Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch
Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and foreh...
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MDPI AG
2021-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/5/733 |
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| author | Muhammad Adnan Shan Olivia Strunge Meyer Mie Refn Niels Morling Jeppe Dyrberg Andersen Claus Børsting |
| author_facet | Muhammad Adnan Shan Olivia Strunge Meyer Mie Refn Niels Morling Jeppe Dyrberg Andersen Claus Børsting |
| author_sort | Muhammad Adnan Shan |
| collection | DOAJ |
| description | Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals also had an average proportion of Sub-Saharan African ancestry of approximately 10%, whereas it was <1% in the Punjabi and Pashtun individuals. The pairwise genetic distances between the Pashtun, Punjabi, and Baloch subpopulations based on the ancestry markers were statistically significantly different. Individuals from the Pashtun subpopulation had statistically significantly lower skin pigmentation than individuals from the Punjabi and Baloch subpopulations (<i>p</i> < 0.05). The proportions of European and Sub-Saharan African ancestry and five SNPs (rs1042602, rs10831496, rs1426654, rs16891982, and rs12913832) were statistically significantly associated with skin pigmentation at either the upper arm, lower arm or forehead in the Pakistani population after correction for multiple testing (<i>p</i> < 10<sup>−3</sup>). A model based on four of these SNPs (rs1426654, rs1042602, rs16891982, and rs12913832) explained 33% of the upper arm skin pigmentation. The four SNPs and the proportions of European and Sub-Saharan African ancestry explained 37% of the upper arm skin pigmentation. Our results indicate that the four likely causative SNPs, rs1426654, rs1042602, rs16891982, and rs12913832 located in <i>SLC24A5, TYR, SLC45A2,</i> and <i>HERC2,</i> respectively, are essential for skin color variation in the admixed Pakistani subpopulations. |
| first_indexed | 2024-03-10T11:27:10Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-10T11:27:10Z |
| publishDate | 2021-05-01 |
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| spelling | doaj.art-c6b906720c9c45f39879329ed587dc142023-11-21T19:33:52ZengMDPI AGGenes2073-44252021-05-0112573310.3390/genes12050733Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and BalochMuhammad Adnan Shan0Olivia Strunge Meyer1Mie Refn2Niels Morling3Jeppe Dyrberg Andersen4Claus Børsting5Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, DenmarkSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, DenmarkSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, DenmarkSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, DenmarkSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, DenmarkSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, DenmarkSkin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals also had an average proportion of Sub-Saharan African ancestry of approximately 10%, whereas it was <1% in the Punjabi and Pashtun individuals. The pairwise genetic distances between the Pashtun, Punjabi, and Baloch subpopulations based on the ancestry markers were statistically significantly different. Individuals from the Pashtun subpopulation had statistically significantly lower skin pigmentation than individuals from the Punjabi and Baloch subpopulations (<i>p</i> < 0.05). The proportions of European and Sub-Saharan African ancestry and five SNPs (rs1042602, rs10831496, rs1426654, rs16891982, and rs12913832) were statistically significantly associated with skin pigmentation at either the upper arm, lower arm or forehead in the Pakistani population after correction for multiple testing (<i>p</i> < 10<sup>−3</sup>). A model based on four of these SNPs (rs1426654, rs1042602, rs16891982, and rs12913832) explained 33% of the upper arm skin pigmentation. The four SNPs and the proportions of European and Sub-Saharan African ancestry explained 37% of the upper arm skin pigmentation. Our results indicate that the four likely causative SNPs, rs1426654, rs1042602, rs16891982, and rs12913832 located in <i>SLC24A5, TYR, SLC45A2,</i> and <i>HERC2,</i> respectively, are essential for skin color variation in the admixed Pakistani subpopulations.https://www.mdpi.com/2073-4425/12/5/733biogeographic ancestrypigmentationskin colorforensic DNA phenotypingexternally visible characteristics |
| spellingShingle | Muhammad Adnan Shan Olivia Strunge Meyer Mie Refn Niels Morling Jeppe Dyrberg Andersen Claus Børsting Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch Genes biogeographic ancestry pigmentation skin color forensic DNA phenotyping externally visible characteristics |
| title | Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch |
| title_full | Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch |
| title_fullStr | Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch |
| title_full_unstemmed | Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch |
| title_short | Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch |
| title_sort | analysis of skin pigmentation and genetic ancestry in three subpopulations from pakistan punjabi pashtun and baloch |
| topic | biogeographic ancestry pigmentation skin color forensic DNA phenotyping externally visible characteristics |
| url | https://www.mdpi.com/2073-4425/12/5/733 |
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