Genetic features and phylogenetic relationship analyses of Guizhou Han population residing in Southwest China via 38 X-InDels

PeerJ. 2023 Mar 8:11:e14964. doi: 10.7717/peerj.14964. eCollection 2023.

Abstract

Background: The insertion/deletion polymorphism (InDel), an ideal forensic genetic marker with a low spontaneous mutation rate and small amplification product fragments, is widely distributed in the genome, combining the advantages of STR and SNP genetic markers. The X-chromosome has high application value in complex paternity testing, and it is an excellent system for evaluating population admixture and studying evolutionary anthropology. However, further research is needed on the population genetics of X-chromosome InDels (X-InDels).

Methods: In this article, a system composed of 38 X-InDel loci was utilized to analyse and evaluate the forensic parameters of the Guizhou Han population in order to explore its forensic application efficiency.

Results: The results showed that expected heterozygosities spanned from 0.0189 to 0.5715, and the cumulative power of discrimination of the 32 X-InDels and three linkage blocks was 0.9999999954 and 0.999999999999741 for males and females, respectively. The combined mean exclusion chance of these loci for trios and duos is 0.999999 and 0.999747, respectively. Multiple methods like principal component analysis, Fst genetic distance, and phylogenetic reconstruction were employed for dissecting the genetic structure of the Guizhou Han population by comparing it with previously reported populations. As expected, the studied Han population displayed relatively close genetic affinities with the East Asian populations. At the same time, there were obvious genetic differentiations between the Guizhou Han population and other continental populations that were discerned, especially for the African populations.

Conclusions: This study further verified the applicability of 38 X-InDels for human personal identification and kinship analyses of Han Chinese, and also showed the application potential of X-InDels in population genetics.

Keywords: Forensic features; Guizhou Han; InDel; Population genetics; X-chromosome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • China
  • Female
  • Gene Frequency
  • Genetics, Population*
  • Humans
  • Male
  • Phylogeny
  • Polymorphism, Genetic* / genetics

Grants and funding

This study was supported by the Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Open Project, KF202207; the Guizhou Provincial Science and Technology Projects (ZK[2022] General 355); the Guizhou Education Department Young Scientific and Technical Talents Project, Qian Education KY No. [2022]215; the Guizhou Scientific Support Project, Qian Science Support [2021] General 448; the Guizhou Province Education Department, Characteristic Region Project, Qian Education KY No. [2021]065; the Guizhou “Hundred” High-level Innovative Talent Project, Qian Science Platform Talents [2020]6012; the Guizhou Scientific Support Project, Qian Science Support [2020] 4Y057; the Guizhou Scientific Support Project, Qian Science Support [2019] 2825; the Guizhou Engineering Technology Research Center Project, Qian High-Tech of Development and Reform Commission No. [2016] 1345; the Guizhou Innovation training program for college students S202210660030; National Natural Science Foundation (No. 82160324); the Guizhou Science Project, Qian Science Foundation [2020] 1Y353; the Guizhou Scientific Cultivation Project, Qian Science Platform Talent [2018] 5779-X. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.