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

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.

Fig 1. Forensic parameters of Guizhou Han and Meta-Han Chinese population.

Parameters were calculated on the basis of allele frequencies in females (A), males (B) and pooled population (C). Forensic parameters estimated based on the haplotype frequencies in males (D).

Fig 2. Genetic structure and population relationship between Guizhou Han and other four Han Chinese population.

(A) Principal component analysis (PCA) revealed the genetic relationship on the basis of the first two components; (B) Multidimensional scaling plots showed the Han population relationship on the basis of Nei’s genetic distances; (C) A Neighbor-Joining tree reveled the phylogenetic relationship of Han Chinese populations; and (D) Genetic structure revealed by Structure among Han female populations.

Fig 3. Principal component analyses between Guizhou Han and other 19 Chinese reference populations.

(A) PCA was constructed on the basis of PCA1 and PCA2; and (B) Dimensional PCA plots were established according PCA2 and PCA3.

Fig 4. Multidimensional scaling plots showed the genetic relationship among 20 populations belonging to four language families.

Fig 5. Phylogenetic tree showed the population relationship between Guizhou Han and other 19 reference populations on the basis of Neighbor-Joining algorithm.

Fig 6. Genetic differences and similarities between Meta-Han Chinese population and other 15 reference populations.

(A) PCA was constructed based on the first two components; (B) MDS was visualized on the basis of the pairwise Reynolds’s genetic distance matrix; (C) Neighbor-Joining tree showed the genetic homogeneity and heterogeneity between Han Chinese and Chinese minority groups.