Association of pigmentation related-genes polymorphisms and geographic environmental variables in the Chinese population

Background Human skin color is highly heritable and one of the most variable phenotypic traits. However, the genetic causes and environmental selective pressures underlying this phenotypic variation have remained largely unknown. To investigate whether the pigmentation related-genes polymorphisms are associated with the geographic environmental variables. We selected randomly 795 healthy individuals from eight ethnic groups in nine provinces in China. Six single nucleotide polymorphisms (SNPs) of SLC45A2 and TYR were genotyped using Agena MassARRAY. The Chi-square test and Spearman correlation analysis were used to compare the frequency distribution of genotypes among different ethnic groups and evaluate the relationship between SNP genetic diversity and environmental variables, respectively. Results The results indicated that rs28777 and rs183671 (SLC45A2) and rs1042602 (TYR) genotype frequency distributions were significantly different between the Xinjiang-Uighur and other ethnic groups (P < 0.05). Spearman correlation analysis found that rs28777-A (r = − 0.090, P = 0.011), rs183671-G (r = − 0.105, P = 0.003), rs1042602-A (r = − 0.108, P = 0.002), rs1126809-A (r = − 0.151, P < 0.001) allele frequencies were negatively correlated with the longitude; rs183671-G (r = 0.151), rs1042602-A (r = 0.157) and rs1126809-A (r = 0.138) allele frequencies were positively associated with the latitude (P < 0.001); rs183671-G (r = 0.116, P = 0.001), rs1042602-A (r = 0.105, P = 0.003) and rs1126809-A (r = 0.070, P = 0.048) allele frequencies were positively correlated with the sunshine hours; rs183671-G (r = − 0.076, P = 0.033), rs1042602-A (r = − 0.079, P = 0.027) and rs1126809-A (r = − 0.076, P = 0.031) were negatively correlated with the annual average temperature. Conclusions Our results confirmed the idea that environmental factors have been an important selective pressure upon pigmentation related gene polymorphisms. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-021-00189-7.


Introduction
Human skin color is highly heritable and one of the most variable phenotypic traits that can vary dramatically within and across ethnic populations [1]. It is known that the human skin color is predominantly determined by pigments include melanin, hemoglobin (red), hemosiderin (brown), carotene (yellow), and bilirubin (yellow) [2]. Among those, the amount, the type, and the distribution of melanin play key roles in determining human skin pigmentation. The studies indicate that the human skin pigmentation in global populations is highly associated with latitude, and fundamentally, the distribution of ultraviolet (UV) radiation [3,4]. Moreover, the researchers believe that geographic variation in skin pigmentation was in uenced by the concerted action of different types of natural selection, including climate, lifestyle, diet, metabolism [1]. However, the genetic causes and environmental selective pressures underlying this range of skin color variation have remained largely unknown.
With the rapid development of genetics and genomics, researchers have gradually realized that the human skin color diversity is due to the natural positive selection of those genes that impact on human pigmentation, especially in the melanosome biogenesis or the melanin biosynthetic pathways [5,6]. Recently, a large number of genome-wide association studies (GWAS) for pigmentation have been established and identi ed that some single nucleotide polymorphisms (SNPs) on TYR, IRF4, TYRP1, OCA2, SLC45A2, MC1R and KITLG genes are signi cantly associated with human skin color [7][8][9][10]. The SLC45A2 (solute carrier family 45, member 2) gene encodes the membrane associated transporter protein (MATP). The SLC45A2 protein expresses in melanocyte cell lines and mediates melanin synthesis by tyrosinase tra cking and proton transportation to melanosomes [11]. SLC45A2 mutations cause oculocutaneous albinism type IV (OCA4) and polymorphisms of this gene are associated with dark skin, hair, and eye pigmentation. [12,13]. In addition, the TYR gene encodes tyrosinase, a multifunctional enzyme that plays a major role in melanin biosynthesis in melanocytes [14]. TYR is commonly known as the albino locus since the homozygous or compound heterozygous mutations of this gene result in oculocutaneous albinism type 1 (OCA1), an autosomal recessive genetic disorder characterized by hypopigmented hair, skin and eyes [15]. The six SNPs (rs11568737, rs28777 and rs183671 in the SLC45A2 gene and rs1042602, rs1393350 and rs1126809 in the TYR gene) were successfully genotyped from 795 samples (call rate > 95%). The basic information (SNP-ID, chromosome number, position, alleles and gene name) and polymerase chain reaction (PCR) primer sequence (1st-PCRP, 2nd-PCRP and UEP-SEQ) of the six SNPs was showed in Table 2. The MAF and HWE-P value of each SNPs are shown in Supplementary Table 1 and Supplementary Table 2, respectively. The results showed that except for rs1393350 in TYR was not in accordance with the HWE in Uighur (P < 0.01), other ve SNPs were in accordance with the HWE in the nine groups (P > 0.01). In addition, we used the chi-square test to evaluate the difference of genotype frequency distribution of the ve SNPs among 8 ethnic groups, as shown in Table 3. The results indicated that the genotype frequency distribution of rs28777 and rs183671 (SLC45A2) and rs1042602 (TYR) were signi cantly different between the Xinjiang-Uighur and other ethnic groups (P < 0.05). The allele frequency distribution of these three signi cantly different SNPs was shown in Fig. 1. Simultaneously, we analyzed the relationship between SNP genetic diversity and environmental variables using Spearman correlation analysis (Table 4). It was found that the allele frequencies of rs28777 (r = -0.090, P = 0.011), rs183671 (r = -0.105, P = 0.003), rs1042602 (r = -0.108, P = 0.002), rs1126809 (r = -0.151, P < 0.001) were negatively correlated with the longitude. However, the positive correlation between the alleles frequencies of rs183671 (r = 0.151), rs1042602 (r = 0.157) and rs1126809 (r = 0.138) and the latitude were extremely signi cant (P < 0.001). The alleles frequencies of rs183671 (r = 0.116, P = 0.001), rs1042602 (r = 0.105, P = 0.003) and rs1126809 (r = 0.070, P = 0.048) were found to be signi cantly positively correlated with the sunshine hours. However, the alleles frequencies of rs183671 (r = -0.076, P = 0.033), rs1042602 (r =-0.079, P = 0.027) and rs1126809 (r = -0.076, P = 0.031) were signi cantly negatively correlated with the annual average temperature. The correlations between the allele frequencies of other SNPs and environmental variables were not signi cant. These ndings indicate that environmental factors have selective pressure on these SNPs.

Discussion
To investigate whether the pigmentation related genes (SLC45A2 and TYR) polymorphisms are associated with the geographic environmental variables (altitude, longitude, latitude, and air pressure, sunshine hours, and annual average temperature), we selected randomly selected 795 healthy individuals from eight ethnic groups in nine provinces in China. The results of this study found that the genotype frequency distribution of rs28777 and rs183671 in SLC45A2 and rs1042602 in TYR were signi cantly different between the Xinjiang-Uighur and other ethnic groups (P < 0.05). Simultaneously, the rs28777, rs183671, rs1042602, rs1126809 polymorphisms were found to be correlated with the geographic environmental variables (longitude, latitude, sunshine hours or annual average temperature).
SLC45A2 (as also AIM1 or MATP) encodes a transporter protein that mediates melanin synthesis, which is expressed in a high percentage of melanoma cell lines. It has been reported that some SLC45A2 mutations cause OCA4 and polymorphisms of this gene were found to be signi cantly associated with human skin, hair, and eye pigmentation, and its mutation frequency varies signi cantly among the global population. Yuko Abe et al. found that rs11568737 in SLC45A2 (T500P) was signi cantly associated with melanin index [16]. A multi-stage GWAS of natural hair color in European ancestry found that the SNP rs28777 in the SLC45A2 gene was associated with skin color and tanning ability [17]. A large Australian population-based case control study reveal that rs28777 exhibited the strongest crude association with risk of cutaneous malignant melanoma [18]. The rs183671 in the SLC45A2 gene is in strong linkage disequilibrium (LD) with rs16891982 (F374L) in CEU. A previous GWAS declared that the frequency of the rs183671 derived allele increased from Southern to Northern Europe, and this SNP was associated with skin pigmentation, and that each copy of the derived allele lightens the skin by 1.2 M index units [19].
Moreover, a previous GWAS demonstrated that the SNP rs183671 can explain skin color variation in three European studies RS, BTNS, and TwinsUK [20].
TYR is located at human chromosome 11q14.3, and encodes tyrosinase, which regulates the biosynthesis of melanin. Previous studies demonstrated that mutations in TYR can cause OCA1 [15]. The non-synonymous polymorphism rs1042602 (Ser192Tyr) in TYR derived allele has speci cally high frequency in Europe, and this SNP was signi cantly associated with eye color, freckles and lighter skin pigmentation [21][22][23][24]. The TYR SNP rs1393350 was found to be associated with human hair, eye and skin color and tanning ability [23,[25][26][27]. A GWAS of melanoma conducted by the GenoMEL consortium identi es the locus rs1393350 associated with melanoma risk [28]. The rs1126809 variant is located in exon 4 of TYR gene and encodes a tyrosinase enzyme with an arginine-to-glutamine substitution at codon 402 (R402Q), and is in LD with rs1393350 [29,30]. The mutation of rs1126809 (A-G) causes the TYR enzyme to be thermosensitive, thus less active [31]. The rs1126809 has previously been used as a marker for skin pigmentation and also in uence brown eye colour formation [23,30]. Previous GWAS indicated that the allele A of rs1042602 (TYR) was highly associated with lighter skin color in a South Asian descent population [32]. In has reported that the allele A of rs1042602 was over-represented in the Indo Europeans population [33]. The two polymorphisms (rs1042602 and rs1126809) in TYR appear at high frequency in Europeans and are largely absent in African populations [34].
This study indicated that the genotype frequency distribution of rs28777 and rs18367 in Xinjiang-Uighur were signi cantly different from other ethnic groups. Moreover, the allele frequencies of rs28777, rs183671, rs1042602, rs1126809 were negatively correlated with the longitude; rs183671, rs1042602 and rs1126809 allele frequencies were positively associated with the latitude and the sunshine hours, while were negatively correlated with the annual average temperature in Chinese population. At present, there are few research reports on the association between genetic polymorphism and environmental factors. In 2010, Ji et al. [35] found that the disease-predisposition polymorphisms of the melatonin receptors were associated with sunshine duration in the global human populations. These results indicated that environmental factors had selective pressure on these loci, and their changes were related to environmental variables, that is, differences in selection caused by differences in environmental factors play an important role in genetic differentiation.
However, this study has some limitations that cannot be ignored. First, the sample size is small and the statistical power is relatively low. Second, this study is the rst to explore the correlation between the allele frequencies of these six SNPs and geographical environmental factors. Third, we only selected 6 SNP loci on two genes to explore their correlation with geographical environmental factors. Finally, this study did not design gene functional experiments to explore how allelic variations at SNPs loci lead to the diversity of skin color phenotypes in the human population. Therefore, we will further collect a larger sample and choose more SNPs and design functional experiments to explore the impact of environmental factors on genetic mutations.

SNP selection and genotyping
We randomly selected the six SNPs (rs11568737, rs28777 and rs183671 in the SLC45A2 gene and rs1042602, rs1393350 and rs1126809 in the TYR gene) based on previously published genes related to pigmentation. The online software Agena Bioscience Assay Design Suite Version 2.0 (https://agenacx.com/online-tools/) was used to design the primers sequence (