Population Genetic Diversity and Clustering Analysis for Chinese Dongxiang Group With 30 Autosomal InDel Loci Simultaneously Analyzed.

Bofeng Zhu,Yuxin Guo,Xiaoye Jin,Qiong Lan,Wei Cui,Tong Xie,Yongsong Zhou,Chong Chen,Yating Fang,Xiaogang Li

doi:10.3389/fgene.2018.00279

Abstract

In comparison with the most preferred genetic marker utilized in forensic science (STR), insertion/deletion analysis possesses further benefits, like absence of stutter peak, low mutation rate, and enabling mixed stain analysis. At present, a total of 169 unrelated healthy Dongxiang individuals dwelling in Dongxiang Autonomous county of Gansu province were recruited in our study to appraise the forensic usefulness of the panel including 30 autosomal diallelic genetic markers. The insertion allele frequencies were in the range of 0.1598 at HLD 111 to 0.8550 at HLD 118. The cumulative match of probability and the combined probability of exclusion were estimated based on independence of pairwise loci, with the values of 3.96 × 10-11 and 0.9886, respectively, which showed tremendous potential of this panel to be qualified for forensic personal identification in Chinese Dongxiang group. And it could also be used as a complementary tool for forensic parentage testing when combined with standard STR genetic markers. Furthermore, calculation of the DA distance and Fst values of pairwise populations, phylogenetic reconstruction, multidimensional scaling analysis, structure clustering analysis were also conducted to probe the genetic relationships between Dongxiang group and the other 30 reference populations. Results demonstrated that Dongxiang ethnic group might be genetically closer related with most Chinese populations involved in our study, especially Tibet groups, Xibe group, and several Han populations.

Highlights

Insertion/deletion (InDel) polymorphic genetic marker characterized by abundance in the genome, relative low mutation rate, small amplicon size, and compatibility with current genotyping platform (Wei et al, 2014) is gradually becoming a possible alternative approach for forensic amplifications to overcome some inevitable limitations of traditional STRs, such as stutterPopulation Genetic Diversity Analysis products, high mutation rate, and so on
In combination with the results of Hardy–Weinberg Equilibrium (HWE) tests and Linkage disequilibrium (LD) analysis, we concluded that our population data were representative and the 30-InDel loci were independent of each other
The product law could be unquestionably utilized to calculate the cumulative match of probability (CMP) and cumulative probability of exclusion (CPE)

Summary

Introduction

Population Genetic Diversity Analysis products, high mutation rate, and so on. It has been proved that the InDels could be useful in human identification (Pereira et al, 2009), mixed stain identification and deconvolution (Oldoni et al, 2017), as well as population genetic analysis including biogeographic ancestry inference and population substructure determination (Santos et al, 2010). Sun et al (2016) verified the considerable potency of a multi-InDel panel in ancestry inference of subpopulations in China and Caputo et al (2017) reported the potential use of a 33 X-InDel panel in Argentina populations. Data in existence did not incorporate Dongxiang ethnic minority in Gansu province of China. That’s the reason why we chose Dongxiang group as our research subject

Methods

Results

Conclusion