Human pigmentation genes break out into several biochemical pathways, including those for tyrosinase enzyme complex formation on the inner surface of the melanosome, hormonal and environmental regulation, melanoblast migration and differentiation, the intracellular routing of new proteins into the melanosome, and the proper transportation of the melanosomes from the body of the cell into the dendritic arms toward the keratinocytes. Depending on how little pigment the melanocytes produce, albinism causes red or violet eyes. Oetting, W. S. & King, R. A. Molecular basis of albinism: mutations and polymorphisms of pigmentation genes associated with albinism. 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). 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. 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. 2001). 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/). 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. In the case of TYR, melanin production will halt entirely, resulting in albinism in the entire body. Use a lab partner to help you determine your phenotype for the traits listed. Others genes such as AIM, OCA2, and TYRP1 harbored haplotypes positively associated with brown but negatively associated with blue color (AIM haplotype 2; OCA2 haplotypes 2, 4, 45, 47; TYRP1 haplotype 4; Table 3) while others, such as the MYO5A, OCA2, TYRP1, and CYP2C8 genes located at 10q23, harbored haplotypes positively associated with one color but not negatively associated with any other color (MYO5A haplotype 5 and haplotype 10, OCA2 haplotype 19, TYRP1 haplotype 3, and CYP2C8 haplotype 1; Table 3). MGG 1, 393394 (1908). In the P protein, the mutation causes residue 419 to change from an arginine to a glutamine. Second, although a roughly equal number of pigmentation and nonpigmentation gene SNPs were tested, of the 34 marginally associated SNPs, 28 of them. Half of the associated SNPs were located on chromosome 15, which corresponds with results that others have previously obtained from linkage analysis. Chi-square P value is shown. .. Bito L Z, Matheny A, Cruickshanks K J, Nondahl D M, Carino O B. Boissy R E, Zhao H, Oetting W S, Austin L M, Wildenberg S C et al. 1999; Flanagan et al. 2002). As mentioned previously, melanogenesis produces two different types of melanin and requires numerous proteins. We did not confine this higher-order analysis to those genes with marginal SNP associations, but we grouped all of the high-frequency SNPs tested for each gene. The most strongly associated 68 genotypes of the 543 genotypes observed for the 16 genes/regions, on the basis of chi-square-adjusted residuals, explained 13% of the variation (last row in Table 4). Montserrat Rabago-Smith. Transcribed image text: P>p Trait Genotype Phenotypic Effect Relationship P. Pigmented Iris (Additional genes give specific Iris Color color, e.g. PTC tasting If you can taste PTC, you have the dominant allele (P). The pedigree in the accompanying illustration shows the inheritance of albinism, a homozygous recessive condition resulting in a total lack of pigment. 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). Although introns are usually viewed as superfluous DNA, intron 86 of HERC2 regulates the expression of OCA2. Google Scholar. Also, if an allele does code for brown, the individual will have brown eyes, except for cases where a critical gene is turned off. The red appearance is the reflection of the eye's blood vessels. Brilliant, M. The mouse p (pink-eyed dilution) and human P genes, ocular albinism type 2 (OCA2), and melanosomal pH. 1993; Valverde et al. 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. 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. Therefore, it seems that our findings indicate that most of the previous results associating pigmentation gene alleles with iris colors, taken independently, represent merely strokes of a larger, more complex portrait. Nine were not and of these 2 were of relatively low frequency with weak evidence for disquilibrium (P value close to 0.05). In this pedigree use "A" to represent the dominant allele and "a" for the recessive allele.A It is toward this goal that we have performed the present study. Forensic Sci Int: Genet. Hum Genet 123, 177187 (2008). The process that produces melanin, known as melanogenesis, requires numerous proteins. Duffy, D. L., Montgomery, G. W., Chen, W., Zhao, Z., Le, L., James, M. R. et al. The remaining SNPs had values and chi-square P values that were not significant on any level of intragenic complexity. The P values we obtained suggested that diplotypes explained more iris color variation than did haplotypes or individual SNPs. Google Scholar. Allele Variations in OCA2 gene (pink-eyed-dilution locus) are associated with genetic susceptibility to melanoma. PubMed Central Sequences of the highest order of complexity within a locus found to be associated with iris colors. Pedigree studies in the mid-1970s suggested that iris color variation is a function of two loci: a single locus responsible for depigmentation of the iris, not affecting skin or hair, and another pleiotropic gene for reduction of pigment in all tissues (Brues 1975). Article CAS In humans, eye color is determined by the amount of light that reflects off the iris, a muscular structure that controls how much light enters the eye. The minor allele frequency for most of these SNPs was relatively high (average F minor allele = 0.22) and most of them were in Hardy-Weinberg equilibrium (HWE; those for which HWE P > 0.05, 28/34; Table 3). Knoll, J. H. M., Nicholls, R. D., Magenis, R. E., Glatt, K., Graham, Jr J. M., Kaplan, L. et al. The SNP, rs12913832, causes a phenotype change from brown to blue eyes, respectively. (2003) within the context of a software program we developed for this purpose, which will be presented elsewhere (T. Frudakis, Z. Gaskin, M. Thomas, V. Ponnuswamy, K. Venkateswarlu, S. Gunjupulli, C. Bonilla, E. Parra and M. Shriver, personal communication). Agonist color refers to the color with which the sequence is positively associated. IRIS pigmentation is a complex genetic trait that has long interested geneticists, anthropologists, and the public at large. (2000) with adjusted residuals to compensate for this risk. 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. This is an example of a hihybrid crosses. Provided by the Springer Nature SharedIt content-sharing initiative, Graefe's Archive for Clinical and Experimental Ophthalmology (2022), Cellular and Molecular Life Sciences (2016), Journal of Human Genetics (J Hum Genet) Nat Genet. 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). Genetic determinants of hair, eye and skin pigmentation in Europeans. (2002). Rather, it seems likely that the structure behind our results is of a finer, more cryptic nature, such as ethnicity or even within-ethnic-group structure. Already, some researchers have started studying hues and saturations. .. Gardner J M, Nakatsu Y, Gondo Y, Lee S, Lyon M F et al. Overall, the diversity of haplotypes associated with brown irises was similar to that of haplotypes associated with blue irises. Here, we present an analysis of iris phenotypes among 16 mouse strains with mutations influencing melanosomes. (Abstr. 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. Linkage studies have implicated certain pigmentation genes as specifically relevant for pigmentation phenotypes, and most of the pigmentation gene SNPs that we identified clustered to certain genes such as OCA2, MYO5A, TYRP1, and AIM. To correct for multiple tests, we used the empirical Bayes adjustments for multiple results method described by Steenland et al. Eumelanin (brown pigment) is a light-absorbing polymer synthesized in specialized melanocyte lysosomes called melanosomes. 1995). .. Ooi C E, Moreira J E, DellAngelica E C, Poy G, Wassarman D A et al. They help with hormone secretion, which affects the pituitary and can lead to dysfunction of the hypothalamus and other protein complexes. Article 1998), but mouse studies have suggested that 14 genes preferentially affect pigmentation in vertebrates (reviewed in Sturm et al. TYR, located from 11q14-q21, begins the melanogenesis pathway. 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. The promoter region for OCA2 is located within the HERC2 gene. Relationship. Legal. Molecular and General Genet. Statistical methods: To test the departures from independence in allelic state within and between loci, we used the exact test, described in Zaykin et al. Box N F, Duffy D L, Irving R E, Russell A, Chen W et al. Petunias with genotype R1R1 are red flowered, R1R2 are pink flowered and R2R2 are white flowered. (2002), although it should be noted that we did not observe this gene association at the level of the SNP as they did; one of the ASIP SNPs that we identified (marker 861, Table 2) is the 8818 G-A SNP transversion that they described to be associated with brown iris colors, but from our study the association was with hazel color at the level of the haplotype. 2. The most strongly associated of the marginally associated SNPs were from the OCA2, TYRP1, and AIM genes, in order of the strength of association, which is the same order as that provided using the number of marginally associated SNPs, rather than their strength. (H represents the non-mutated HERC2 SNP, and O represents the OCA2 allele for brown eyes). Nature 361, 7276 (1993). 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. 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. 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). 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. Haplotypes were inferred using the Stephens et al. J Hum Genet 56, 57 (2011). Predicting phenotype from genotype: normal pigmentation. 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. Sequences associated with human iris pigmentation. 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. 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. 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. A change in rs1800407 causes a change in the protein, Arg419Gln, and a change from brown to blue eyes. 1997; Lloyd et al. However, single-gene studies have not provided a sound basis for understanding the complex genetics of human iris color. et al. At the level of the haplotype, each gene or region had unique numbers and types of associations. (gray/blue). In the population sample, we were also able to examine the correlation between genotype at the W locus and iris color . The eumelanin/pheomelanin switch triggered by the MC1R gene may account for some cases of this disorder. Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene. In the traditional view of eye color, it was taught that two blue-eyed individuals could only produce blue-eyed offspring. Clearly work remains to be done, objectifying the collection of iris colors from subjects, enhancing the sample size so that epistatic interactions can be explored, possibly screening other regions of the genome not screened here, and modeling the sequences that we have described to enable classification of iris colors from DNA. 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. In other words, the distribution of SNPs among the various gene types was also not random. Hum Mutat 13, 99115 (1999). 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. Liu, F., Wollstein, A., Hysi, P. G., Ankra-Badu, G. A., Spector, T. D., Park, D. et al. Linkage disequilibrium (LD) for pairs of SNPs within a gene was determined using the Zaykin exact test and a cutoff value of |D| 0.05 (P value < 0.05; Zaykin et al. PLoS Genet 6, e1000934 (2010). .. Steenland K, Bray I, Greenland S, Boffetta P. Strobel M C, Seperack P K, Copeland N G, Jenkins N A. Valverde P, Healy E, Jackson I, Rees J L, Thody A J. Wilson S M, Yip R, Swing D A, OSullivan T N, Zhang Y et al. .. Krude H, Biebermann H, Luck W, Horn R, Brabant G et al. Peripheral scalloping of the posterior pigmented iris layer. For each gene, we inferred haplotypes and used contingency analyses to determine which haplotypes were statistically associated with iris colors. Different SNPs on these two genes were investigated and analyzed for melanoma risk.24, 25. Jannot, A- S., Meziani, R., Bertrand, G., Gerard, B., Descamps, V., Archibaud, A. et al. Accessibility StatementFor more information contact us atinfo@libretexts.orgor check out our status page at https://status.libretexts.org. These genes are of the greatest importance for eye color.9, 10, 11, Numerous ubiquitin ligases are coded for throughout the body. .. Chintamaneni C D, Ramsay M, Colman M-A, Fox M F, Pickard R T et al. The overlap among these SNP sets was high but not perfect. A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation. Without cysteine, the synthesis cannot be carried out. Many more genes affect brown and blue more than the other eye colors. 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. PubMed Central Redei, G. Encyclopedia of Genetics, Genomics, Proteomics, and Informatics, 3rd edn (Springer, New York City, NY, 2008). Other genes determine the nature and density of the pigment, giving us brown, hazel, violet, green and other eye colors. What is your genotype for this trait? Duffy, D. L., Box, N. F., Chen, W., Palmer, J. S., Montgomery, G. W., James, M. R. et al. At the cellular level, variable iris color in healthy humans is the result of the differential deposition of melanin pigment granules within a fixed number of stromal melanocytes in the iris (Imesch et al. Sulem, P., Gudbjartsson, D., Stacey, S., Helgason, A., Rafnar, T., Magnusson, K. P. et al. 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. An ASIP polymorphism is reported to be associated with both brown iris and hair color (Kanetsky et al. 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. 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. 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. (1995) and Koppula et al. Using a chi-square test, determine whether those numbers are consistent with . The front layer of the iris (called the stroma) can make eyes appear brown, blue or green. 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). It is around 12 . Aside from these two genes, the genes involved in melanogenesis and other minor genes also contain regions that account for eye color. 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. _____ Pigmented Iris If you are homozygous for the recessive allele "p", you do not produce pigment in the front layer of your iris. Eye color phenotypes demonstrate both epistasis and incomplete dominance. .. Schioth H B, Phillips S R, Rudzish R, Birch-Machin M A, Wikberg J E et al. Am J Hum Genet 47, 149155 (1990). 2001) and that disparate regions of the TYR and other OCA genes are functionally distinct for determining the pigmentation in different tissues. SNP discovery: We obtained candidate SNPs from the National Center for Biotechnology Information (NCBI) Single Nucleotide Polymorphism Database (dbSNP), which generally provided more candidate SNPs than were possible to genotype. In studies with HERC2 functions, deletions caused hypopigmentation even though the protein has nothing to do with pigmentation. When a T is replaced with a C in rs12913832 of intron 86, OCA2 transcription is depressed, resulting in a blue-eyed individual. CAS Similar to a lack of TYR, other conditions cause ocular albinism. .. Lee S-T, Nicholls R D, Schnur R E, Guida L C, Lu-Kuo J 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. Haplotype order refers to the order of the SNPs in the haplotypes shown in Table 4 and described in the text. 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 . To determine whether and how common polymorphisms are associated with natural distributions of iris colors, we surveyed 851 individuals of mainly European descent at 335 SNP loci in 13 pigmentation genes and 419 other SNPs distributed throughout the genome and known or thought to be informative for certain elements of population structure. as a function of BGA (Frudakis et al. Gene 277, 4962 (2001). 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. 2003). Am J Hum Genet 80, 241252 (2007). Although this could indicate that the SNPs are in LD with other phenotypically active loci, it may also be a reflection that variability in message transcription and/or turnover may explain part of the variability observed in human iris colors. TYR catalyzes the rate-limiting step of melanin biosynthesis and the degree to which human irises are pigmented correlates well with the amplitude of TYR message levels (Lindsey et al. ), 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. .. 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. Having little effect on eye color, many of them deal primarily with hair and skin pigmentation. 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. The "P" allele produces the pigment which gives you eye color. Complete the table. 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. The first is that for most of the genes for which we identified marginally associated SNPs, multiple such SNPs were identified. PCR amplification was accomplished using pfu Turbo polymerase according to the manufacturer's guidelines (Stratagene, La Jolla, CA). Twin Res 7, 197210 (2004). Google Scholar. 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). (2000). If no haplotypes or diplotypes for a locus were found to be associated, only the SNP alleles are shown. 1998; Flanagan et al. 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. Biogeographical ancestry admixture proportions were determined using the methods of Hanis et al. Flower-color pigments are synthesized by gene action in two separate pigment-producing biochemical pathways. Frequency of the minor allele and the major and minor allele nucleotide. 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. The recessive allele (b) encodes blue eyes.