pigmented iris genotype

In studies with HERC2 functions, deletions caused hypopigmentation even though the protein has nothing to do with pigmentation. People with blue eyes have no pigment at all in this front layer, causing the fibers to scatter and absorb some of the longer wavelengths of light that come in. Tyrosinase (TYR), the enzyme responsible for pigment production in the body, starts the synthesis of both types of melanin by catalyzing a reaction between tyrosine and dopa, forming dopaquinone. 1997; Box et al. On the basis of population studies, scientists speculate that the blue-eyed mutation originated in peoples of Northern Europe (Scandinavian countries). Despite the color of the eye, the number of melanocytes does not differ. 1998), but mouse studies have suggested that 14 genes preferentially affect pigmentation in vertebrates (reviewed in Sturm et al. Transcribed image text: P>p Trait Genotype Phenotypic Effect Relationship P. Pigmented Iris (Additional genes give specific Iris Color color, e.g. Digital quantification of human eye color highlights genetic association of three new loci. 1995). In addition, the evolutionary and population roles of the different expressions are significant. CAS The "P" allele produces the pigment which gives you eye color. Before the revelation of the effect of HERC2, rs1800407 in exon nine was thought to be the main factor for eye color. Pigmented iris: If a person is homozygous recessive for eye color, there is no pigment in the front part of the eyes, and the blue color of the back of the iris shows through, giving blue eyes . Pigmented iris A person with the B allele has brown eyes. 2) although some associations were found within nonpigmentation genes such as CYP2C8 at 10q23, CYP2C9 at 10q24, CYP1B1 at 2p21, and MAOA at Xp11.3. 2003) and it is possible that alleles for these SNPs are associated with elements of population structure that correlate with iris colors. Tony Frudakis, Matthew Thomas, Zach Gaskin, K Venkateswarlu, K Suresh Chandra, Siva Ginjupalli, Sitaram Gunturi, Sivamani Natrajan, Viswanathan K Ponnuswamy, K N Ponnuswamy, Sequences Associated With Human Iris Pigmentation, Genetics, Volume 165, Issue 4, 1 December 2003, Pages 20712083, https://doi.org/10.1093/genetics/165.4.2071. This test showed that each of our 851 Caucasian samples was of majority Indo-European BGA, and although 58% of the samples were of significant (>4%) non-Indo-European BGA admixture, there was no correlation among low levels (<33%) of East Asian, sub-Saharan African, or Native American admixture and iris colors. The overlap among these SNP sets was high but not perfect. The large HERC2 gene requires 211kb and 93 exons that codes for a 528kDa protein made of 4834 residues.12. Collin College Faculty Web Directory This also explains why deletions within HERC2 would cause a decrease in melanin without interacting with the P protein itself. The iris consists of five cell layers, the anterior border layer, stroma, the sphincter and dilator muscles fibers, and the posterior pigment epithelium ( Figure 1 ), of which the most important for the appearance of eye colour are the anterior layer and its underlying stroma ( Eagle, 1988; Imesch et al., 1996; Wilkerson et al., 1996 ). The recessive allele (b) encodes blue eyes. PDF HUMAN SINGLE GENE TRAITS - Winston-Salem/Forsyth County Schools Eumelanin (brown pigment) is a light-absorbing polymer synthesized in specialized melanocyte lysosomes called melanosomes. Different SNPs on these two genes were investigated and analyzed for melanoma risk.24, 25. Aside from these two genes, the genes involved in melanogenesis and other minor genes also contain regions that account for eye color. Relationship. A battery of genetic tests, of which one for the inference of iris color could be a part, could enable the construction of a more objective and science-based (partial) physical profile from crime-scene DNA, and an investigator using these tests would be less interested in the biological mechanism of the phenotype than in an ability to make an accurate inference of trait value. Gene 277, 4962 (2001). The SNPs between the 2p21 and 2p23 regions were also in LD (P < 0.01). Frudakis, T., Thomas, M., Gaskin, Z., Venkateswarlu, K., Chandra, K. S., Ginjupalli, S. et al. Our results show that a surprisingly large number of polymorphisms in a large number of genes are associated with iris colors, suggesting that the genetics of iris color pigmentation are quite complex. Genetic determinants of hair, eye and skin pigmentation in Europeans. The solid figures represent albino individuals. Both genes are located on chromosome 15. Eye color genes. However, a number of the associations we identified were for SNPs located in other types of genes. Although cysteine is not an essential amino acid and its deficiency rarely occurs, the lack of it halts the production of pheomelanin. The LibreTexts libraries arePowered by NICE CXone Expertand are supported by the Department of Education Open Textbook Pilot Project, the UC Davis Office of the Provost, the UC Davis Library, the California State University Affordable Learning Solutions Program, and Merlot. 2001) are necessary for normal human iris pigmentation. In the most elementary form, the inheritance of eye color is classified as a Mendelian trait.1 On the basis of the observation of more than two phenotypes, eye color has a more complex pattern of inheritance. For these genes we performed resequencing and of the genes discussed in this article, 113 SNPs were discovered in CYP1A2 (7 gene regions, 5 amplicons, 10 SNPs found), CYP2C8 (9 gene regions, 8 amplicons, 15 SNPs found), CYP2C9 (9 gene regions, 8 amplicons, 24 SNPs found), OCA2 (16 gene regions, 15 amplicons, 40 SNPs found), TYR (5 gene regions, 5 amplicons, 10 SNPs found), and TYRP1 (7 gene regions, 6 amplicons, 14 SNPs found). The mammalian iris has three main tissue layers, all pigmented with melanin: an anterior fibrovascular stroma; a middle smooth-muscle layer consisting of the circumferential sphincter muscle at . In the pheomelanin pathway, the presence of cysteine has a major role. Phakomatoses. A dominant allele of this gene (P) causes pigment to be deposited in the front of the iris, thus masking the blue to various degrees. Traits.html - Rowan University There are two. To an investigator interested in elucidating a biological mechanism, association due to population structure might not seem to be very satisfying, but when classification is the goal rather than the elucidation of a biological mechanism, it would seem to matter little why a marker is associated with a trait. This gene is often referred to as the red-headed gene because of its prevalent expression in people with red hair and green eyes.4 Dopachrome tautomerase also contains regions for hazel and green eyes.5 Regions for brown eyes dominate the effects of these genes, though. PubMed Even at this level of complexity, the sequences from no single gene could be used to make reliable iris color inferences, which suggests an element of intergenic complexity (i.e., epistasis) for iris color determination as well. Sturm, R. & Frudakis, T. Eye Colour: portals into pigmentation genes and ancestry. Blue is confined mostly to people who originated from Europe.11 Green eyes permeate the lowest amount of the population (excluding the disorders), probably due to the lack of coding for it within the genome. The P values we obtained suggested that diplotypes explained more iris color variation than did haplotypes or individual SNPs. What Causes Hazel Eyes? - All About Vision For full access to this pdf, sign in to an existing account, or purchase an annual subscription. Mutations in the pigmentation genes are the primary cause of oculocutaneous albinism so it was natural to expect that common variations in their sequences might explain some of the variance in natural iris colors, and this is in fact what we observed. Depending on how little pigment the melanocytes produce, albinism causes red or violet eyes. To identify SNP loci associated with variable human pigmentation, we genotyped for 754 SNPs: 335 SNPs within pigmentation genes (AP3B1, ASIP, DCT, MC1R, OCA2, SILV, TYR, TYRP1, MYO5A, POMC, AIM, AP3D1, and RAB; Table 1), and 419 other SNPs distributed throughout the genome. Duffy, D. L., Box, N. F., Chen, W., Palmer, J. S., Montgomery, G. W., James, M. R. et al. Am J Hum Genet 80, 241252 (2007). 1997; Smith et al. Phenotypic Effect. The P values we obtained for this particular SNP association (P = 0.010.05, depending on the color criteria) were less significant than those described (P = 0.002) by Rebbeck et al. Thank you for visiting nature.com. Lastly, disorders involved in eye color include ocular albinism and heterochromia. 2. (2000) with adjusted residuals to compensate for this risk. With the help of dopachrome tautomerase and TYR-related protein 1, eumelanin, the darker pigment, is synthesized; with cysteine, pheomelanin, a yellow-red pigment, is produced. For most of the genes, multilocus gene-wise genotype sequences were more strongly associated with iris colors than were haplotypes or SNP alleles. Genotype-phenotype correlations have been reported with specific mutations possibly associated with certain angle abnormalities. Donors checked a box for blue, green, hazel, brown, black, or unknown/not clear iris colors, and each had the opportunity to identify whether iris color had changed over the course of their lives or whether the color of each iris was different. The disorder is characterized by different-colored irises or different colors within the iris. Within the melanosomes, the tyrosinase (TYR) gene product catalyzes the rate-limiting hydroxylation of tyrosine to 3, 4-dihydroxyphenylanine (DOPA), and the resulting product is oxidized to DOPAquinone to form the precursor for eumelanin synthesis. Inheritance in humans 2023 | PDF | Genotype | Eye Color Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. (a) List all possible genotypes for an individual with pigmented iris and dimpled chin. It is inherited or caused by somatic mutations within the cells.2 In addition, it can be caused by the inactivation of particular genes within the cells. Hum Mol Genet 13, 447461 (2004). b) Give the genotype of an individual who is homozygous recessive for brown eye color. When there is too little pigment to produce a strong blue color, the red reflections interact with the small amount of blue, producing a violet color.3, The biological process for producing melanin, melanogenesis, involves numerous protein interactions. Red and violet eyes come from a lack of pigment. However, this result would not have necessarily been obtained were we working with SNPs that were not truly associated with iris colors. Most of the SNPs within a gene or region were in LD with others in that gene or region (|D| 0.05); only 32 SNP pairsin the MC1R (1 pair), OCA2 (27 pairs), TYR (2 pairs), and TYRP1 (2 pairs) geneswere found to be in linkage equilibrium (not shown). Multiple SNPs were identified on chromosome 10q; the CYP2C8-10p23 region had 1 marginally associated SNP, and the neighboring region, CYP2C9-10p24, also had one. What determines eye color? - Medical News Today .. Gardner J M, Nakatsu Y, Gondo Y, Lee S, Lyon M F et al. Google Scholar. Peripheral scalloping of the posterior pigmented iris layer. b) List the possible genotypes for an individual with pigmented iris but lacking a dimpled chin. Because most human traits have complex genetic origins, wherein the whole is often greater than the sum of its parts, innovative genomics-based study designs and analytical methods for screening genetic data in silico that are respectful of genetic complexity are neededfor example, the multifactorial and/or phase-known components of dominance and epistatic genetic variance. Valenzuela, R., Henderson, M., Walsh, M., Garrison, N., Kelch, J., Cohen-Barak, O. et al. The little that isn't absorbed by the iris is reflected back, producing what we see as eye color. Duffy, D. L., Montgomery, G. W., Chen, W., Zhao, Z., Le, L., James, M. R. et al. .. The first parent contains the mutation in the HERC2 intron in both alleles but possesses an allele with the coding for brown eyes. Resequencing for these genes was performed by amplifying the proximal promoter (average 700 bp upstream of transcription start site), each exon (average size 1400 bp), the 5 and 3 ends of each intron (including the intron-exon junctions, average size 100 bp), and 3 untranslated region (UTR; average size 700 bp) sequences from a multi-ethnic panel of 672 individuals (450 individuals from the Coriell Institute's DNA Polymorphism Discovery Resource, 96 additional European Americans, 96 African Americans, 10 Pacific Islanders, 10 Japanese, and 10 Chinese; these 672 individuals represented a set of samples separate from that used for the association study described herein). Teaching the genetics of eye colour & colour vision. Place the PTC paper on your tongue for a few seconds. A golden-brown iris indicates the mixture of both eumelanin and pheomelanin (produces the yellow color), and hazel is usually a mixture of brown and green or blue and green, depending on the shade. As the eye color lightens, less melanin is present in the cells, reflecting more of the visible spectrum. For example, OCA2, AIM, DCT, and TYRP1 harbored haplotypes both positively associated with blue irises and negatively associated with brown irises (OCA2 haplotypes 1, 37, 38, 42; AIM haplotype 1; DCT haplotype 2; and TYRP1 haplotype 1; Table 3). Iris phenotypes and pigment dispersion caused by genes influencing 1997, 2001; Akey et al. volume56,pages 57 (2011)Cite this article. (1995) and Koppula et al. An individual that is homozygous W is much more likely to have blue iris, exhibiting odds 77.25-times larger than the odds of having blue irises of a genotype other than W/W (P < 0.0001). .. Hanis C, Chakraborty R, Ferrell R, Schull W. Jackson I J, Chambers D M, Tsukamoto K, Copeland N G, Gilbert D J et al. PCR amplification was accomplished using pfu Turbo polymerase according to the manufacturer's guidelines (Stratagene, La Jolla, CA). Most of the marginally associated SNPs were found within the pigmentation genes OCA2 (n = 10), TYRP1 (n = 4), AIM (n = 3), MYO5A (n = 2), and DCT (n =, SNPs marginally (independently) associated with iris pigmentation and SNPs associated only within the context of haplotypes and/or diplotypes. For example, the OCA2 has 200 known candidate SNPs in NCBI's dbSNP, and it is possible that this gene has more to teach us about variable human iris pigmentation than what we have learned from the work presented herein. More than likely, their offspring would have blue eyes, but a 25% chance stands that offspring would have brown eyes. Zaumseger, D., Rothschild, M. & Schneider, P. SNPs for the analysis of human pigmentation genes--A comparative study. Eye color is determined by the pattern of brown and red pigment, collagen fibers, and the topography of the iris. For some genes, the number of SNPs in the database was low and/or some of the SNPs were strongly associated with iris colors, warranting a deeper investigation. Am J Hum Genet 82, 411423 (2008). We also acknowledge previous National Science Foundation support under grant numbers 1246120, 1525057, and 1413739. Tully, G. Genotype versus phenotype: human pigmentation. 20, 327332 (2004). Agonist color refers to the color with which the sequence is positively associated. 1998; Schioth et al. Although research on pigment mutants has made clear that a small subset of genes is largely responsible for catastrophic pigmentation defects in mice and humans, it remains unclear whether or how common single-nucleotide polymorphisms (SNPs) in these genes contribute toward (or are linked to) natural variation in human iris color. ), Ectopic expression of the agouti gene in transgenic mice causes obesity, features of type II diabetes, and yellow fur, Identification of common polymorphisms in the coding sequence of the human MSH receptor (MCIR) with possible biological effects, Severe early-onset obesity, adrenal insufficiency and red hair pigmentation caused by POMC mutations in humans, Pigmentation genes: the tyrosinase gene family and the pmel 17 gene family, Molecular basis of mouse Himalayan mutation, A melanocyte-specific gene, Pmel 17, maps near the silver coat color locus on mouse chromosome 10 and is in a syntenic region on human chromosome 12, Molecular structure and chromosomal mapping of the human homolog of the agouti gene, Diverse mutations of the P gene among African-Americans with type II (tyrosinase-positive) oculocutaneous albinism (OCA2), Induction of tyrosinase gene transcription in human iris organ cultures exposed to latanoprost, Not just pretty eyes: Drosophila eye-colour mutations and lysosomal delivery, Genetic and molecular analysis of recessive alleles at the pink-eyed dilution (p) locus of the mouse, Mutations in the human orthologue of the mouse underwhite gene (uw) underlie a new form of oculocutaneous albinism, OCA4, Mutations within the promoter region of the tyrosinase gene in type I (tyrosinase-related) oculocutaneous albinism. Garcia-Gonzalo, F. R. & Rosa, J. L. The HERC proteins: functional and evolutionary insights. 1994, 1996), tyrosinase-like protein (TYRP1; Abbott et al. 3. . Molecular and General Genet. In terms of disease, OCA2 and MC1R were linked to melanoma. Apart from representing the first comprehensive candidate gene study for variable iris pigmentation and constituting a first step toward developing a classification model for the inference of iris color from DNA, our results suggest that cryptic population structure might serve as a leverage tool for complex trait gene mapping if genomes are screened with the appropriate ancestry informative markers. One SNP has been studied to show a large significance for eye color. All of the major sequences (count 13) for each locus with at least one significantly associated sequence are shown. Eye color ranges include varying shades of brown, hazel, green, blue, gray, and in rare cases, violet and red. Fig. PubMed The possible changes in the DNA sequence are GCT to GTT and GCC to GTC. MGG 1, 393394 (1908). On the HERC2/OCA2 A/A and A/G genotype background there was an increasing proportion of blue eye colour when carrying the IRF4 T allele (P = 3 10 4) and a higher number of iris pigmented lesions with the IRF4 T/T homozygote (P . If no haplotypes or diplotypes for a locus were found to be associated, only the SNP alleles are shown. 2003). Google Scholar. .. Ooi C E, Moreira J E, DellAngelica E C, Poy G, Wassarman D A et al. In this case, pleiotropic effects change eye color. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. One method of grouping colors is light = blue + green and dark = hazel + brown, and this grouping would seem to more clearly distinguish individuals with respect to the detectible level of eumelanin (brown pigment). Melanin undergoes a packaging process and if large amounts of P protein are not available to process and transport it, the quality of the darker pigment is compromised and lighter shades will result.14 Demonstrating epistasis, the HERC2 gene affects the results produced by the OCA2 gene. As mentioned previously, melanogenesis produces two different types of melanin and requires numerous proteins. .. Kwon H Y, Bultman S J, Loffler C, Chen W-J, Furdon P J et al. .. Durham-Pierre D, King R A, Naber J M, Laken S, Brilliant M H. Flanagan N, Healy E, Ray A, Philips S, Todd C et al. E_ Free earlobes. Chromosome 15 contains HERC1 and HERC2. Human Genetics: Simple inheritance - Antranik .. Kanetsky P, Swoyer J, Panossian S, Holmes R, Guerry D et al. . Zhu, G., Evans, D., Duffy, D., Montgomery, G., Medland, S., Gillespie, N. A. et al. To determine the extent to which extant iris color variation could be explained by various models, we calculated R2 values for SNPs, haplotypes, and multilocus genotype data by first assigning the phenotypic value for blue eye color as 1, green eye color as 2, hazel eye color as 3, and brown eye color as 4. 1997). However, it is yet to be completely understood. Diplotypes for these 61 alleles explained most of the iris color variance in our sample; the lowest amount was explained at the level of the SNP, suggesting an element of intragenic complexity to iris color determination (i.e., dominance). An individual with this disorder produces little or no pigment in their ocular melanocytes. Genetics of human iris colour and patterns - Sturm - 2009 - Pigment In mice and humans where the P protein is nonfunctional, albinism occurs, indicating its crucial role in pigmentation.13, 14 The gene located 11.7kb from HERC2 requires 345kb, but it requires only 24 exons to produce a 110kDa protein with 838 residues. Melanopsin signalling in mammalian iris and retina | Nature Without cysteine, the synthesis cannot be carried out. Green eyes require more pigment than blue and not much less than brown, and because the shades of hazel (brown with blue or green) are more versatile, hazel is still more popular than green. Each chromosome contains thousands of individual genes. Antagonist color refers to the color with which the sequence is negatively associated. The density of granules appears to reach genetically determined levels by early childhood and usually remains constant throughout later life, although a small minority of individuals exhibit changes in color during later stages of life (Bito et al. In this pedigree use "A" to represent the dominant allele and "a" for the recessive allele.A Two major genes on chromosome 15 affect the quantity and quality of the melanin produced by melanogenesis. We will explore some of these single gene traits in the laboratory. A few of the genes/regions not harboring a marginally associated SNP had haplotypes and diplotypes positively and/or negatively associated with iris colors (ASIP gene, 1 haplotype; MC1R gene, 2 haplotypes; Tables 2 and 3). From a screen of 754 SNP loci, we have identified 61 that are statistically associated with variable iris pigmentation at one level of intragenic complexity or another. HERC2/OCA2 rs12913832 and IRF4 rs12203592 influenced both eye colour and the number of iris pigmented lesions. This page titled 8.2: Human Traits Determined by Single Genes is shared under a CC BY 4.0 license and was authored, remixed, and/or curated by Ellen Genovesi, Laura Blinderman, & Patrick Natale via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request. A few disorders are associated with eye color. In the case of TYR, melanin production will halt entirely, resulting in albinism in the entire body. A gene for the mouse pink-eyed dilution locus and for human type II oculocutaneous albinism. Furthermore, with all genetic expression, aberration also occurs. 11. These two seemingly unrelated genes have a major effect on eye color in humans. Pigment Cell Res 14, 8693 (2001). Although introns are usually viewed as superfluous DNA, intron 86 of HERC2 regulates the expression of OCA2. A simple cross is provided in Figure 1: Blue-eyed Cross. Other very minor genes are responsible for eye color production, such as agouti signaling protein, but they usually have miniscule effects.5, Finally, two major genes are responsible for eye color: HERC2 and OCA2. 1997). Edridge Green Lecture RCOphth Annual Congress Glasgow May 2019, A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia, A multiethnic genome-wide analysis of 44,039 individuals identifies 41 new loci associated with central corneal thickness, A large Canadian cohort provides insights into the genetic architecture of human hair colour, Environment and culture shape both the colour lexicon and the genetics of colour perception, A systematic review of skin ageing genes: gene pleiotropy and genes on the chromosomal band 16q24.3 may drive skin ageing, White matter variability, cognition, and disorders: a systematic review, Quantitative changes in iris vasculature and blood flow in patients with different refractive errors, The Effect of Ambient Light Conditions on Quantitative Pupillometry, Functional and pathological relevance of HERC family proteins: a decade later. For these, it would seem more prudent to eliminate false positives downstream of SNP identification, such as from tests of higher-order association, using various other criteria, such as those described above, or possibly using the utility of the SNP for the generalization of a complex classification model when one is finally described. For this population a. Representatives of the resulting PCR products were checked on an agarose gel, and first-round PCR product was diluted and then used as template for a second round of PCR. Box N F, Duffy D L, Irving R E, Russell A, Chen W et al. BLAST searches confirmed the specificity of all primers used. These observations suggest that the genetic determinants for pigmentation in the various tissues are distinct and that these determinants have been subject to a common set of systematic and evolutionary forces that have shaped their distribution in world populations. Pigmented irises. The range in eye color, from blue to hazel to brown (see figure one), depends on the level of melanin pigment stored in the melanosome "packets" in the melanocytes of the iris. (d) List the possible genotypes of a blue eyed individual lacking a dimpled chin. For some, associations with iris colors were found only within the context of diplotypes, but not at the level of the SNPs or the haplotype (i.e., SILV and GSTT2 genes located at 22q11.23). Diplotypes explained 15% of the variation, whereas haplotypes explained 13% and SNPs explained only 11% (Table 4) after correcting for the number of variables. Genotypes for these 754 candidate SNPs were scored for 851 European-derived individuals of self-reported iris colors (292 blue, 100 green, 186 hazel, and 273 brown). 2002). J Forensic Sci 55, 315322 (2010). Eiberg, H., Troelsen, J., Nielsen, M., Mikkelsen, A., Mengel-From, J., Kjaer, K. et al. Second, although a roughly equal number of pigmentation and nonpigmentation gene SNPs were tested, of the 34 marginally associated SNPs, 28 of them. The OCA2 gene also contains numerous regions for eye color expression. 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