Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

Caiyong Yin; Kaiyuan Su; Ziwei He; Dian Zhai; Kejian Guo; Xueyun Chen; Li Jin; Shilin Li

doi:10.3390/genes11070743

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

Genes (Basel). 2020 Jul 3;11(7):743. doi: 10.3390/genes11070743.

Authors

Caiyong Yin^{1

2}, Kaiyuan Su^{1

2}, Ziwei He^{1

2}, Dian Zhai³, Kejian Guo^{1

4}, Xueyun Chen³, Li Jin^{1

2}, Shilin Li^{5

6}

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 Yunnan Province, Kunming 650021, China.
⁴ Public Security Bureau of Zibo City, Zibo 255000, China.
⁵ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China.
⁶ Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.

Abstract

Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male-female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler^™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants ("DYS518~.2" alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.

Keywords: Y-SNP; Y-STR; population differentiation; population investigation.

Publication types

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

MeSH terms

China
Chromosomes, Human, Y / genetics*
Forensic Genetics / methods*
Genotyping Techniques / methods
Humans
Male
Microsatellite Repeats*
Pedigree
Polymorphism, Single Nucleotide*
Population / genetics*