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Coat colour in livestock speciesis one of the most distinctive traits that characterise many different breeds. Pigmentation does not affect only skin and hairs but also the eyes. Few genomic studies in cattle and horses also investigated iris pigmentation, but no similar studies was conducted in pigs thus far. In this study we analysed eye colour diversity in a Large White pig population (n=897) and reported the results of genome-wide association studies based on several comparisonsincluding pigs having four main eye colour categories(three with both pigmented eyes of different brown grades: pale, 17.9%; medium, 14.8%; and dark, 54.3%; another one with both eyes completely depigmented, 3.8%) and heterochromia patterns (heterochromia iridis, i.e. depigmented iris sectors in pigmented irises, 3.2%; heterochromia iridium, i.e. a whole eye iris of depigmented phenotype and the other eye with the iris completely pigmented, 5.9%). Pigs were genotyped with the Illumina PorcineSNP60 BeadChip and GEMMA was used for the association analyses. The results indicated that the eye pigmented patterns (different grades of brown pigmentation), the total absence of pigmentation in the both eyes, and heterochromia iridis defect were under controlled of SLC45A2 (on chromosome 16, SSC16), EDNRB (SSC11) and KITLG (SSC5), respectively. In addition, to new candidate associations for the eye depigmented patterns were also identified for SNPs on two SSC4 regions (including two candidate genes: NOTCH2 and PREX2) and on SSC6, SSC8 and SSC14 (including COL17A1 as candidate gene). This study provided useful information to understand the genetic mechanisms affecting eye pigmentation in pigs.

Approximately 1-2% of cutaneous melanoma (CM) is classified as strongly familial. We sought to investigate unexplained CM predisposition in families negative for the known susceptibility genes using next generation sequencing of affected individuals. Segregation of germline variants of interest within families was assessed by Sanger sequencing. Several heterozygous variants in oculocutaneous albinism (OCA) genes: TYR, OCA2, TYRP1 and SLC45A2, were present in our CM cohort. OCA is a group of autosomal recessive genetic disorders, resulting in pigmentation defects of the eyes, hair and skin. Missense variants classified as pathogenic for OCA were present in multiple families and some fully segregated with CM. The functionally compromised TYR p.T373K variant was present in three unrelated families. In OCA2, known pathogenic variants: p.V443I and p.N489D, were present in three families and one family, respectively. We identified a likely pathogenic SLC45A2 frameshift variant that fully segregated with CM in a family of four cases. Another four-case family harboured cosegregating variants (p.A24T and p.R153C) of uncertain functional significance in TYRP1. We conclude that rare, heterozygous variants in OCA genes confer moderate risk for CM. This article is protected by copyright. All rights reserved.

Non‐syndromic oculocutaneous albinism (nsOCA) is a group of genetically heterogeneous autosomal recessive disorders with complete lack or decrease pigmentation in skin, hair, and eyes. TYR, OCA2, TYRP1, SLC45A2, SLC24A5, and LRMDA were reported to cause OCA1‐4 and OCA6‐7, respectively. By sequencing all the known nsOCA genes in 114 unrelated Chinese nsOCA patients combined with In silico analyses, splicing assay, and classification of variants according to the standards and guidelines of American College of Medical Genetics and Genomics, we detected seventy‐one different OCA‐causing variants separately in TYR, OCA2, SLC45A2, and SLC24A5, including thirty‐one novel variants (13 in TYR, 11 in OCA2, and 7 in SLC45A2). This study shows that OCA1 is the most common (75/114) and OCA2 ranks the second most common (16/114) in Chinese. 99 patients of our cohort were caused by variants of all the known nsOCA genes. Cutaneous phenotypes of OCA1, OCA2, and OCA4 patients were shown in this study. The second OCA6 case in China was identified here. These data expand the spectrum of OCA variants as well phenotype and facilitate clinical implement of Chinese OCA patients.

Variations in the SLC45A2 gene are responsible for the dilution phenotypes cream and pearl in domestic horses. Cream dilution is inherited in an incomplete dominant manner, diluting only red in the heterozygous state but both red and black pigments when two alleles are present. The pearl dilution is recessive and dilutes only the red and black pigment in the homozygous state or when paired with a cream allele. Horses that inherit one copy of pearl (Cprl ) and one copy of the dominant cream allele (CC r ) display a dilution phenotype similar to that of homozygous cream, suggesting that pearl is the result of a different variation in the same gene responsible for cream. We sequenced SLC45A2 in two 'false double dilute' horses that appeared phenotypically homozygous cream but tested as possessing only a single CC r allele. We also sequenced one known pearl carrier to screen for putative causal variants. The missense variant ECA21:SLC45A2:c.985G>A; p.Ala329Thr (Cprl ) was present in one false double dilute and the pearl carrier and was also genotyped in an additional 126 horses for statistical evaluation. The genotype matched the expected phenotype in all horses (P-value = 6.5 × 10-41 ) and is identical to a pearl variant found previously. The second false double dilute horse and one non-dilute offspring genotyped as heterozygous for a novel missense variant ECA21:SLC45A2:c.568G>A (p.Gly190Arg), the proposed Csun variant (for the name of the horse). This variant produces a recessive dilution similar to pearl and indicates that multiple alleles of SLC45A2 result in dilution phenotypes in the domestic horse.

Four loci seem responsible for the dilution of the basic coat colours in horse: Dun (D), Silver Dapple (Z), Champagne (CH) and Cream (C). Apart from the current phenotypes ascribed to these loci, pearl has been described as yet another diluted coat colour in this species. To date, this coat colour seems to segregate only in the Iberian breeds Purebred Spanish horse and Lusitano and has also been described in breeds of Iberian origin, such as Quarter Horses and Paint Horse, where it is referred to as the 'Barlink Factor'. This phenotype segregates in an autosomal recessive manner and resembles some of the coat colours produced by the champagne CHCH and cream CCr alleles, sometimes being difficult to distinguish among them. The interaction between compound heterozygous for the pearl Cprl and cream CCr alleles makes SLC45A2 the most plausible candidate gene for the pearl phenotype in horses. Our results provide documented evidence for the missense variation in exon 4 [SLC45A2:c.985G>A; SLC45A2:p.(Ala329Thr)] as the causative mutation for the pearl coat colour. In addition, it is most likely involved as well in the cremello, perlino and smoky cream like phenotypes associated with the compound CCr and Cprl heterozygous genotypes (known as cream pearl in the Purebred Spanish horse breed). The characterization of the pearl mutation allows breeders to identify carriers of the Cprl allele and to select this specific coat colour according to personal preferences, market demands or studbook requirements as well as to verify segregation within particular pedigrees.

Oculocutaneous albinism (OCA) type 4 is one of the most common types of albinism among Japanese population. In some patients who were clinically diagnosed with OCA, we have found a heterozygous pathological mutation in the coding region of SLC45A2, the gene responsible for OCA4, not leading to a DNA-based diagnosis. In this study, we evaluated pathological variants in the promoter region of SLC45A2 in these patients. The results indicated that the majority of the patients had a 4-bp deletion in the said region (c.-492_489delAATG; GenBank accession number: NM_016180; rs984225803) in the contralateral allele. These patients displayed a mild phenotype, especially regarding eye manifestations. The results of the luciferase reporter assay and electrophoretic mobility shift assay supported the pathological role of the variant. In addition, four of 220 alleles in Japanese normal control subjects also showed the deletion variant, indicating that this variant could possibly be a skin color-associated variant.

Background/Purpose: Recent GWAS studies, mostly performed in populations of North European origin, have identified the genetic loci associated with pigmentation, sun sensitivity, freckling and skin cancer susceptibility. Here, we aimed at addressing the genetic determinants of sunlight sensitivity in Spain, a southern European population.Methods: Nine SNPs located in 8 pigmentation- related genes (IRF4,TYR,ASP,HERC2,OCA2,BNC2,SLC24A4 and SLC45A2) were genotyped in 456 Spaniards. Additionally, the complete sequence of the MC1R gene was obtained, testing each nonsynony-mous mutation supported by the classification as R or r alleles. A standardised ques-tionnaire was used to collect demographic characteristics, pigmentation and sun sensitivity traits, as well as sun exposure habits.Results: MC1R R alleles and IRF4 rs12203592 were significantly associated with sun-light sensitivity at the Bonferroni-corrected level (P- value < 4.54 × 10−3). Genetic variants in SLC45A2 (rs16891982) and HERC2 (rs12913832) were also found to be significantly associated with skin photosensitivity in our Spanish sample. Interaction analysis using the MDR method revealed epistatic effects when these four variants were considered together.Conclusion: MC1R, IRF4,HERC2 and SLC45A2 play a significant role in skin sensitivity to sunlight in the Spanish population. Moreover, interaction among these four loci seems to modulate the ability of the skin to respond to UV radiation.

Molecular methods for the detection of mammalian coat color phenotypes have expanded greatly within the past decade. Many phenotypes are associated with a single nucleotide polymorphism mutation in the genetic sequence. Traditionally, these mutations are detected through sequencing, hybridization assays or mini-sequencing. However, these techniques can be expensive and tedious. Previously, CE-SSCP using the F-108 polymer was able to distinguish SNPs for the melanocortin-1 receptor (mc1r) coat color gene in horses (Equus caballus) that differed by one nucleotide substitution. The objective of this study was to expand the detection of coat color SNPs in horses. The genes for the solute carrier family member 2 (slc45a2/matp), type III receptor protein-tyrosine kinase (kit) and mc1r genes using CE-SSCP and F-108 polymer were compared to mini-sequencing with the SNaPshotTM kit. The F-108 polymer reproducibly resolved homozygous and heterozygous individuals for the mc1r and kit markers, but was unable to resolve heterozygous individuals for slc45a2 at 38oC. The need for temperatures

Oculocutaneous albinism type IV (OCA4) is an autosomal recessive inherited disorder which is characterized by reduced biosynthesis of melanin pigmentation in skin, hair, and eyes and caused by the genetic mutations in the membrane-associated transporter protein (MATP) encoded by SLC45A2 gene. The MATP protein consists of 530 amino acids which contains 12 putative transmembrane domains and plays an important role in pigmentation and probably functions as a membrane transporter in melanosomes. We scrutinized the most OCA4 disease-associated mutation and their structural consequences on SLC45A2 gene. To understand the atomic arrangement in 3D space, the native and mutant structures were modeled. Further the structural behavior of native and mutant MATP protein was investigated by molecular dynamics simulation (MDS) approach in explicit lipid and water background. We found Y317C as the most deleterious and disease-associated SNP on SLC45A2 gene. In MDS, mutations in MATP protein showed loss of stability and became more flexible, which alter its structural conformation and function. This phenomenon has indicated a significant role in inducing OCA4. Our study explored the understanding of molecular mechanism of MATP protein upon mutation at atomic level and further helps in the field of pharmacogenomics to develop a personalized medicine for OCA4 disorder. J. Cell. Biochem. 117: 2608-2619, 2016. © 2016 Wiley Periodicals, Inc.

Oculocutaneous albinism type 4 (OCA4) in humans and similar phenotypes in many animal species are caused by variants in the SLC45A2 gene, encoding a putative sugar transporter. In dog, two independent SLC45A2 variants are known that cause oculocutaneous albinism in Doberman Pinschers and several small dog breeds respectively. For the present study, we investigated a Bullmastiff with oculocutaneous albinism. The affected dog was highly inbred and resulted from the mating of a sire to its own grandmother. We obtained whole genome sequence data from the affected dog and searched specifically for variants in candidate genes known to cause albinism. We detected a single base deletion in exon 6 of the SLC45A2 gene (NM_001037947.1:c.1287delC) that has not been reported thus far. This deletion is predicted to result in an early premature stop codon. It was confirmed by Sanger sequencing and perfectly co-segregated with the phenotype in the available family members. We genotyped 174 unrelated dogs from diverse breeds, all of which were homozygous wildtype. We therefore suggest that SLC45A2:c.1287delC causes the observed oculocutaneous albinism in the affected Bullmastiff.

Human eye colour is a polygenic trait with a heritability of close to 100%, with seven leading factors explaining three-quarters of the genetic variance: OCA2, TYR, TYRP1, IRF4, SLC45A2, SLC24A5 and SLC24A4. Many of these genes were already known to be mutated in oculocutaneous albinism, and all are involved in melanin biosynthesis, coding for key enzymes, transcription factors controlling expression of key enzymes or transporters that maintain the acidity of the melanosome interior. At least two of the variants of largest effect abrogate regulatory elements in the associated gene, causing changes in expression level. The differences in eye colour between different populations suggest strong selection, either on correlated traits such as skin colour or perhaps directly. Key Concepts Variation in eye colour is polygenic, with seven major genes explaining 75% of European population variance. Blue eye colour is strongly predicted by a single nucleotide polymorphism near the OCA2 gene – this is the classical recessive gene inferred from family data. Intermediate eye colours such as hazels and greens are less well predicted. Two of the major loci are in non-coding regulatory regions, a pattern common to trait loci for other complex traits. The large effect sizes make this an excellent model for the investigation of the architecture of gene action, especially gene-by-gene interactions (epistasis), as well as multi-trait action (pleiotropy). Iris pigmentation loci generally exhibit genomic evidence of strong Darwinian selection, and this may not be completely explained by pleiotropic effects on skin colour. Keywords: iris colour; Darwinian selection; tyrosinase; oculocutaneous albinism; melanin; TYRP1 ; TYRP2 ; OCA2 ; IRF4 ; SLC45A2

Summary We present here the positional cloning of the Danio rerio albino mutant and show that the affected gene encodes Slc45a2. The human orthologous gene has previously been shown to be involved in human skin color variation, and mutations therein have been implicated in the disease OCA4. Through ultrastructural analysis of the melanosomes in albino alleles as well as the tyrosinase-deficient mutant sandy, we add new insights into the role of Slc45a2 in the production of melanin. To gain further understanding of the role of Slc45a2 and its possible interactions with other proteins involved in melanization, we further analyzed the role of the V- ATPase as a melanosomal acidifier. We show that it is possible to rescue the melanization potential of the albino melanosomes through genetic and chemical inhibition of V-ATPase, thereby increasing internal melanosome pH.

Phenotypic variation between human populations in skin pigmentation correlates with latitude at the continental level. A large number of hypotheses involving genetic adaptation have been proposed to explain human variation in skin colour, but only limited genetic evidence for positive selection has been presented. To shed light on the evolutionary genetic history of human variation in skin colour we inspected 118 genes associated with skin pigmentation in the Perlegen dataset, studying single nucleotide polymorphisms (SNPs), and analyzed 55 genes in detail. We identified eight genes that are associated with the melanin pathway (SLC45A2, OCA2, TYRP1, DCT, KITLG, EGFR, DRD2 and PPARD) and presented significant differences in genetic variation between Europeans, Africans and Asians. In six of these genes we detected, by means of the EHH test, variability patterns that are compatible with the hypothesis of local positive selection in Europeans (OCA2, TYRP1 and KITLG) and in Asians (OCA2, DCT, KITLG, EGFR and DRD2), whereas signals were scarce in Africans (DCT, EGFR and DRD2). Furthermore, a statistically significant correlation between genotypic variation in four pigmentation candidate genes and phenotypic variation of skin colour in 51 worldwide human populations was revealed. Overall, our data also suggest that light skin colour is the derived state and is of independent origin in Europeans and Asians, whereas dark skin color seems of unique origin, reflecting the ancestral state in humans.

with OCA4 (The Human Gene MutationDatabase, HGMD 2013.1). However, thisGlycine 518 residue appears to be con-served through all available vertebrategenomes investigated, hence suggestinga relevant functional role at this position,plus it is true that other glycine-to-argi-nine amino acid changes in the SLC45A2protein have been already associatedwith OCA4 (data from HGMD 2013.1:p.G44R; p.G89R; p.G110R; p.G349R;p.G370R; p.G404R). Some indirect evi-dence of an altered association of themutant protein with membranes wasalso reported by the authors. However, itis probably expected, for a protein with12 transmembrane domains, that itwould remain associated with mem-branes, even in the presence of somedisruptive mutations, although theseminor topological alterations might actu-ally result in a loss-of-function pheno-type. The ultimate proof should beprovided by engineering this mutation inan experimental animal model (i.e.mouse or zebrafish) and/or, simply, byreporting its presence in human subjectsdiagnosed as OCA4.Finally, the authors investigated thelandscape where this SLC45A2 muta-tion was found in Snowflake’s genomeand showed that it is nicely locatedwithin a large run (40 Mbps) of homo-zygosity, orthologous to human chro-mosome 5 (where the humanSLC45A2 gene is located), indicatingthis allele was inside a block identicalby descent, characteristic for Mende-lian recessive disorders. Furthermore,by investigating the patterns of hetero-zygosity in the Snowflake’s genome,the authors inferred that it was likely aresult of inbreeding. Through computa-tional simulations they concluded thatthe most probable scenarios for Snow-flake’s parents were uncle/niece oraunt/nephew.It is always rewarding to put an endto previously unexplained observations,especially if these refer to remarkableindividuals such this unique albino gor-illa. Therefore, the authors of thisstudy must be praised for having com-pleted the quest for the genetic causeof the albinism of Snowflake. Person-ally, as someone born in Barcelonajust 1 yr before Snowflake and some-one that had the chance to witnesshis life through my visits at the Zoo,as many other visitors worldwide, it isalso good that the conservation plightof Snowflake’s relatives has beenhighlighted; let us hope that this is intime to contribute to the efforts toconserve these remarkable but endan-gered primates.

Objectives Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing to phenotypic variation in skin pigmentation within and among South Asian populations are still poorly understood. The present study uses data from the Phase 3 of the 1000 genomes project focusing on two South Asian populations—GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK), so as to decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations. Methods Statistical tests included were (1) tests to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima's D, Fay and Wu's H and Fu and Li's D* and F*), (2) tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb), and (3) tests based on genetic differentiation between populations (LSBL). Results Twenty-two pigmentation genes fall in the top 1% for at least one statistic in the GIH population, 5 of which (LYST, OCA2, SLC24A5, SLC45A2, and TYR) have been previously associated with normal variation in skin, hair, or eye color. In comparison, 17 genes fall in the top 1% for at least one statistic in the ITU population. Twelve loci which are identified as outliers in the ITU scan were also identified in the GIH population. Conclusions These results suggest that selection may have affected these loci broadly across the region.

Oculocutaneous albinism (OCA) affects 1/17000 person. It is characterized by hypopigmentation of the skin, hair and eyes. The main handicap in patients is at the ophthalmologic level. There are 6 known OCA genes (TYR, OCA2, TYRP1, SLC45A2, SLC24A5, C10ORF11) (OCA1,2,3,4,6,7 respectively). An OCA5 locus has been localized, but the gene is not known yet. Apart from the OCA types, an X-linked ocular albinism gene (OA1, GPR143) as well as 17 genes involved in syndromic forms (HPS, CHS, WS, GS) of albinism have been identified. We routinely search for mutations (point mutations, deletions) in the OCA1, 2, 3, 4, 6 ,7, OA1 and HPS1 genes. Our data in more than 400 patients show 36% OCA1, 25% OCA2, 2% OCA3, 11% OCA4, 1.25% OCA6, 0% OCA7, 6% OA1, 1% HPS1. 17.75% of patients remain without a molecular diagnostic either because only one mutation (6%)or no mutation at all (11.75%) was found. This suggests two main alternative hypotheses. First of all the patient may have a hitherto clinically undiagnosed form of syndromic albinism. For this reason, we are now heading towards analyzing all 24 known albinism genes by next generation sequencing. Secondly, it is likely that additional OCA genes remain to be identified.

Oculocutaneous albinism type 4 (OCA4) is an autosomal recessive hypopigmentary disorder caused by mutations in the Membrane-Associated Transporter Protein gene (SLC45A2). The SLC45A2 protein is a 530-amino-acid polypeptide that contains 12 putative transmembrane domains, and appears to be a transporter that mediates melanin synthesis. Eighteen pathological mutations have been reported so far. In this study, six novel mutations, p.Y49C (c.146A > G), p.G89R (c.265G > A), p.C229Y (c.686G > A), p.T437A (c.1309A > G), p.T440A (c.1318A > G) and p.G473D (c.1418G > A) were found in eight Japanese patients with various clinical phenotypes. The phenotypes of OCA4 were as various as the other types of OCA and probably depended on the mutation sites in the SLC45A2 gene.