Cell Mol Life Sci 62, 18261838 (2005). J Hum Genet 56, 57 (2011). Am J Hum Genet 82, 411423 (2008). Sturm, R. A., Teasdale, R. D. & Box, N. F. Human pigmentation genes: identification, structure and consequences of polymorphic variation. 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. In addition, for 103 of the subjects, iris colors were reported using a number from 1 to 11 as well, where 1 is the darkest brown/black and 11 is the lightest blue, identified using a color placard. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. Red and violet eyes come from a lack of pigment. Decreased expression of OCA2 affects the pathway for melanosome maturation. 11. If you have no pigment you have either blue or gray eyes. Eye color is determined by the pattern of brown and red pigment, collagen fibers, and the topography of the iris. PubMed The process that produces melanin, known as melanogenesis, requires numerous proteins. Eye colors are green, hazel, brown or black. By analyzing the DNA from a crime scene, the general phenotypic traits of the suspect may be pieced together.21, 22, 23 Tully suggests that it may help eliminate particular groups of suspects in circumstances with few leads. We identified numerous SNPs, haplotypes, and diplotypes (diploid pairs of haplotypes) within the OCA2, MYO5A, TYRP1, AIM, DCT, and TYR genes and the CYP1A2-15q22-ter, CYP1B1-2p21, CYP2C8-10q23, CYP2C9-10q24, and MAOA-Xp11.4 regions as significantly associated with iris colors. Since most individuals of non-European or minority European descent exhibit low variability in iris colors (on average of darker shade than individuals of European descent), this improvement may not seem surprising. Many more genes affect brown and blue more than the other eye colors. .. Kanetsky P, Swoyer J, Panossian S, Holmes R, Guerry D et al. For R2 computation, we used the following function: Adj-R2 = 1 [n/(n p)](1 R2), where n is the model degrees of freedom and n p is the error degrees of freedom. Before screening these genotypes for association with iris colors, we used the 73 nonxenobiotic metabolism AIMs to determine BGA admixture proportions for each sample and we tested for correlation between BGA admixture and iris colors. Some phenotypes however, are determined by a single gene. 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). Genotype-phenotype correlations have been reported with specific mutations possibly associated with certain angle abnormalities. Nonetheless, the complexity of OCA phenotypes illustrates that TYR is not the only gene involved in iris pigmentation (Lee et al. Corresponding author: DNAPrint Genomics, 900 Cocoanut Ave., Sarasota, FL 34236. Depending on how little pigment the melanocytes produce, albinism causes red or violet eyes. Alleles for these latter SNPs were known to be informative for certain elements of population structure; 73 were selected from a screen of the human genome because they were exceptional ancestry informative markers (AIMs, based on high values) for Indo-European, sub-Saharan African, Native American, and East Asian biogeographical ancestry (BGA; Shriver et al. As the eye color lightens, less melanin is present in the cells, reflecting more of the visible spectrum. 1996), melanocortin receptor (MC1R; Robbins et al. OCA2 ranges from 15q11.2-12 and HERC 2 starts at 15q13. One SNP has been studied to show a large significance for eye color. For example, forensics investigators construct physical profiles using surprisingly unscientific means; only in rare cases are eye-witness accounts available, and in certain circumstances these accounts are subjective and unreliable. For these subjects, we obtained digital photographs of the right iris, where subjects peered into a box at one end at the camera at the other end to standardize lighting conditions and distance and from which a judge assigned the sample to a color group. Sequences associated with human iris pigmentation. Am J Hum Genet 82, 424431 (2008). MYO5A alleles were not found to be in LD with those of OCA2, suggesting that these results were independently obtained and that Eiberg and Mohr's results may have been a reflection of the activity of two separate genes. If you cannot taste anything, you do not possess the dominant allele. Google Scholar. Department of Chemistry and Biochemistry, Kettering University, Flint, MI, USA, You can also search for this author in An intron in HERC2 contains the promoter region for OCA2, affecting its expression. Lastly, disorders involved in eye color include ocular albinism and heterochromia. Using a chi-square test, determine whether those numbers are consistent with . CAS Alternatively, as a research tool, the common haplotypes that we have identified and the complex, biologically relevant contexts within which they are found may help researchers more accurately define risk factors for pigmentation-related diseases such as cataracts and melanoma. ., Oxford University Press is a department of the University of Oxford. For example, dissection of the oculocutaneous albinism (OCA) trait in humans has shown that many pigmentation defects are due to lesions in the TYR gene, resulting in their designation as TYR-negative OCAs (Oetting and King 1991, 1992, 1993, 1999; see albinism database at http://www.cbc.umn.edu/tad/). Flower-color pigments are synthesized by gene action in two separate pigment-producing biochemical pathways. This condition is pronounced in people who produce little to no pigment throughout their entire body, but it can be localized to the eyes.2 When they produce no pigment at all, it is usually due to a nonfunctioning TYR.10 With this condition, a complete lack of pigment produces red eyes, and a small amount of pigment may produce violet eyes. When this work is more fully developed, it may be possible to assign an iris color to an individual sample with reasonable certainty, and surely in this case the results herein will have some tangible value for the field of forensic science. Refer to TABLE II. Haplotype order refers to the order of the SNPs in the haplotypes shown in Table 4 and described in the text. Montserrat Rabago-Smith. Sulem, P., Gudbjartsson, D., Stacey, S., Helgason, A., Rafnar, T., Magnusson, K. P. et al. 1993; Valverde et al. Last, we thank the reviewers of this manuscript who suggested a number of important improvements. In other words, their SNPs were associated with iris colors only within the context of gene haplotypes or diplotypes. TYR, the enzyme responsible for pigment throughout the body, uses tyrosine to begin the chemical pathway. 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. Most of what we have learned about pigmentation since has been derived from molecular genetics studies of rare pigmentation defects in humans and model systems such as mouse and Drosophila. 2001). Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. Number of times the haplotype was observed in our sample of 851. groups of the world that are of darker average iris color (Frudakis et al. The eumelanin/pheomelanin switch triggered by the MC1R gene may account for some cases of this disorder. Brilliant, M. The mouse p (pink-eyed dilution) and human P genes, ocular albinism type 2 (OCA2), and melanosomal pH. These analyses resulted in the identification of 61 SNPs in 16 genes/chromosomal regions associated with iris colors on one level or another; details for each and whether the SNP is marginally associated or associated within the context of the haplotype and/or diplotype are shown in Table 2. 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). We selected those for which at least two instances of PHRED identified variants that scored 24, and each of these SNPs discovered through resequencing were used for genotyping. ISSN 1434-5161 (print), Genotypephenotype associations and human eye color, Further insight into the global variability of the OCA2-HERC2 locus for human pigmentation from multiallelic markers, The distinctive geographic patterns of common pigmentation variants at the OCA2 gene, Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability, What colour are your eyes? Blue Iris (non-pigmented) MG-3: Jeremy has attached earlobes and pigmented irises. What is your genotype for this trait? BLAST searches confirmed the specificity of all primers used. 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. (2001) haplotype reconstruction method. . In the absence of melanin brown pigment, the iris is blue. 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. Before the revelation of the effect of HERC2, rs1800407 in exon nine was thought to be the main factor for eye color. Each of these genes is part of the main (TYR) human pigmentation pathway. 20, 327332 (2004). Genotyping was performed for individual DNA specimens using a single base primer extension protocol and an SNPstream 25K/ultra-high throughput (UHT) instrument (Beckman Coulter, Fullerton, CA, and Orchid Biosystems, Princeton, NJ). The rest were found in or around xenobiotic metabolism genes, which we have previously shown exhibit dramatic sequence variation, Candidate genes tested for sequence associations with human iris pigmentation. The first parent contains the mutation in the HERC2 intron in both alleles but possesses an allele with the coding for brown eyes. .. Shriver M, Parra E, Dios S, Bonilla C, Norton H et al. Of the 17 that did not, 6 were brown/hazel, 7 were green/hazel, and 4 were blue/green discrepancies although none were gross discrepancies such as brown/green, brown/blue, or hazel/blue. 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). ISSN 1435-232X (online) In contrast, between-population comparisons show good concordance; populations with darker average iris color also tend to exhibit darker average skin tones and hair colors. 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 ). 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). Knoll, J. H. M., Nicholls, R. D., Magenis, R. E., Glatt, K., Graham, Jr J. M., Kaplan, L. et al. The large HERC2 gene requires 211kb and 93 exons that codes for a 528kDa protein made of 4834 residues.12. IRIS pigmentation is a complex genetic trait that has long interested geneticists, anthropologists, and the public at large. Specify the following genotypes using A and a to indicate dominant and recessive alleles, respectively. 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Hum Genet 123, 177187 (2008). Further studies of this region and its sequence revealed that a change in one nucleotide, single-nucleotide polymorphism (SNP), regulates the binding site for the transcription of the OCA2 gene, altering its expression.9 The base changes from a thymine to a cytosine. 1997; Smith et al. Eye color phenotypes demonstrate both epistasis and incomplete dominance. A few disorders are associated with eye color. All of the major sequences (count 13) for each locus with at least one significantly associated sequence are shown. 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. Specimens for genotyping were of self-reported European descent, of different age, sex, hair, iris, and skin shades and they were collected using informed consent guidelines under Investigational Review Board guidance. This information revealed more factors for determining eye color in European populations.20 Tully, Valenzuela and Zaumseger suggest using genotype data for forensic analysis. The overlap among these SNP sets was high but not perfect. A dark iris pigment (green/brown/black) is dominant over the light pigmentation. volume56,pages 57 (2011)Cite this article. Similar to a lack of TYR, other conditions cause ocular albinism. 1998; Flanagan et al. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. .. Hanis C, Chakraborty R, Ferrell R, Schull W. Jackson I J, Chambers D M, Tsukamoto K, Copeland N G, Gilbert D J et al. The recessive allele (b) encodes blue eyes. Producing multicolored irises, heterochromia stems from mutations in certain cells of the iris. Gardner, J., Nakatsu, Y., Gondo, Y., Lee, S., Lyon, M., King, R. et al. That is, the occurrence of an allele for eye pigmentation in a gamete has nobearing on which allele for chin form will occur in that same gamete. .. Kwon B S, Chintamaneni C, Kozak C A, Copeland N G, Gilbert D J et al. Pathway I contains gene A that produces an enzyme to catalyze conversion of a colorless pigment designated white1 to blue pigment. 1997, 2001; Akey et al. Aside from the fact that many of the SNPs we identified were significant after imposing the Steenland correction for multiple testing, there are three lines of evidence that the SNPs we have identified are not spuriously associated. A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation. The MC1R gene harbored haplotypes associated only with green color in our sample and the POMC gene harbored a single SNP with genotypes weakly associated with iris colors (no significant haplotypes or diplotypes were found). is called your "genotype" 2 matching alleles = "homozygous" 2 different alleles = "heterozygous" In heterozygous individuals, the allele that is "expressed" (seen in individual's appearance) is the "dominant" allele. Sturm, R. & Frudakis, T. Eye Colour: portals into pigmentation genes and ancestry. Eye color ranges include varying shades of brown, hazel, green, blue, gray, and in rare cases, violet and red. These genes are of the greatest importance for eye color.9, 10, 11, Numerous ubiquitin ligases are coded for throughout the body. Alternatively, the mechanism for the associations could be LD with phenotypically active loci in nearby pigment genes. To test this, we performed a corrected ANOVA analysis for our data on each of these three levels. Over 300 SNPs for eye color have been identified on the gene, but classification of their results proved too arduous. (82%) were in pigmentation genes. They help with hormone secretion, which affects the pituitary and can lead to dysfunction of the hypothalamus and other protein complexes. .. Lee S-T, Nicholls R D, Schnur R E, Guida L C, Lu-Kuo J et al. Therefore, the residue change causes a problem with the P protein, and melanin maturation decreases. Article the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in The pigmented structure inside the eye that surrounds the pupil and gives eyes their color is called the iris. The traditional view was correct in which an allele that codes for brown is dominant over green or blue, and green takes precedence over blue.2, Melanocytes in the stroma and anterior layers of the eye hold melanin in their cytoplasms. Once the pigment is produced, MC1R, membrane-associated transporter protein, and p proteins (OCA2) mature the melanosomes to be used in the cells. The P values we obtained suggested that diplotypes explained more iris color variation than did haplotypes or individual SNPs. Science 257, 1121 (1992). 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 . Google Scholar. 2000), and adaptin 3B (AP3B) loci (Ooi et al. In other words, the distribution of SNPs among the various gene types was also not random. Second, although a roughly equal number of pigmentation and nonpigmentation gene SNPs were tested, of the 34 marginally associated SNPs, 28 of them. genotype - all alleles present in the cell ; phenotype - physical appearance of a trait ; . Petunias with genotype R1R1 are red flowered, R1R2 are pink flowered and R2R2 are white flowered. Although we screened a large number of SNPs, some of the genes harbor a large number of candidate SNPs and we did not test them all. a) Give the genotype of an individual, who is homozygous dominant for Brown eye color, where "B" is the letter used to distinguish this trait. Without cysteine, the synthesis cannot be carried out. record your observations. Question: In albinism (a recessive disorder), the formation of melanin, a dark skin pigment, are blocked so that albinos have extremely light skin and hair. Problems with just HERC2 lead to nerve tissue malfunctioning, small size and semi-sterility or sterility. Melanocortin 1 receptor (MC1R) instructs a melanocyte to switch production between eumelanin and pheomelanin.3, 4, 5 Therefore, these two proteins affect the quality and quantity of the melanin in the cell. Genetics 165, 20712083 (2003). Accessibility StatementFor more information contact us atinfo@libretexts.orgor check out our status page at https://status.libretexts.org. Allele Variations in OCA2 gene (pink-eyed-dilution locus) are associated with genetic susceptibility to melanoma. et al. We found that most of the associations were still significant after this correction (those with asterisks in Table 2), and since the analysis was conducted using adjusted residuals, some new associations were observed (i.e., MAOA marker 2 had a chi-square P value of 0.24 but was associated using the corrected testing procedure; Table 2). Genotypes were subject to several quality controls: two scientists independently pass/fail inspected the calls, requiring an overall UHT signal intensity >1000 for >95% of genotypes and clear signal differential between the averages for each genotype class (i.e., clear genotype clustering in two-dimensional space using the UHT analysis software). PubMed Central We developed a program (T. Frudakis, M. Thomas, Z. Gaskin, K. Venkateswarlu, K. Suresh Chandra, S. Ginjupalli, S. Gunturi, S. Natrajan, V. K. Ponnuswamy and K. N. Ponnuswamy, unpublished results) to design resequencing primers in a manner respectful of homologous sequences in the genome, to ensure that we did not coamplify pseudogenes or amplify from within repeats. Aside from these two genes, the genes involved in melanogenesis and other minor genes also contain regions that account for eye color. Article More than likely, their offspring would have blue eyes, but a 25% chance stands that offspring would have brown eyes. PubMed Central One leads to eumelanin, a darker pigment (brown-black), and the other to pheomelanin, a light pigment (red-yellow). Membrane-associated transporter protein and p protein oculocutaneous albinism II (OCA2) transport melanosomes for melanin maturation. Each chromosome contains thousands of individual genes. One of these, the Arg305TRP SNP, was one of the 13 OCA2 SNPs that we found to be strongly associated with iris colors using all four of our color criteria, although its association was only the ninth strongest among the OCA2 SNPs that we identified and the eleventh strongest among all of the associated SNPs that we identified. When light passes through a large amount of melanin, most of the visible light is absorbed, and the little that is reflected back appears brown.