CAS 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. CAS Nonetheless, the complexity of OCA phenotypes illustrates that TYR is not the only gene involved in iris pigmentation (Lee et al. We thank D. C. Rao, Director of the Division of Biostatistics, Washington University, St. Louis, for help preparing this manuscript; Mark Shriver, Department of Anthropology and Human Genetics at The Pennsylvania State University for his help with the biogeographical ancestry admixture aspect of the project; and Murray Brilliant, professor of Pediatrics and Molecular and Cellular Biology at the University of Arizona for their kind advice and support of our work. Flower-color pigments are synthesized by gene action in two separate pigment-producing biochemical pathways. European J Hum Genet 13, 913920 (2005). Nature 361, 7276 (1993). 1998), but mouse studies have suggested that 14 genes preferentially affect pigmentation in vertebrates (reviewed in Sturm et al. Third, when applied to a sample including individuals of multiple ancestries, the linear and nonlinear variables from these and the other genes combined performed even better than when applied just to individuals of majority European ancestry (not shown). A few disorders are associated with eye color. PubMed Central .. Gardner J M, Nakatsu Y, Gondo Y, Lee S, Lyon M F et al. 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. Biogeographical ancestry admixture proportions were determined using the methods of Hanis et al. In the absence of melanin brown pigment, the iris is blue. In studies with HERC2 functions, deletions caused hypopigmentation even though the protein has nothing to do with pigmentation. In Drosophila, iris pigmentation defects have been ascribed to mutations in >85 loci contributing to a variety of cellular processes in melanocytes (Ooi 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. 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. Twin Res 7, 197210 (2004). In all, 27 SNPs were significantly associated with iris pigmentation using at least one of the four criteria, and we refer to these as marginally associated. We will explore some of these single gene traits in the laboratory. 1997; Lloyd et al. as a function of BGA (Frudakis et al. 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. We fixed significance levels at 5%, and the alleles of 20 SNPs were found to be associated with specific iris colors, 19 with iris color shades, 19 with blue/brown color comparisons, and 18 using the brown/not brown comparison. The first is that for most of the genes for which we identified marginally associated SNPs, multiple such SNPs were identified. PHRED-qualified sequences were imported into the CLUSTAL X alignment program and the output of this was used with a second program that we developed (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 identify quality-validated discrepancies between sequences. Am J Hum Genet 82, 411423 (2008). Specify the following genotypes using A and a to indicate dominant and recessive alleles, respectively. During pigment distribution in an infant, a diet low in cysteine or methionine, which it is synthesized from, would likely affect the color of the child's eyes until the amino acid is supplemented. Dopachrome tautomerase (13q32) and TYR-related protein 1 (9p23) will continue the pathway to form eumelanin.15 Therefore, if any of these proteins are not coded for correctly, the eumelanin production may be hindered, producing lighter eyes. 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. Cell Mol Life Sci 62, 18261838 (2005). 1997; Box et al. pigmented iris genotype 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 = 3 10-9 ). Hurst, C. C. On the inheritance of eye colour in man. 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. Corresponding author: DNAPrint Genomics, 900 Cocoanut Ave., Sarasota, FL 34236. When there is no pigment in the front part of the eyes, then a blue layer at the back of the iris shows through, resulting in blue eyes. Phakomatoses. 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. 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. Although TYR is centrally important for this process, pigmentation in animals is not simply a Mendelian function of TYR or of any other single protein product or gene sequence. In the case of TYR, melanin production will halt entirely, resulting in albinism in the entire body. The two rounds were necessary due to the fact that many of the genes we queried were members of gene families, the SNPs resided in regions of sequence homology, and our genotyping platform required short (100 bp) amplicons. & Driscoll, D. J. Prader-Willi syndrome. No significant SNP associations within the pigmentation genes SILV, MC1R, ASIP, POMC, RAB, or TYR were found, although TYR had one SNP with a P = 0.06. Sturm, R. & Frudakis, T. Eye Colour: portals into pigmentation genes and ancestry. 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. 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. The OCA2 gene also contains numerous regions for eye color expression. HERC2/OCA2 rs12913832 and IRF4 rs12203592 influenced both eye colour and the number of iris pigmented lesions. In other words, the distribution of SNPs among the various genes tested was not random. .. Lindsey J D, Jones H L, Hewitt E G, Angert M, Weinreb R N. Lyon M F, King T R, Gondo Y, Gardner J M, Nakatsu Y et al. 1993; Valverde et al. Redei, G. Encyclopedia of Genetics, Genomics, Proteomics, and Informatics, 3rd edn (Springer, New York City, NY, 2008). Sequences associated with human iris pigmentation. If you have no pigment you have either blue or gray 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. OCA2 contains regions for the numerous eye colors, but one SNP is a strong predictor for brown/blue eyes. From the chi-square and adjusted residuals, we found 43 haplotypes for 16 different loci to be either positively (agonist) or negatively (antagonist) associated with iris colors (Table 3). 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. Abbott C, Jackson I J, Carritt B, Povey S. Akey J M, Wang H, Xiong M, Wu H, Liu W et al. Genetics 165, 20712083 (2003). Amplification products were subcloned into the pTOPO (Invitrogen, San Diego) sequencing vector and 96 insert-positive colonies were grown for plasmid DNA isolation (the use of 670 individuals for the amplification step reduced the likelihood of an individual contributing more than once to this subset of 96 selected). .. Newton J M, Cohen-Barak O, Hagiwara N, Gardner J M, Davisson M T et al. Eye colors are green, hazel, brown or black. Google Scholar. J Forensic Sci 55, 315322 (2010). 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. Aside from HERC2 and OCA2, the other genes involved in melanin production have some regions that correlate to other eye colors.5 MC1R contains regions that increase the probability of obtaining green eyes. Article Eye color results from varying degrees of melanin produced in the melanocytes of the iris. An ASIP polymorphism is reported to be associated with both brown iris and hair color (Kanetsky et al. 39, 14431452 (2007). 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. 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. These two seemingly unrelated genes have a major effect on eye color in humans. Department of Chemistry and Biochemistry, Kettering University, Flint, MI, USA, You can also search for this author in PubMedGoogle Scholar. It is toward this goal that we have performed the present study. 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. 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? In other words, their SNPs were associated with iris colors only within the context of gene haplotypes or diplotypes. Finally, in addition to the OCA2 (15q11.2q12) and MYO5A (15q21) sequences, a single SNP (15q22ter) was also implicated on chromosome 15q, but SNPs between each of these three loci were not found to be in LD (data not shown). PLoS Genet 6, e1000934 (2010). Attached earlobes. One SNP has been studied to show a large significance for eye color. What is your genotype for this trait? (82%) were in pigmentation genes. (1995). 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). 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. Multiple SNPs were also identified on chromosome 2; the C/C genotype for the POMC SNP located at 2p23 was associated with blue iris color (Table 3) and a CYP1B1-2p21-region SNP was also marginally associated at the level of iris shade (Table 2), as well as within the context of a 2-SNP haplotype (Table 3). Google Scholar. _____ Pigmented Iris If you are homozygous for the recessive allele "p", you do not produce pigment in the front layer of your iris. Hum Mol Genet 13, 447461 (2004). Only about half of the 61 SNPs that we identified were associated with iris colors independentlythe others were associated only in the context of haplotypes or diplotypes. An intron in HERC2 contains the promoter region for OCA2, affecting its expression. Tully, G. Genotype versus phenotype: human pigmentation. The sequences we have identified constitute a good first step toward developing a classifier model for the inference of iris colors from DNA, and the nature of some of these as markers of population structure might have implications for the design of other complex trait gene-mapping studies. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in IRIS pigmentation is a complex genetic trait that has long interested geneticists, anthropologists, and the public at large. .. Smith R, Healy E, Siddiqui S, Flanagan N, Steijlen P M et al. The colored area at the front of the eye is called the iris. Two major genes on chromosome 15 affect the quantity and quality of the melanin produced by melanogenesis. Rinchik, E. M., Bultman, S. J., Horsthemke, B., Lee, S., Strunk, K. M., Spritz, R. A. et al. (1997), suggesting that these sequences are indeed associated with iris pigmentation as suggested by these authors, although we note that the associations described by these authors were with blue irises and at the level of the SNP, while those that we observed were with green irises and apparent only at the level of the haplotypes and diplotypes. 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. Human Earlobe attachment. Correspondence to When a T is replaced with a C in rs12913832 of intron 86, OCA2 transcription is depressed, resulting in a blue-eyed individual. If you have no pigment you have either blue or gray eyes. 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. 1994). Indeed, some, but not all, of our nonpigment gene SNPs are found in regions within the vicinity of pigmentation genes; CYP2C8 and CYP2C9 are located on chromosome 10 near the HPS1 and HPS2 pigmentation genes (which we did not test directly), CYP1A2 is located at 15q22ter on the same arm as OCA2 and MYO5A, CYP1B1 is located at 2p21 in the vicinity of the POMC gene at 2p23, and MAOA is located on the same arm of chromosome X (Xp11.411.3) as the OA1 pigmentation gene (which we also did not test directly). In melanocyte-specific organelles known as melanosomes, two pathways for melanogenesis occur. 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. Therefore, single-nucleotide polymorphisms in either of these two genes have a large role in the eye color of an individual. Aside from these two genes, the genes involved in melanogenesis and other minor genes also contain regions that account for eye color. We sequenced with an ABI3700 using PE Applied Biosystems BDT chemistry and we deposited the sequences into a commercial relational database system (iFINCH, Geospiza, Seattle). iris contact lenses, or a cosmetic iris implant inserted at the time of cataract surgery . 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. In the meantime, to ensure continued support, we are displaying the site without styles The strongest associations were observed for genes with SNPs that were marginally associated (Table 2) and most of the genes with marginal SNP associations had haplotypes and diplotypes (sometimes referred to as multilocus gene-wise genotypes or diploid pairs of haplotypes) positively (agonist) or negatively (antagonist) associated with at least one iris color (Table 3).