Pigmentation Phenotypes Research Articles

Variation under domestication in animal models: the case of the Mexican axolotl

BackgroundSpecies adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Yet despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is particularly the case of the Mexican axolotl, which has been bred in captivity since 1864.ResultsUsing gene expression data from nine different projects, nucleotide sequence variants were characterised, and distinctive genetic background of the experimental specimens was uncovered. This study provides a catalogue of thousands of nucleotide variants along predicted protein-coding genes, while identifying genome-wide differences between pigment phenotypes in laboratory populations.ConclusionsAwareness of the genetic variation could guide a better experimental design while helping to develop molecular tools for monitoring genetic diversity and studying gene functions in laboratory axolotls. Overall, this study highlights the cross-taxa utility that transcriptomic data might have to assess the genetic variation of the experimental specimens, which might help to shorten the journey towards reproducible research.

Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis).

Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3′ truncated and containing only 5′ UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5′ UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.

The impact of correlations between pigmentation phenotypes and underlying genotypes on genetic prediction of pigmentation traits

Predicting appearance phenotypes from genotypes is relevant for various areas of human genetic research and applications such as genetic epidemiology, human history, anthropology, and particularly in forensics. Many appearance phenotypes, and thus their underlying genotypes, are highly correlated, with pigmentation traits serving as primary examples. However, all available genetic prediction models, including those for pigmentation traits currently used in forensic DNA phenotyping, ignore phenotype correlations. Here, we investigated the impact of appearance phenotype correlations on genetic appearance prediction in the exemplary case of three pigmentation traits. We used data for categorical eye, hair and skin colour as well as 41 DNA markers utilized in the recently established HIrisPlex-S system from 762 individuals with complete phenotype and genotype information. Based on these data, we performed genetic prediction modelling of eye, hair and skin colour via three different strategies, namely the established approach of predicting phenotypes solely based on genotypes while not considering phenotype correlations, and two novel approaches that considered phenotype correlations, either incorporating truly observed correlated phenotypes or DNA-predicted correlated phenotypes in addition to the DNA predictors. We found that using truly observed correlated pigmentation phenotypes as additional predictors increased the DNA-based prediction accuracies for almost all eye, hair and skin colour categories, with the largest increase for intermediate eye colour, brown hair colour, dark to black skin colour, and particularly for dark skin colour. Outcomes of dedicated computer simulations suggest that this prediction accuracy increase is due to the additional genetic information that is implicitly provided by the truly observed correlated pigmentation phenotypes used, yet not covered by the DNA predictors applied. In contrast, considering DNA-predicted correlated pigmentation phenotypes as additional predictors did not improve the performance of the genetic prediction of eye, hair and skin colour, which was in line with the results from our computer simulations. Hence, in practical applications of DNA-based appearance prediction where no phenotype knowledge is available, such as in forensic DNA phenotyping, it is not advised to use DNA-predicted correlated phenotypes as predictors in addition to the DNA predictors. In the very least, this is not recommended for the pigmentation traits and the established pigmentation DNA predictors tested here.

Elucidation of Melanogenesis Cascade for Identifying Pathophysiology and Therapeutic Approach of Pigmentary Disorders and Melanoma.

Melanogenesis is the biological and biochemical process of melanin and melanosome biosynthesis. Melanin is formed by enzymic reactions of tyrosinase family proteins that convert tyrosine to form brown-black eumelanin and yellow-red pheomelanin within melanosomal compartments in melanocytes, following the cascades of events interacting with a series of autocrine and paracrine signals. Fully melanized melanosomes are delivered to keratinocytes of the skin and hair. The symbiotic relation of a melanocyte and an associated pool of keratinocytes is called epidermal melanin unit (EMU). Microphthalmia-associated transcription factor (MITF) plays a vital role in melanocyte development and differentiation. MITF regulates expression of numerous pigmentation genes for promoting melanocyte differentiation, as well as fundamental genes for maintaining cell homeostasis. Diseases involving alterations of EMU show various forms of pigmentation phenotypes. This review introduces four major topics of melanogenesis cascade that include (1) melanocyte development and differentiation, (2) melanogenesis and intracellular trafficking for melanosome biosynthesis, (3) melanin pigmentation and pigment-type switching, and (4) development of a novel therapeutic approach for malignant melanoma by elucidation of melanogenesis cascade.

Functional divergence of white genes in Henosepilachna vigintioctopunctata revealed by RNA interference.

Henosepilachna vigintioctopunctata is a serious pest of Solanaceae and Cucurbitaceae in many Asian countries. RNA interference (RNAi) can effectively reduce transcript abundance in this beetle, offering opportunities to explore the biological function of specific genes. The white gene encodes a half-type ATP-binding cassette transporter that plays an essential role in tryptophan, guanine and uric acid transport across membranes. Mutations that disrupt the function of white are known to cause eye pigmentation phenotypes in many insect species. Here, we found evidence for five white gene paralogues present in H. vigintioctopunctata transcriptome datasets sequenced from a range of developmental stages. We individually knocked down each of the five white genes through the injection of corresponding double-stranded RNAs (dsRNAs) to the fourth-instar larvae to determine whether functional divergence has occurred. We found that injecting 1 μg dswhite3 caused compound eye colour of pupae and adults to develop as red/brown and brown, respectively, compared with black eyes in control beetles. Injection of 2 μg dswhite3 increased RNAi efficacy and produced a clearer eye colour phenotype. At both doses, the ocular diaphragm (a ring of black pigment surrounding each eye) did not change in the white3 RNAi hypomorphs. Moreover, our data revealed that injection of dswhite2 at the fourth-instar larval stage impaired the climbing ability of both male and female adults. Our results confirmed, for the first time, functional divergence of duplicated white genes in an insect species.

Mutated SASH1 promotes Mitf expression inaheterozygous mutated SASH1 knock‑in mouse model.

The SAM and SH3 domain-containing 1 (SASH1) genes have been identified as the causal genes of dyschromatosis universalis hereditaria (DUH); these genes cause the pathological phenotypes of DUH, and SASH1 variants have been shown to regulate the abnormal pigmentation phenotype in human skin in various genodermatoses. However, investigations into the mutated SASH1 gene have been limited to in vitro studies. In the present study, to recapitulate the molecular pathological phenotypes of individuals with DUH induced by SASH1 mutations, a heterozygous BALB/c mouse model, in which the human SASH1 c.1654 T>G (p. Tyr 551Asp, Y551D) mutation was knocked in was first generated. The in vivo functional experiments on Y551D SASH1 indicated that the increased expression of microphthalmia-associated transcription factor (Mitf) was uniformly induced in the tails of heterozygous BALB/c mice, and an increased quantity of Mitf-positive epithelial cells was also detected. An increased expression of Mitf- and Mitf-positive cells was also demonstrated in the epithelial tissues of Y551D-SASH1 affected individuals. In the present study, Mitf expression was also found to be increased by Y551D SASH1 in vitro. Taken together, these findings indicate that the upregulation of Mitf is the bona fide effector of the Y551D SASH1-mediated melanogenesis signaling pathway in vivo. SASH1 may function as a scaffold molecule for the assembly of a SASH1-Mitf molecular complex to regulate Mitf expression in the cell nucleus and thus to promote the hyperpigmented phenotype in the pathogenesis of DUH and other genodermatoses related to pigment abnormalities.

Insights on hair, skin and eye color of ancient and contemporary Native Americans

Over the past few years, tools capable of predicting pigmentation phenotypes have been developed aiming to contribute for criminal and anthropological investigations. In this study, we used eight genetic systems to infer eye, hair, and skin color of ancient and contemporary Native Americans. To achieve this goal, we retrieved 61 SNPs from 42 samples available in free online repositories of DNA sequences. We performed pigmentation predictions using two freely available tools, HIrisPlex-S and Snipper, in addition to two other published models. This workflow made possible to predict all three phenotypes with at least one tool for 29 out of the 42 samples. Considering these 29 individuals, predictions for eye, hair, and skin color were obtained with HIrisPlex-S for 27, 28 and 27 individuals, respectively, while 24, 25 and 25 individuals had such predictions with Snipper. In general, ancient and contemporary Native Americans were predicted to have intermediate/brown eyes, black hair, and intermediate/darker skin pigmentation.

Mutations in Domestic Animals Disrupting or Creating Pigmentation Patterns

The rich phenotypic diversity in coat and plumage color in domestic animals is primarily caused by direct selection on pigmentation phenotypes. Characteristic features are selection for viable alleles with no or only minor negative pleiotropic effects on other traits, and that alleles often evolve by accumulating several consecutive mutations in the same gene. This review provides examples of mutations that disrupt or create pigmentation patterns. White spotting patterns in domestic animals are often caused by mutations in KIT, microphthalmia transcription factor (MITF), or endothelin receptor B (EDNRB), impairing migration or survival of melanoblasts. Wild boar piglets are camouflage-colored and show a characteristic pattern of dark and light longitudinal stripes. This pattern is disrupted by mutations in Melanocortin 1 receptor (MC1R), implying that a functional MC1R receptor is required for wild-type camouflage color in pigs. The great majority of pig breeds carry MC1R mutations disrupting wild-type color and different mutations causing dominant black color were independently selected in European and Asian domestic pigs. The European allele evolved into a new allele creating a pigmentation pattern, black spotting, after acquiring a second mutation. This second mutation, an insertion of two C nucleotides in a stretch of 6 Cs, is somatically unstable and creates black spots after the open reading frame has been restored by somatic mutations. In the horse, mutations located in an enhancer downstream of TBX3 disrupt the Dun pigmentation pattern present in wild equids, a camouflage color where pigmentation on the flanks is diluted. A fascinating example of the creation of a pigmentation pattern is Sex-linked barring in chicken which is caused by the combined effect of both regulatory and coding mutations affecting the function of CDKN2A, a tumor suppressor gene associated with familial forms of melanoma in human. These examples illustrate how evolution of pigmentation patterns in domestic animals constitutes a model for evolutionary change in natural populations.

Analysis of KRT5 and KRT14 gene mutations and mode of inheritance in Iranian patients with clinical suspicion of Epidermolysis bullosa simplex.

Background: Epidermolysis bullosa simplex is a hereditary skin disorder caused by mutations in several genes such as KRT5 and KRT14 . Skin fragility in basal keratinocytes presence regions led to the cytolysis of epidermis and blistering. Aim of this study was to detect the molecular defects in KRT5 and KRT14 genes hot spots in patients with clinical suspicion of EBS and investigation of their probable genotype-phenotype correlations. Methods: Exons 1 and 6-7 of KRT5 and exons 1 and 4-7 of KRT14 amplification and mutation detection were performed by polymerase chain reaction and Sanger sequencing, respectively. Novel variants pathogenicity evaluated by bioinformatics tools. Results: Nine important variants detected in seven different patients within 6 Iranian families affected by Epidermolysis bullosa simplex, of which four variants were novel. Three patients had a mottled pigmentation phenotype [G96D (p.Gly96Asp) and F97I (p.Phe97Ile) in KRT5 ]. One of them showed a Dowling–Meara phenotype [A417P (p.Ala417Pro) and E477D (p.Glu477Asp) in KRT5 ] and another had a Koebner type phenotype [R397I (p.Arg397Ile) and Q444* (p.Gln444Ter) in KRT5 ]. A novel variant [G92E (p.Gly92Glu) in KRT5 ] in a double heterozygous state with a challenging variant [A413T (p.Ala413Thr) in KRT14 ] identified in one patient with Koebner type phenotype. Also, a previously reported mutation [I377T (p.Ile377Thr) in KRT14 gene] identified in this study. Conclusion: The results of molecular data analysis showed that the most severe phenotypes were associated with mutations in highly conserved regions. In some cases, different inheritance modes were observed.

Differential influence of Slc7a11 expression and body condition on pheomelanin‐based pigmentation in two Eurasian nuthatch Sitta europaea populations with different predation risk

The expression of the gene Slc7a11 promotes the antioxidant capacity of cells by providing them with cysteine that can be used for the synthesis of glutathione (GSH), the most important intracellular antioxidant. In melanocytes, intracellular cysteine can also enter melanosomes and get incorporated in the pheomelanin pigment synthesis pathway, thus decreasing cysteine availability for GSH synthesis and potentially creating chronic oxidative stress. We thus hypothesized that a mechanism limiting the use of intramelanocytic cysteine for pheomelanin synthesis in environmental conditions generating oxidative stress may be physiologically advantageous and favored by natural selection. Here we searched for evidence of such a mechanism by comparing the influence of melanocytic Slc7a11 expression on pheomelanin‐based pigmentation in developing Eurasian nuthatch Sitta europaea nestlings from two populations differing in predation risk, a natural source of oxidative stress. Pheomelanin synthesis and pigmentation tended to increase with Slc7a11 expression in the low‐risk population as expected from the activity of this gene, but decreased with Slc7a11 expression in the high‐risk population. The same was not observed in the expression of five other genes influencing pheomelanin synthesis without affecting cysteine availability in melanocytes. The influence of body condition on the intensity of pheomelanin‐based pigmentation also differed between populations, being positive in the low‐risk population and negative in the high‐risk population. The resulting pigmentation of birds was more intense in the high‐risk population. These findings suggest that birds perceiving high predation risk may limit the use of cysteine for pheomelanin synthesis, which becomes independent of Slc7a11 expression. Some birds may have thus evolved the ability to adjust their pigmentation phenotype to environmental stress.

Risk Factors for Keratinocyte Carcinoma in Recipients of Allogeneic Hematopoietic Cell Transplants

Allogeneic hematopoietic cell transplant (alloHCT) is known to increase the risk for keratinocyte carcinoma. The extent to which host characteristics, including pigmentary phenotype and UV radiation exposure, contribute is unknown. To identify and validate independent risk factors for keratinocyte carcinoma after alloHCT, including those associated with the transplant and the host. This retrospective cohort study analyzed a consecutive sample of alloHCT recipients from January 1, 2000, to December 31, 2014, at the Mayo Clinic, Rochester, Minnesota (n = 872) and University Hospitals Cleveland Medical Center, Cleveland, Ohio (n = 147). Participants from the Mayo Clinic were randomly allocated (2:1) into discovery (n = 581) and validation (n = 291) cohorts. Time to first keratinocyte carcinoma and information about transplant- and host-associated risk factors were extracted. A multivariate keratinocyte carcinoma risk model was created using a stepwise Cox proportional hazards regression model with P ≤ .05 for entry that incorporated all covariates that were individually statistically significant at α = 0.05 in the discovery cohort. The risk model was first internally validated using the Mayo Clinic validation cohort and then externally validated using the independent cohort of alloHCT recipients at University Hospitals Cleveland Medical Center. Data were analyzed from March 13, 2018, to June 12, 2019. Allogeneic hematopoietic cell transplant. The primary outcome was time to development of the first cutaneous keratinocyte carcinoma after alloHCT; secondary outcome, time to development of the first individual basal and/or squamous cell carcinoma after alloHCT. Of the 872 alloHCT recipients identified in the Mayo Clinic cohort (520 men [59.6%]; mean [SD] age, 48.3 [12.6] years), 95 (10.9%) developed keratinocyte carcinoma after alloHCT during 5349 person-years of follow-up. Of the 147 alloHCT recipients in the exernal validation cohort (86 men [58.5%]; mean [SD] age, 47.9 [17.5] years), 18 (12.2%) developed keratinocyte carcinoma after alloHCT in 880 person-years of follow up. Risk factors independently associated with keratinocyte carcinoma after alloHCT included age (hazard ratio [HR] per 10 years, 1.72; 95% CI, 1.21-2.42), chronic lymphocytic leukemia (HR, 2.47; 95% CI, 1.20-5.09), clinically photodamaged skin (HR, 3.47; 95% CI, 1.87-6.41), and history of cutaneous squamous cell carcinoma (HR, 2.60; 95% CI, 1.41-5.91). Harrell concordance statistics were 0.81 (95% CI, 0.72-0.90) and 0.86 (95% CI, 0.74-0.98) for internal and external validation of the keratinocyte carcinoma risk model, respectively. This study found validated independent risk factors for keratinocyte carcinoma after alloHCT that are enriched with host- compared with transplant-associated risk factors. These findings highlight the importance of assessing host-associated risk factors for keratinocyte carcinoma in patients eligible for alloHCT. Future studies should examine whether keratinocyte carcinoma risk stratification before alloHCT may inform long-term surveillance strategies.

Association of Melanophilin (MLPH) gene polymorphism with coat colour in Rex rabbits

Rex rabbit, with multiple phenotypes and colourful fur, is an interesting model for assessing the effect of coat colour gene mutations on characteristic pigmentation phenotype. Based on previous study, the <em>melanophilin</em> (<em>MLPH</em>) gene is a positional candidate gene related coat colour dilution. The fur colours are a lighter shade, e.g. grey instead of black. We sequenced 1689 base pairs of the <em>MLPH</em> gene in Chinchilla and black Rex rabbit. A total of 13 polymorphisms were identified, including seven missense mutations. The rabbit <em>MLPH</em> gene has a very high GC content and the protein shows 64.87% identity to the orthologous human protein (lack of homologous amino acids encoded by human MLPH exon 9). Hardy-Weinberg test showed that, except for the g.606C>A single nucleotid polymorphism (SNP), all other SNPs were in Hardy-Weinberg equilibrium. Haplotype analysis revealed that the seven missense mutation SNPs of two strains of Rex rabbits formed 10 haplotypes, but there were only seven major types of haplotypes (haplotype frequency <em>P</em>>0.05). The major haplotypes of the Chinchilla and black Rex rabbits were H1/H2/H3/H4/H5 and H1/H2/H3/H6/H8, respectively. The special haplotypes of Chinchilla Rex rabbit (H4, H5, H7) were consistently associated with the Chinchilla phenotype. This study provides evidence that different coat colour formation may be caused by one or more mutations within <em>MLPH</em> gene in several Rex rabbit strains. The data on polymorphisms that are associated with the Chinchilla phenotype facilitate the breeding of rabbits with defined coat colours.

Metabolomics Study of Flavonoids and Anthocyanin-Related Gene Analysis in Kiwifruit (Actinidia chinensis) and Kiwiberry (Actinidia arguta)

This study investigated the flavonoid compounds in Actinidia chinensis and Actinidia arguta fruits. A total of 125 flavonoids, including 9 anthocyanins, 12 catechins, 17 flavanones, 48 flavones (including 14 flavone C-glycosides), 29 flavonols, 6 isoflavones, and 4 proanthocyanidins, were identified in “Hongyang” kiwifruit (red flesh), “Jintao” kiwifruit, “Mini Amethyst” kiwiberry (purple flesh), and “Kuilv” kiwiberry. Thirty-nine metabolites showed significantly different contents between “Hongyang” and “Jintao,” and 38 of them showed higher content in “Hongyang,” whereas 39 metabolites showed significantly different contents between “Mini Amethyst” and “Kuilv,” and 31 of them showed higher content in “Mini Amethyst.” This result indicates the superior nutritional value of the pigmented kiwi cultivars in terms of flavonoids. Multivariate statistical analysis indicates that the variation in flavonoid profiles contributes to the pigmentation phenotypes of “Hongyang” and “Mini Amethyst.” Further comparative transcriptomic analysis revealed that structural genes in the anthocyanin synthesis pathway (AcF3H, AcF3′H, AcDFR, AcUFGT) and transcription factors (AcMYB10, AcbHLH5) may be involved in the pigmentation of the red-fleshed A. chinensis, whereas AaF3H, AaF3GT, and AaMYB110 may play important roles in the pigmentation of the purple-fleshed A. arguta. This study provides broader insight into the variation in flavonoid profiles among kiwifruit/berry, evaluates the flavonoid nutrition of the four cultivars, and provides additional evidence for the correlation between the genes and metabolites involved in flavonoid synthesis.

Yeast glutaredoxin, GRX4, functions as a glutathione S-transferase required for red ade pigment formation in Saccharomyces cerevisiae

The adenine biosynthetic mutants ade1 and ade2 of Saccharomyces cerevisiae accumulate a characteristic red pigment in their vacuoles under adenine limiting conditions. This red pigmentation phenotype, widely used in a variety of genetic screens and assays, is the end product of a glutathione-mediated detoxification pathway, where the glutathione conjugates are transported into the vacuole. The glutathione conjugation step, however, has still remained unsolved. We show here, following a detailed analysis of all the members of the thioredoxinfold superfamily, the involvement of the monothiol glutaredoxin GRX4 as essential for pigmentation. GRX4 plays multiple roles in the cell, and we show that the role in ade pigmentation does not derive from its regulatory role of the iron transcription factor, Aft1p, but a newly identified GST activity of the protein that we could demonstrate using purified Grx4p. Further, we demonstrate that the GRX domain of GRX4 and its active site cysteine C171 is critical for this activity. The findings thus solve a decades old enigma on a critical step in the formation of this red pigmentation.

Impairment of mixed melanin-based pigmentation in parrots.

Parrots and allies (Order Psittaciformes) have evolved an exclusive capacity to synthesize polyene pigments called psittacofulvins at feather follicles, which allows them to produce a striking diversity of pigmentation phenotypes. Melanins are polymers constituting the most abundant pigments in animals, and the sulphurated form (pheomelanin) produces colors that are similar to those produced by psittacofulvins. However, the differential contribution of these pigments to psittaciform phenotypic diversity has not been investigated. Given the color redundancy, and physiological limitations associated to pheomelanin synthesis, we hypothesized that the latter would be avoided by psittaciform birds. Here we test this by using Raman spectroscopy to identify pigments in feathers exhibiting colors suspicious of being produced by pheomelanin (i.e., dull red, yellow and grey- and green-brownish) in 26 species from the three main lineages of Psittaciformes. We detected the non-sulphurated melanin form (eumelanin) in black, grey and brown plumage patches, and psittacofulvins in red, yellow and green patches, but no evidence of pheomelanin. As natural melanins are assumed to be composed of eumelanin and pheomelanin in varying ratios, our results represent the first report of impairment of mixed melanin-based pigmentation in animals. Given that psittaciforms also avoid the uptake of circulating carotenoid pigments, these birds seem to have evolved a capacity to avoid functional redundancy between pigments, likely by regulating follicular gene expression. Ours study provides the first vibrational characterization of different psittacofulvin-based colors and thus helps to determine the relative polyene chain length in these pigments, which is related to their antireductant protection activity.

MC1R and KIT Haplotypes Associate With Pigmentation Phenotypes of North American Yak (Bos grunniens).

Small numbers of domestic yak (Bos grunniens) were imported to North America in the late 19th century indirectly from the Qinghai-Tibetan Plateau. Coat color of yak is of interest for fiber production, aesthetics, and as a potential indicator of recent hybridization with cattle. North American yak are classified into 3 major coat color patterns depending upon the presence and extent of white markings. They are further classified by nose pigmentation (black or gray). The aim of this study was to identify loci involved in white patterning and nose pigmentation of North American yak. Genotyping by mass spectrometry of markers identified through Sanger and whole-genome sequencing revealed a 388 kb haplotype of KIT associated in a semi-dominant manner with white coloration in this population of yak. This KIT haplotype is similar to both a haplotype found in white-faced Chinese yak and to haplotypes found in cattle but is divergent from other Bos species such as bison, gaur, and banteng. Melanocortin 1 receptor (MC1R) was implicated as a dominant determinant of black nose color with a single haplotype containing 2 missense mutations perfectly associated with the phenotype. The MC1R haplotype associated with black nose pigment is also similar to cattle haplotypes. No cattle studied, however, shared either of the 2 haplotypes associated with color in yak, suggesting these alleles were introgressed into yak before they were imported to North America. These results provide molecular insight into the history of North American yak and information from which breeders can determine possible color outcomes of matings.

Pigmentation Phenotype Prediction of Chinese Populations from Different Language Families.

Objective To predict the pigmentation phenotypes of Chinese populations from different language families, analyze the differences and provide reference data for forensic anthropology and genetics. Methods The HIrisPlex-S multiplex amplification system with 41 loci related to pigmentation phenotypes was constructed in the laboratory, and 2 666 DNA samples of adult males of 17 populations from six language families, including Indo-European, Sino-Tibetan, Altaic, Hmong-Mien, Tai-Kadai and Austro-Asiatic language families distributed in different regions of China were genotyped. The pigmentation phenotype category of each individual was predicted using the online prediction system （https://HIrisPlex.erasmusmc.nl/）, and then the output data were statistically analyzed. Results About 1.92% of the individuals of Asian-European admixed populations from Indo-European and Altaic language families had blue eyes and 34.29% had brown or gold hair. The phenotypes of the color of eyes and hair of other populations had no significant difference, all individuals had brown eyes and black hair. There were differences in skin color of populations of different language families and geographical areas. The Indo-European language family had the lightest skin color, and the Austro-Asiatic language family had the darkest skin color; the southwestern minority populations had a darker skin color than populations in the plain areas. Conclusion The prediction results of pigmentation phenotype of Chinese populations are consistent with the perception of the appearance of each population, proving the reliability of the system. The color of eyes and hair are mainly related to ancestral components, while the skin color shows the differences between language families, and is closely related to geographical distribution of populations.

Development and external validation study of a melanoma risk prediction model incorporating clinically assessed naevi and solar lentigines.

Melanoma risk prediction models could be useful for matching preventive interventions to patients' risk. To develop and validate a model for incident first-primary cutaneous melanoma using clinically assessed risk factors. We used unconditional logistic regression with backward selection from the Australian Melanoma Family Study (461 cases and 329 controls) in which age, sex and city of recruitment were kept in each step, and we externally validated it using the Leeds Melanoma Case-Control Study (960 cases and 513 controls). Candidate predictors included clinically assessed whole-body naevi and solar lentigines, and self-assessed pigmentation phenotype, sun exposure, family history and history of keratinocyte cancer. We evaluated the predictive strength and discrimination of the model risk factors using odds per age- and sex-adjusted SD (OPERA) and the area under curve (AUC), and calibration using the Hosmer-Lemeshow test. The final model included the number of naevi ≥2mm in diameter on the whole body, solar lentigines on the upper back (a six-level scale), hair colour at age 18 years and personal history of keratinocyte cancer. Naevi was the strongest risk factor; the OPERA was 3·51 [95% confidence interval (CI) 2·71-4·54] in the Australian study and 2·56 (95% CI 2·23-2·95) in the Leeds study. The AUC was 0·79 (95% CI 0·76-0·83) in the Australian study and 0·73 (95% CI 0·70-0·75) in the Leeds study. The Hosmer-Lemeshow test P-value was 0·30 in the Australian study and <0·001 in the Leeds study. This model had good discrimination and could be used by clinicians to stratify patients by melanoma risk for the targeting of preventive interventions. What's already known about this topic? Melanoma risk prediction models may be useful in prevention by tailoring interventions to personalized risk levels. For reasons of feasibility, time and cost many melanoma prediction models use self-assessed risk factors. However, individuals tend to underestimate their naevus numbers. What does this study add? We present a melanoma risk prediction model, which includes clinically-assessed whole-body naevi and solar lentigines, and self-assessed risk factors including pigmentation phenotype and history of keratinocyte cancer. This model performs well on discrimination, the model's ability to distinguish between individuals with and without melanoma, and may assist clinicians to stratify patients by melanoma risk for targeted preventive interventions.

Understanding pseudo-albinism in sole (Solea senegalensis): a transcriptomics and metagenomics approach

Pseudo-albinism is a pigmentation disorder observed in flatfish aquaculture with a complex, multi-factor aetiology. We tested the hypothesis that pigmentation abnormalities are an overt signal of more generalised modifications in tissue structure and function, using as a model the Senegalese sole and two important innate immune barriers, the skin and intestine, and their microbiomes. Stereological analyses in pseudo-albino sole revealed a significantly increased mucous cell number in skin (P < 0.001) and a significantly thicker muscle layer and lamina propria in gut (P < 0.001). RNA-seq transcriptome analysis of the skin and gut identified 573 differentially expressed transcripts (DETs, FDR < 0.05) between pseudo-albino and pigmented soles (one pool/tissue from 4 individuals/phenotype). DETs were mainly linked to pigment production, skin structure and regeneration and smooth muscle contraction. The microbiome (16 S rRNA analysis) was highly diverse in pigmented and pseudo-albino skin but in gut had low complexity and diverged between the two pigmentation phenotypes. Quantitative PCR revealed significantly lower loads of Mycoplasma (P < 0.05) and Vibrio bacteria (P < 0.01) in pseudo-albino compared to the control. The study revealed that pseudo-albinism in addition to pigmentation changes was associated with generalised changes in the skin and gut structure and a modification in the gut microbiome.

The complementary effect of rs1042522 in TP53 and rs1805007 in MC1R is associated with an elevated risk of cutaneous melanoma in Latvian population.

Genetic factors serve important roles in melanoma susceptibility. Although much genetic variation has been associated with cutaneous melanoma (CM), little is known about the interactions between genetic variants. The current study investigated the joint effect of rs1042522 in the tumour protein 53 (TP53) gene, rs2279744 in the murine double minute-2 (MDM2) gene and several single nucleotide polymorphisms (SNPs) in the melanocortin 1 receptor (MC1R) gene. All of these genes are interconnected in a single signalling pathway that regulates pigmentation. The current study included 479 individuals, of which, 255 were patients with CM and 224 were controls from the Latvian population. Multifaceted analyses of potential interactions between SNPs were performed, whilst taking into account the pigmentation phenotypes of individuals and tumour characteristics (Breslow thickness and ulceration). Univariate analyses revealed a borderline significant association between rs1042522 in the TP53 gene and CM risk. The results also confirmed a known association with rs1805007 in the MC1R gene. The rs1042522 was also selected as a CM risk factor in multivariate models, suggesting an effect that is independent from and complementary to that of rs1805007. The results indicated that these SNPs need to be taken into account when determining melanoma risk. A strong association between CM and red hair was identified for rs1805007, and rs1805008 in the MC1R gene was mainly associated with red hair. An association was also determined between rs2279744 in the MDM2 gene and brown eye colour. No convincing associations were identified between the analysed SNPs and Breslow thickness of tumours or ulcerations.