Manjari Jonnalagadda1, Neeraj Bharti2, Yatish Patil2, Shantanu Ozarkar3, Sunitha Manjari K2, Rajendra Joshi2, Heather Norton4. 1. Symbiosis School for Liberal Arts (SSLA), Symbiosis International University (SIU), Pune, 411014, India. 2. HPC-MBA Group, Centre for Development of Advanced Computing, Pune, 411007, India. 3. Department of Anthropology, Savitribai Phule Pune University, Pune, 411007, India. 4. Department of Anthropology, University of Cincinnati, Cincinnati, Ohio.
Abstract
OBJECTIVES: Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing to phenotypic variation in skin pigmentation within and among South Asian populations are still poorly understood. The present study uses data from the Phase 3 of the 1000 genomes project focusing on two South Asian populations-GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK), so as to decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations. METHODS: Statistical tests included were (1) tests to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima's D, Fay and Wu's H and Fu and Li's D* and F*), (2) tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb), and (3) tests based on genetic differentiation between populations (LSBL). RESULTS: Twenty-two pigmentation genes fall in the top 1% for at least one statistic in the GIH population, 5 of which (LYST, OCA2, SLC24A5, SLC45A2, and TYR) have been previously associated with normal variation in skin, hair, or eye color. In comparison, 17 genes fall in the top 1% for at least one statistic in the ITU population. Twelve loci which are identified as outliers in the ITU scan were also identified in the GIH population. CONCLUSIONS: These results suggest that selection may have affected these loci broadly across the region.
OBJECTIVES:Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing to phenotypic variation in skin pigmentation within and among South Asian populations are still poorly understood. The present study uses data from the Phase 3 of the 1000 genomes project focusing on two South Asian populations-GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK), so as to decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations. METHODS: Statistical tests included were (1) tests to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima's D, Fay and Wu's H and Fu and Li's D* and F*), (2) tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb), and (3) tests based on genetic differentiation between populations (LSBL). RESULTS: Twenty-two pigmentation genes fall in the top 1% for at least one statistic in the GIH population, 5 of which (LYST, OCA2, SLC24A5, SLC45A2, and TYR) have been previously associated with normal variation in skin, hair, or eye color. In comparison, 17 genes fall in the top 1% for at least one statistic in the ITU population. Twelve loci which are identified as outliers in the ITU scan were also identified in the GIH population. CONCLUSIONS: These results suggest that selection may have affected these loci broadly across the region.
Authors: Nicholas G Crawford; Derek E Kelly; Matthew E B Hansen; Marcia H Beltrame; Shaohua Fan; Shanna L Bowman; Ethan Jewett; Alessia Ranciaro; Simon Thompson; Yancy Lo; Susanne P Pfeifer; Jeffrey D Jensen; Michael C Campbell; William Beggs; Farhad Hormozdiari; Sununguko Wata Mpoloka; Gaonyadiwe George Mokone; Thomas Nyambo; Dawit Wolde Meskel; Gurja Belay; Jake Haut; Harriet Rothschild; Leonard Zon; Yi Zhou; Michael A Kovacs; Mai Xu; Tongwu Zhang; Kevin Bishop; Jason Sinclair; Cecilia Rivas; Eugene Elliot; Jiyeon Choi; Shengchao A Li; Belynda Hicks; Shawn Burgess; Christian Abnet; Dawn E Watkins-Chow; Elena Oceana; Yun S Song; Eleazar Eskin; Kevin M Brown; Michael S Marks; Stacie K Loftus; William J Pavan; Meredith Yeager; Stephen Chanock; Sarah A Tishkoff Journal: Science Date: 2017-10-12 Impact factor: 47.728