Y-chromosome Evidence: Genetic Structure Analysis Among Populations From Southern Littoral And North-central Esophageal Cancer High-risk Areas In China

BackgroundChaoshan, Fujian and Henan Taihang Mountain EC high-risk areas were geographically distant and furthermore their living environment was very diverse, but they were all famous for their high incidence and mortality rate for EC, and populations among these regions share similar pedigree of malignancy. According to historical records, Han inhabitants of north-central China (Henan and Shanxi Hans) continuously migrated into Chaoshan area via Fujian due to warfare and famines, and gradually became the predominant inhabitants of Chaoshan area, which were confirmed by the records on genealogy, stone tablet and archaeological discovery and the language-speaking. Therefore we hypothesized that these three EC high-risk populations might share common genetic traits and descended from a recent common ancestor.ObjectivesTo obtain the polymorphism information of Y-chromosome DNA on the four studied populations and provide the patrilineal genetic evidence to verify our hypothesis. In the same time, it also could provide the reference data for individual identification in the three study areas and would abundant the Y-chromosome database among these regions。Methods1. 16 SNP loci that were highly informative in East Asians and 7 STR markers were selected to study. Three strategies were introduced to type Y-SNP and Y-STR. For SNPs without length changes, was typed using PCR-RFLP assay. For SNPs with length variation, and Y-STRs, fluorescence PCR was used. The product of PCR was electrophoresed on a 3100 genetic analyzer to type. Genotype of M1 was conducted by agarose gel electrophoresis directly after PCR. Y-SNP haplogroup and Y-STR haplotype assignments were made based on the three typing results.2. The Y-SNP haplogroup of every individual was defined according to the typing results and following the Y-chromosome consortium nomenclature. Their frequencies and diversities were calculated and compared among the three EC high-risk populations and Chaoshan area EC high-risk populations. Chi-square test was performed to show the difference of haplogroup distribution in the studied populations. Meanwhile, the allele diversity values (DP) and the haplotype diversity for each Y-STR locus was directly calculated.3. Principal component analysis and correlation analysis were carried out to show the genetic affinity among the three EC high-risk populations and other groups for comparision. The paternal genetic relationship among the EC high-risk populations was further displayed by hierarchical cluster analysis. The extent of genetic differentiation of the populations was estimated by the Rst statistic on the basis of the Y-STR haplotypes. Neighbor joining tree was constructed according to the Rst distance matrix to show the phylogenic structure among the populations. O2a* and O3e1 haplogroup network was drawn to show the detailed difference and association among the four studied populations and other populations for compared.Results1. O3*, O3e* and O3e1*, sharing M122 mutation, were the predominant haplogroups in the three high-risk populations. The overall frequencies of these three haplogroups in Taihang mountain, Fujian and Chaoshan EC high-risk populations were 60.42%, 66.22% and 65.16%, respectively. X2 test showed no significant difference among them (p>0.05). These three haplogroups were also frequent in Chaoshan area EC population (30.0%), but they were significantly lower than those in the three EC high-risk populations (p<0.05). In addition, haplogroup O2a* was more frequent in Chaoshan area EC population than in EC high-risk populations (p<0.05).2. Principal component analysis was carried out among the populations of all three studied areas and other five language families'populations in East Asia. Using the values of PC1 and PC2 as height values, the principal components plot was drawn. The result showed that those from the three studied areas clustered together in the rightmost part of the PC map, especially the three EC high-risk populations. They all located among Sino-Tibetan population. Correlation analysis displayed that only haplogroup O3e* was consistent with the distribution of Sino-Tibetan populations. 3. Principal component and hierarchical clustering analysis based on the Y-SNP and Y-STR frequencies among populations coming from the three studied areas and other regions of China displayed that the four studied populations formed a distinctive cluster. Correlation analysis showed that haplogroup frequency distribution in the Chaoshan EC high-risk population was significantly positively correlated to those in the Taihang Mountain and Fujian EC high-risk populations. Chaoshan area EC patients were also significantly positively correlated to Taihang Mountain high-risk population.4. Rst values showed a close relationship among Taihang Mountain,Fujian and Chaoshan high-risk population. The close genetic affinity among the three high-risk populations was also displayed by the N-J phylogeny.5. O2a* network analysis showed that compared with other Chinese and East Asia populations, populations in the three studied areas formed a close cluster and distributed at the edge of the network. O3el haplogroup network showed that the O3e1 individuals from the three studied areas shared the same Y-STR mutations in the central and sub-central node of the network.6. The allele diversity values (DP) of these loci was higher than 0.5 except for that of DYS391 in the four studied populations and DYS389II in Chaoshan area EC patients. The haplotype diversity for the seven Y-STRs was all above 0.980.Conclusions1. Taihang Mountain, Fujian and Chaoshan EC high-risk populations were all typical Sino-Tibetan population. They might share similar patrilineal genetic background and descended from a recent common ancestor, which also confirmed that our hypothesis on genetic backgroundd of Chaoshan EC high-risk population was relatively creditable.2. Chaoshan area EC population also showed closer genetic affinity with the three high-risk populations, however, it might have more gene flow between the ancestor of Chaoshan area EC population and the Baiyue populations. Esophageal cancer might not occur randomly in Chaoshan area population. Haplgroups O2a* might be a candidate genetic background marker for screening population susceptible to EC in Chaoshan area.3. The 7 Y-STR loci had high discriminating ability and their haplotypes were highly polymorphic in the three studied area populations. They were suitable for forensic individual identification and paternity testing.