title: Genotype-Phenotype Study of the Middle Gangetic Plain in India Shows Association of rs2470102 with Skin Pigmentation.
abstract: Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians.
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Anshuman
authors.initials: A
authors.lastname: Mishra
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Sheikh
authors.initials: S
authors.lastname: Nizammuddin
authors.affiliation: Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Estonian Biocentre, Tartu, Estonia.
authors.forename: Chandana Basu
authors.initials: CB
authors.lastname: Mallick
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Sakshi
authors.initials: S
authors.lastname: Singh
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Satya
authors.initials: S
authors.lastname: Prakash
authors.affiliation: Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India.
authors.forename: Niyamat Ali
authors.initials: NA
authors.lastname: Siddiqui
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Niraj
authors.initials: N
authors.lastname: Rai
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: S Justin
authors.initials: SJ
authors.lastname: Carlus
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Digumarthi V S
authors.initials: DVS
authors.lastname: Sudhakar
authors.affiliation: Department of Biotechnology, V.B.S. Purvanchal University, Jaunpur, India.
authors.forename: Vishnu P
authors.initials: VP
authors.lastname: Tripathi
authors.affiliation: Estonian Biocentre, Tartu, Estonia; Insitute of Mathematical Statistics, University of Tartu, Tartu, Estonia.
authors.forename: Märt
authors.initials: M
authors.lastname: Möls
authors.affiliation: Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma, USA.
authors.forename: Xana
authors.initials: X
authors.lastname: Kim-Howard
authors.affiliation: Department of Anthropology, Delhi University, New Delhi, India.
authors.forename: Hemlata
authors.initials: H
authors.lastname: Dewangan
authors.affiliation: Oriental Institute of Science and Technology, Bhopal, India.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Mishra
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Alla G
authors.initials: AG
authors.lastname: Reddy
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Biswajit
authors.initials: B
authors.lastname: Roy
authors.affiliation: Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India.
authors.forename: Krishna
authors.initials: K
authors.lastname: Pandey
authors.affiliation: Estonian Biocentre, Tartu, Estonia.
authors.forename: Gyaneshwer
authors.initials: G
authors.lastname: Chaubey
authors.affiliation: Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Das
authors.affiliation: Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma, USA.
authors.forename: Swapan K
authors.initials: SK
authors.lastname: Nath
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Lalji
authors.initials: L
authors.lastname: Singh
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India. Electronic address: thangs@ccmb.res.in.
authors.forename: Kumarasamy
authors.initials: K
authors.lastname: Thangaraj
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D017920:Antiporters / Q000235:genetics; D044466:Asian People / Q000235:genetics; D002648:Child; D015331:Cohort Studies; D005260:Female; D005787:Gene Frequency; D056726:Genetic Association Studies; D005843:Geography; D006239:Haplotypes; D006801:Humans; D007194:India; D008297:Male; D008875:Middle Aged; D010641:Phenotype; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012880:Skin Pigmentation / Q000235:genetics*; D012923:Social Class; D055815:Young Adult
chemical_list: D017920:Antiporters; C506584:SLC24A5 protein, human