Population genetic study of 34 X-Chromosome markers in 5 main ethnic groups of China

Identification of the genetic information of populations is an important task for which different types of genetic markers can be used, including autosomal1,2, mtDNA2,3, Y-Chromosome2,3,4 and X-Chromosome5,6,7. The use of autosomal markers is a typical strategy to disclose population patterns, as these markers account for both paternal and maternal inheritance. Nevertheless, X-Chromosome is gaining significant importance in population and forensic genetic studies due to the special transmission property5,6,7. The X-Chromosome is transmitted between both sexes in each generation, telling a different story from uniparental genomes. Moreover, its effective population size is reduced in relation to autosomes, making it more sensitive to the effects of population substructure and genetic drift6,7. And X-Chromosome markers show higher efficiency parameters than autosomes in special kinship investigations involving mainly female offspring, making them suitable for forensic application6,7. Thus, growing number of scientists is becoming interested in X-Chromosome research, using X markers (X-STRs, X-SNPs and more recently X-Indels) for studying the genetic structure of human populations, ancestry proportions in admixed populations as well as for forensic investigations5,6,7,8,9. Genetic markers of STRs or SNPs are predominantly applied to dissect patterns of genetic variation for human genetic studies. Indels represent another type of DNA variation that is increasingly studied and applied in genetics6,8,9. However, studies of X-Chromosome markers in Chinese population have only been related to genetic parameters, home-system development or evaluation. As a large united multi-ethnic state, composed of 56 ethnic groups, studies on the genetic background of China are necessary. This study was focused on 5 main ethnic groups, including HAN and 4 main minority ethnic groups (HUI, Uygur, Mongolian and Tibetan). HAN Chinese account for almost 92% of China’s population, and make up roughly 20% of the international population, making it the world’s largest ethnic group. Here, HAN population in Shanghai City was chosen to be studied since the highest proportion of Shanghai’s residents are members of China’s vast floating population. Additionally, the 4 minority ethnic groups are mainly located in Northwest of China. All of them have populations of more than 5 million according to 2010 national data and are regarded as typical examples of Chinese ethnic minorities. The detail location of each ethnic group is depicted in Supplementary Fig. S1. Some Chinese investigators have examined population differentiation and admixture patterns for Chinese ethnic groups and some Central Asian populations with mtDNA or Y chromosomes10,11. Previous studies demonstrated that high genetic differentiation exists among Chinese ethnic groups and that the gene flow and genetic admixture are very complex. Addressing major issues in the field of human genetics requires multiple types of genetic markers, various analytical methods and statistical models. In the present study, a set of 34 X- chromosomal markers (16 X-STRs and 18 X-Indels) was evaluated in the 5 main ethnic groups of China. The 4 minority ethnic groups along the Silk Road in the Northwest of China display clear differences in culture and social customs, perhaps as a result of geographic isolation and different traditions. However, extensive trade and interactions probably facilitated the admixture of different gene pools between these ethnic groups over the last two millennia. The aim was to obtain detailed genetic information of the 34 X-Chromosome markers and to improve the current knowledge on the genetic background of the 5 ethnic groups of China.