Biochemical Genetics

, Volume 45, Issue 7–8, pp 535–542 | Cite as

Distribution of Two Asian-Related Coding SNPs in the MC1R and OCA2 Genes

  • I. YuasaEmail author
  • K. Umetsu
  • S. Harihara
  • A. Kido
  • A. Miyoshi
  • N. Saitou
  • B. Dashnyam
  • F. Jin
  • G. Lucotte
  • P. K. Chattopadhyay
  • L. Henke
  • J. Henke


Very little is known about the genes and mechanisms affecting skin lightening in Asian populations. In this study, two coding SNPs, c.G1129A (R163Q) at the MC1R (melanocortin 1 receptor) gene and c.A1962G (H615R) at the OCA2 (oculocutaneous albinism type II) gene, were investigated in a total of 1,809 individuals in 16 populations from various areas. The Q163 and R615 alleles prevailed almost exclusively in East and Southeast Asian populations. Wright’s F ST was 0.445 for R163Q and 0.385 for H615R among the 16 populations. The frequency of the Q163 allele was higher in Northeast Asians than in Southeast Asians. The frequency of the R615 allele was highest in South China and unlikely to be associated with levels of ultraviolet radiation. This allele may be a good marker to study the genetic affinity among East Asians because of its restricted distribution and marked difference in allele frequency.


MC1R OCA2 Pigmentation Polymorphism Population study Skin color 


  1. Akey JM, Wang H, Xiong M, Wu H, Liu W, Shriver M, Jin L (2001) Interaction between the melanocortin-1 receptor and P genes contributes to inter-individual variation in skin pigmentation phenotypes in a Tibetan population. Hum Genet 108:516–520PubMedCrossRefGoogle Scholar
  2. Excoffier L, Laval G, Schneider S (2005) Arlequin ver 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50Google Scholar
  3. Graf J, Hodgson R, van Daal A (2005) Single nucleotide polymorphisms in the MATP gene are associated with normal human pigmentation variation. Hum Mutat 25:278–284PubMedCrossRefGoogle Scholar
  4. Harding RM, Healy E, Ray AJ, Ellis NS, Flanagan N, Todd C, Dixon C, Sajantila A, Jackson IJ, Birch-Machin MA, Rees JL (2000) Evidence for variable selective pressures at MC1R. Am J Hum Genet 66:1351–1361PubMedCrossRefGoogle Scholar
  5. Hartl DL, Clark AG (1997) Principles of population genetics 3rd edn. Sunderland, Sinauer AssociatesGoogle Scholar
  6. Jablonski NG, Chaplin G (2000) The evolution of skin coloration. J Hum Evol 39:57–106PubMedCrossRefGoogle Scholar
  7. Lamason RL, Mohideen MA, Mest JR, Wong AC, Norton HL, Aros MC, Jurynec MJ, Mao X, Humphreville VR, Humbert JE, Sinha S, Moore JL, Jagadeeswaran P, Zhao W, Ning G, Makalowska I, McKeigue PM, O’Donnell, Kittles R, Parra EJ, Mangini NJ, Grunwald DJ, Shriver MD, Canfield VA, Cheng KC (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310:1782–1786PubMedCrossRefGoogle Scholar
  8. Lee S-T, Nicholls RD, Jong MTC Fukai K, Spritz AS (1995) Organization and sequence of the human P gene and identification of a new family of Transport proteins. Genomics 26:354–363PubMedCrossRefGoogle Scholar
  9. Makova K, Norton H (2005) Worldwide polymorphism at the MC1R locus and normal pigmentation variation in humans. Peptides 26:1901–1908PubMedCrossRefGoogle Scholar
  10. McEvoy B, Beleza S, Shriver MD (2006) The genetic architecture of normal variation in human pigmentation: an evolutionary perspective and model. Hum Mol Genet 15:R176–R181PubMedCrossRefGoogle Scholar
  11. Myles S, Somel M, Tang K, Kelso J, Stoneking M (2007) Identifying genes underlying skin pigmentation differences among human populaions. Hum Genet 120:613–621PubMedCrossRefGoogle Scholar
  12. Nakayama K, Fukamachi S, Kimura H, Koda Y, Soemantri A, Ishida T (2002) Distinctive distribution of AIM1 polymorphism among major human populations with different skin color. J Hum Genet 47:92–94PubMedCrossRefGoogle Scholar
  13. Nakayama K, Soemantri A, Jin F Dashnyam B, Ohtsuka R, Duanchang P, Isa MN, Settheetham-Ishida W, Harihara S, Ishida T (2006) Identification of novel functional variants of the melanocortin 1 receptor gene originated from Asians. Hum Genet 119:322–330PubMedCrossRefGoogle Scholar
  14. Oetting WS, Garrett SS, Brott M, King RA (2005) P gene mutations associated with occulocutaneous albinism type II (OCA2) Hum Mutat 25:323PubMedCrossRefGoogle Scholar
  15. Puri N, Gardner JM, Brilliant MH (2000) Aberrant pH of melanosomes in pink-eyed dilution (p) mutant melanocytes. J Invest Dermatol 115:607–613PubMedCrossRefGoogle Scholar
  16. Rana BK, Hewett-Emmett D, Jin L Chang BH, Sambuughin N, Lin M, Watkins S, Bamshad M, Jorde LB, Ramsay M, Jenkins T, Li WH (1999) High polymorphism at the human melanocortin 1 receptor locus. Genetics 151:1547–1557PubMedGoogle Scholar
  17. Relethford JH (2002) Apportionment of global human genetic diversity based on craniometrics and skin color. Am J Phys Anthropol 118:393–398PubMedCrossRefGoogle Scholar
  18. Ringholm A, Klovins J, Rudzish R, Phillips S, Rees JL, Schioth HB (2004) Pharmacological characterization of loss of function mutations of the human melanocortin 1 receptor that are associated with red hair. J Invest Dermatol 123:917–923PubMedCrossRefGoogle Scholar
  19. Shi P, Lu XM, Luo HR, Xiang-Yu J, Zhang YP (2001) Melanocortin-1 receptor gene variants in four Chinese ethnics populations. Cell Res 11:81–84CrossRefGoogle Scholar
  20. Soejima M, Tachida H, Ishida T, Sano A, Koda Y (2006) Evidence for recent positive selection at the human AIM1 locus in a European population. Mol Biol Evol 23:179–188PubMedCrossRefGoogle Scholar
  21. Valverde P, Healy E, Jackson I, Rees JL, Thody AJ (1995) Variants of the melanocyte-stimulating hormone receptor gene are associated with red hair and fair skin in humans. Nat Genet 11:328–330PubMedCrossRefGoogle Scholar
  22. Watanabe G, Umetsu K, Yuasa I, Suzuki T (1997) Amplified product length polymorphism (APLP): a novel strategy for genotyping the ABO blood group. Hum Genet 99:34–37PubMedCrossRefGoogle Scholar
  23. Yuasa I, Umetsu K, Watanabe G, Nakamura H, Endoh M, Irizawa Y (2004) MATP polymorphisms in Germans and Japanese: L374F mutation as a population marker for Caucasoids. Int J Legal Med 118:364–366PubMedCrossRefGoogle Scholar
  24. Yuasa I, Umetsu K, Harihara S, Kido A, Miyoshi A, Saitou N, Dashnyam B, Jin F, Lucotte G, Chattopadhyay PK, Henke L, Henke J (2006) Distribution of the F374 allele of the SLC45A2 (MATP) gene and founder-haplotype analysis. Ann Hum Genet 70:802–811PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • I. Yuasa
    • 1
    Email author
  • K. Umetsu
    • 2
  • S. Harihara
    • 3
  • A. Kido
    • 4
  • A. Miyoshi
    • 5
  • N. Saitou
    • 6
  • B. Dashnyam
    • 7
  • F. Jin
    • 8
  • G. Lucotte
    • 9
  • P. K. Chattopadhyay
    • 10
  • L. Henke
    • 11
  • J. Henke
    • 11
  1. 1.Division of Legal Medicine, Faculty of MedicineTottori UniversityYonagoJapan
  2. 2.Department of Experimental and Forensic Pathology, Faculty of MedicineYamagata UniversityYamagataJapan
  3. 3.Department of Biological Sciences, Graduate School of ScienceUniversity of TokyoTokyoJapan
  4. 4.Department of Legal Medicine, Faculty of MedicineUniversity of YamanashiNakakomaJapan
  5. 5.Department of Forensic MedicineFukuoka University School of MedicineFukuokaJapan
  6. 6.Division of Population GeneticsNational Institute of GeneticsMishimaJapan
  7. 7.Institute of Biological Sciences, Mongolian Academy of SciencesUlaan BaatorMongolia
  8. 8.Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
  9. 9.Center of Molecular NeurogeneticsParisFrance
  10. 10.Amity Institute of Forensic Sciences, Defence ColonyNew DelhiIndia
  11. 11.Institut für BlutgruppenforschungCologneGermany

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