Forensic characterization and genetic polymorphisms of 19 X-chromosomal STRs in 1344 Han Chinese individuals and comprehensive population relationship analyses among 20 Chinese groups.

Pengyu Chen,Fuquan Jia,Jida Li,Xing Zou,Mengge Wang,Guanglin He,Jian Yu,Yanyan Han,Huiru Bai,Chuan-Chao Wang

doi:10.1371/journal.pone.0204286

Pengyu Chen, Fuquan Jia + Show 8 more

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https://doi.org/10.1371/journal.pone.0204286

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Abstract

X-chromosomal short tandem repeats (X-STRs) may assist resolution of complex forensic kinship cases and complement autosomal and Y-chromosomal STRs in routine forensic practice and population genetics. In the present study, we investigated the allele/haplotype diversity and forensic genetic characteristics of 19 X- STRs in 206 Guizhou Han and 1344 Meta-Han Chinese individuals using AGCU X19 PCR amplification system. Population relationships within five Han Chinese population groups (1344 individuals), between Guizhou Han and other 19 Chinese reference populations belonging to four language families (5074 individuals), as well as between Meta-Han Chinese and other 15 minorities (3730 individuals) were performed using Reynolds’s, Nei’s and Fst genetic distances, principal component analysis (PCA), multidimensional scaling (MDS), Structure and Neighbor-Joining tree. Mean paternity exclusion chance (MEC) in Duos > 0.99999999453588 and in trios > 0.99999999999781, as well as power of discrimination (PD) > 0.99999999999980 in Guizhou Han on the basis of allele frequencies. Consistent high MECs and PDs can be observed in Meta-Han Chinese population based on both allele diversities of 19 markers and haplotype diversities of seven linkage groups (LG). DXS10135 and LG1 are the most informative and polymorphic in Han Chinese group. The comprehensive population comparisons reveal that Han Chinese is a homogenous population and has the genetically closer relationship with Hmong-Mien-speaking groups than Tibetan-Burman-speaking and Turkic-speaking populations. In summary, AGCU X19 PCR amplification system is highly polymorphic and informative in Guizhou Han and Han Chinese populations. The comprehensive population data from 20 Chinese populations analyzed in this study may be used as a reference Chinese frequency database of X-STRs for forensic casework applications.

Highlights

Short tandem repeats (STRs), known as microsatellites and composed of repeating 2–6 base pair motifs, are highly variable variants with the number of approximately 700,000 in the human genome, play a pivotal role in population genetics, anthropology, genetic genealogy and forensics
Tremendous progresses have been made in exploring the genetic variations and establishing the forensic reference database of 12 X-chromosomal short tandem repeats (X-STRs) included in the Investigator1 Argus X-12 Kit in China [14, 17], while forensic information focused on 19 X-STRs included in the AGCU X19 kit in Chinese ethnically/geographically diverse populations keep largely underrepresented [19,20,21,22,23,24,25,26,27,28,29].Han Chinese, who traces a common ancestry to the initial Neolithic Huaxia agricultural confederation residing in Yellow River and shares and exchanges culture and language with non-Han Chinese population when Huaxia culture continuous expansion toward southern China, exceeds 1.3 billion in the world and 1.282 billion in China (2010 census) [30, 31]
Autosomal STRs have been the gold standard in forensic science and much effort has been made based on the genetic variations of autosomal or Ychromosomal STRs in diverse populations [51,52,53,54,55,56], X-STRs have begun to draw more attention by forensic scientist with the appearance of Investigator1 Argus X-12 and AGCU X19 STR Kits

Summary

Introduction

Short tandem repeats (STRs), known as microsatellites and composed of repeating 2–6 base pair motifs, are highly variable variants with the number of approximately 700,000 in the human genome, play a pivotal role in population genetics, anthropology, genetic genealogy and forensics. AGCU X19 amplification system (AGCU ScienTech Inc., Wuxi, Jiangsu, China) was designed to facilitate the X-STRs into the applications of forensic routine cases This system is a five-dye, multiplex that allows co-amplification and fluorescent detection of 19 loci belonging to seven linkage groups (LG), in which DXS10148, DXS10135 and DXS8378 comprise the LG1 [11, 12], DXS10159, DXS10162 and DXS10164 comprise the LG2 [13], DXS7132, DXS10079, DXS10074 and DXS10075 comprise the LG3 [14], DXS6809 and DXS6789 comprise the LG4 [15], DXS7424 and DXS101 comprise the LG5 [16], DXS10103, HPRTB and DXS10101 comprise the LG6 [12], and DXS10134 and DXS7423 comprise the LG7 [14]. Han Chinese nowadays account for more than 60% of the population in Guizhou and are mostly the descants of the ancient Han soldiers, who massively moved into Guizhou during the 8th and 9th centuries in the Tang Dynasty (https://en.wikipedia.org/wiki/Guizhou)

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