs, suggesting that complex regulatory networks of coding and non-coding genes underlie the coat color trait in Wuzhishan pigs. Our study provides a foundation for understanding how lncRNA, miRNA and genes interact to regulate coat color in black-back/white-belly pigs. We also constructed lncRNA–miRNA–gene interaction networks to elucidate the complex molecular mechanisms underlying skin physiology and melanogenesis. The results extend our knowledge about the diversity of coat color among different domestic animals and provide a foundation for studying novel mechanisms that control coat color in Chinese indigenous pigs.

Identification of copy number variations using high density whole-genome SNP markers in Chinese Dongxiang spotted pigs

Objective

Copy number variations (CNVs) are a major source of genetic diversity complementary to single nucleotide polymorphism (SNP) in animals. The aim of the study was to perform a comprehensive genomic analysis of CNVs based on high density whole-genome SNP markers in Chinese Dongxiang spotted pigs.

Methods

We used customized Affymetrix Axiom Pig1.4M array plates containing 1.4 million SNPs and the PennCNV algorithm to identify porcine CNVs on autosomes in Chinese Dongxiang spotted pigs. Then, the next generation sequence data was used to confirm the detected CNVs. Next, functional analysis was performed for gene contents in copy number variation regions (CNVRs). In addition, we compared the identified CNVRs with those reported ones and quantitative trait loci (QTL) in the pig QTL database.

Results

We identified 871 putative CNVs belonging to 2,221 CNVRs on 17 autosomes. We further discarded CNVRs that were detected only in one individual, leaving us 166 CNVRs in total. The 166 CNVRs ranged from 2.89 kb to 617.53 kb with a mean value of 93.65 kb and a genome coverage of 15.55 Mb, corresponding to 0.58% of the pig genome. A total of 119 (71.69%) of the identified CNVRs were confirmed by next generation sequence data. Moreover, functional annotation showed that these CNVRs are involved in a variety of molecular functions. More than half (56.63%) of the CNVRs (n = 94) have been reported in previous studies, while 72 CNVRs are reported for the first time. In addition, 162 (97.59%) CNVRs were found to overlap with 2,765 previously reported QTLs affecting 378 phenotypic traits.

Conclusion

The findings improve the catalog of pig CNVs and provide insights and novel molecular markers for further genetic analyses of Chinese indigenous pigs.