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. 2021 May 13;12(5):733.
doi: 10.3390/genes12050733.

Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch

Muhammad Adnan Shan  1   2 , Olivia Strunge Meyer  1 , Mie Refn  1 , Niels Morling  1 , Jeppe Dyrberg Andersen  1 , Claus Børsting  1
Affiliations

Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch

Muhammad Adnan Shan et al. Genes (Basel). .

Abstract

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 (p < 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 (p < 10-3). 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 SLC24A5, TYR, SLC45A2, and HERC2, respectively, are essential for skin color variation in the admixed Pakistani subpopulations.

Keywords: biogeographic ancestry; externally visible characteristics; forensic DNA phenotyping; pigmentation; skin color.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Boxplots of skin pigmentation measurements (pigment protection factor) of the upper arm, lower arm, and forehead in three Pakistani subpopulations. The pigment protection factor was measured in triplicate at each measured skin area.
Figure 2
Figure 2
STRUCTURE analysis with K = 4 using 160 ancestry informative markers (AIMs) and six meta-populations. Each cluster (K) is represented by a color. Population abbreviations used: SS Africa: Sub-Saharan Africa; N Africa: North Africa; M East: Middle East; SC Asia: South-Central Asia; E Asia: East Asia.
Figure 3
Figure 3
Cumulative correlations between (1) four SNPs and ancestry and (2) upper arm, lower arm, and forehead pigmentation. The SNPs were ranked based on their correlations with skin color (adjusted R2). Ancestry is the proportion of Sub-Saharan African and European ancestry.
Figure 4
Figure 4
Boxplots showing the skin color category predicted with the HIrisPlex-S prediction model and the pigmentation protection factor on the upper arm, lower arm, and forehead.
See this image and copyright information in PMC

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