Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs

Xiao Zhang; Zhen Tang; Bin Wang; Xindao Zhou; Limin Zhou; Gongying Zhang; Junzhe Tian; Yiqi Zhao; Zhiqing Yao; Lu Tian; Suhua Zhang; Hao Xia; Li Jin; Chengtao Li; Shilin Li

doi:10.3390/genes13081363

Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs

Genes (Basel). 2022 Jul 29;13(8):1363. doi: 10.3390/genes13081363.

Authors

Xiao Zhang^{1

2}, Zhen Tang^{1

2}, Bin Wang³, Xindao Zhou⁴, Limin Zhou⁴, Gongying Zhang³, Junzhe Tian^{1

2}, Yiqi Zhao^{1

2}, Zhiqing Yao³, Lu Tian³, Suhua Zhang⁵, Hao Xia⁶, Li Jin^{1

2}, Chengtao Li⁵, Shilin Li^{1

2}

Affiliations

¹ Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China.
² Human Phenome Institute, Fudan University, Shanghai 200438, China.
³ Criminal Investigation Department of Shanghai, Pudong New Area, Shanghai 200120, China.
⁴ Criminal Investigation Department of Shanghai, Chongming Island, Shanghai 202150, China.
⁵ Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China.
⁶ School of Mathematical Sciences, Tongji University, Shanghai 200092, China.

Abstract

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation.

Keywords: Chongming island; Y-SNP; Y-STR; population differentiation.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

China
Chromosomes, Human, Y* / genetics
Ethnicity / genetics
Genetics, Population
Humans
Male
Microsatellite Repeats
Phylogeny
Polymorphism, Single Nucleotide* / genetics

Grants and funding

This study was supported by the grants from the National Natural Science Fund of China (81930056), National Youth Top-notch Talent of Ten Thousand Program (WRQB2019), and the Youth Science and Technology Innovation Leader of Ten Thousand Program (2018RA2102). The funders had no role in study design, data analysis, publishing decisions, or manuscript preparation.