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Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population

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Oncotarget. 2017; 8:55443-55452. https://doi.org/10.18632/oncotarget.19317

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Yao-Shun Liu, Jian-Gang Chen, Ting Mei, Yu-Xin Guo, Hao-Tian Meng, Jian-Fei Li, Yuan-Yuan Wei, Xiao-Ye Jin, Bo-Feng Zhu and Li-Ping Zhang _

Abstract

Yao-Shun Liu1,2,3,4,*, Jian-Gang Chen1,6,*, Ting Mei1,2,3, Yu-Xin Guo2,3, Hao-Tian Meng2,3, Jian-Fei Li5, Yuan-Yuan Wei2,3, Xiao-Ye Jin2,3, Bo-Feng Zhu2,3,4,** and Li-Ping Zhang1,**

1Department of Biochemistry and Molecular Biology, Basic Medicine College of Xinjiang Medical University, Urumqi, Xinjiang 830011, P. R. China

2Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China

3Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, Shaanxi 710004, P. R. China

4Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China

5School of Marxism, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, P.R. China

6Science and Technology Institute, Xinjiang Public Security Department, Urumqi, Xinjiang 830006, P.R. China

*The first two authors were equal to this article

**These authors have contributed equally to this work and were co-corresponding authors

Correspondance to:

Li-Ping Zhang, email: [email protected]

Keywords: genetic polymorphisms, Southern Shaanxi Han population, forensic characteristic analysis, autosomal STR, Y-STR

Received: April 15, 2017     Accepted: June 05, 2017     Published: July 18, 2017

ABSTRACT

We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations.


INTRODUCTION

Short tandem repeats (STRs) are widely distributed in human genome and play a significant role in forensic DNA analysis. Autosomal STRs have been the most common genetic markers in forensic applications and could be used to solve most of the personal identification and paternity testing cases [1, 2]. However, Y-chromosomal STRs (Y-STRs) would be more helpful in some special cases, such as mixed stain detection for sexual-assault cases, the paternal migration history tracing [3], and so on, because STRs on the non-recombining region of Y-chromosome do not participate in meiotic recombination and are unaltered when inherited from father to son [46]. At present, autosomal STRs or Y-STRs are often used alone in forensic applications. However, when autosomal STRs and Y-STRs were co-amplification in a single fluorescence multiplex system, they would be useful in both personal identification and paternity testing cases, for those Y-STRs could be helpful in the determination of gender and the reconstruction of paternal lineage [7, 8].

Southern Shaanxi region is the south part of Shaanxi province, covering the area from the south of Qinling Mountains to the north of Ba Mountain with the Han River flowing through from west to east; Southern Shaanxi consists of three cities: Hanzhong, Ankang and Shangluo, from west to east where mainly reside the Han population [9, 10]. To further understand the genetic background of Southern Shaanxi Han population and provide population genetic data for forensic identification, we firstly studied 15 autosomal STR loci and 10 Y-STR loci together in Chinese Han population from Southern Shaanxi region, calculated the forensic parameters, and collected previously published population data with overlapping loci of both autosomal STRs and Y-STRs, to discuss the genetic relationships between the studied population and other populations.

RESULTS AND DISCUSSIONS

The analysis of allelic frequencies and forensic parameters for the 15 autosomal STRs

According to the results of Hardy-Weinberg equilibrium (HWE) tests (presented in Table 1), all the autosomal STR loci showed no deviations from HWE (p>0.05). Tests of linkage disequilibrium (LD) were performed for all pairs of autosomal STR loci and the results were shown in Table 2. No LD was observed at a significance level of 0.0033 (α = 0.05/15) after Bonferroni correction, which indicated these autosomal STR loci were relatively independent. As summarized in Table 3, there were totally 150 alleles found at the 15 autosomal STR loci in the Southern Shaanxi Han population. As summarized in Table 1, the observed heterozygosity (Ho) in the studied population ranged from 0.6075 (TPOX locus) to 0.8411 (D8S1179 and D18S51 loci). The loci D18S51 and TPOX showed the highest and lowest expected heterozygosity (He), respectively. The power of discrimination (PD) and power of exclusion (PE) ranged from 0.7944 (TPOX locus) to 0.9623 (D2S1338 locus); and 0.2999 (TPOX locus) to 0.6774 (D8S1179 and D18S51 loci), respectively. The combined PD and PE were 0.99999999999999998866 and 0.999998491, respectively. All the 15 autosomal STR loci were found to be highly polymorphic in Southern Shaanxi Han population and the high value, which indicated their large potentiality for forensic individual identification.

Table 1: Forensic efficiency parameters of 15 autosomal STR loci in Southern Shaanxi Han (n = 214; 108 males and 106 females)

Loci

MP

PD

PIC

PE

TPI

Ho

He

P

D3S1358

0.1284

0.8716

0.6795

0.5058

1.9815

0.7477

0.7311

0.5469

D13S317

0.0762

0.9238

0.7753

0.6593

2.9722

0.8318

0.8079

0.3396

D7S820

0.0814

0.9186

0.7581

0.6060

2.5476

0.8037

0.7924

0.6354

D16S539

0.0742

0.9258

0.7677

0.6413

2.8158

0.8224

0.8020

0.4141

D19S433

0.0617

0.9383

0.7903

0.6235

2.6750

0.8131

0.8177

0.9201

TPOX

0.2056

0.7944

0.5485

0.2999

1.2738

0.6075

0.6167

0.8143

TH01

0.1652

0.8348

0.6147

0.3808

1.5070

0.6682

0.6629

0.8320

D2S1338

0.0377

0.9623

0.8432

0.6593

2.9722

0.8318

0.8630

0.2174

CSF1PO

0.1197

0.8803

0.6805

0.4593

1.7833

0.7196

0.7272

0.8481

vWA

0.0717

0.9283

0.7706

0.6060

2.5476

0.8037

0.8047

0.9718

D5S818

0.0812

0.9188

0.7535

0.5973

2.4884

0.7991

0.7897

0.6879

FGA

0.0413

0.9587

0.8361

0.6147

2.6098

0.8084

0.8559

0.0597

D8S1179

0.0426

0.9574

0.8321

0.6774

3.1471

0.8411

0.8541

0.6524

D21S11

0.0494

0.9506

0.8182

0.6683

3.0571

0.8364

0.8409

0.9216

D18S51

0.0401

0.9599

0.8468

0.6774

3.1471

0.8411

0.8658

0.3338

MP, matching probability; PD, power of discrimination; PIC, polymorphism information content; PE, probability of exclusion; TPI, typical paternity index; Ho, observed heterozygosity; He, expected heterozygosity; P, probability values of exact tests for Hardy–Weinberg equilibrium.

Table 2: P-value in pairwise linkage disequilibrium test at 15 autosomal STR loci in the Southern Shaanxi Han

Loci

D18S51

D21S11

D8S1179

FGA

D5S818

vWA

CSF1PO

D2S1338

TH01

TPOX

D19S433

D16S539

D7S820

D13S317

D21S11

0.6296

D8S1179

0.5324

0.5499

FGA

0.9829

0.9916

0.5286

D5S818

0.5533

0.3886

0.1205

0.2850

vWA

0.7924

0.5526

0.6802

0.6905

0.8789

CSF1PO

0.4312

0.0657

0.5942

0.3433

0.1912

0.6657

D2S1338

0.2196

0.0498

0.1329

0.5224

0.5909

0.2480

0.1339

TH01

0.2324

0.8556

0.2354

0.0941

0.1334

0.1961

0.5523

0.7025

TPOX

0.7221

0.8615

0.9330

0.5244

0.4134

0.0419

0.2683

0.0599

0.6112

D19S433

0.8361

0.6447

0.4450

0.9006

0.6020

0.5437

0.5998

0.0914

0.5520

0.5389

D16S539

0.1618

0.0346

0.3984

0.4926

0.0547

0.7402

0.7314

0.6914

0.8953

0.6968

0.9795

D7S820

0.2090

0.7743

0.5845

0.6665

0.8183

0.2245

0.5539

0.7382

0.1664

0.7873

0.7797

0.9245

D13S317

0.3965

0.8040

0.9324

0.8956

0.3898

0.9323

0.8857

0.7502

0.9283

0.7024

0.3950

0.2245

0.9659

D3S1358

0.2112

0.3818

0.7652

0.9047

0.2617

0.6080

0.8065

0.2471

0.0870

0.1014

0.1553

0.0909

0.3529

0.8748

Table 3: Allele frequency distributions of 15 autosomal STR loci in Southern Shaanxi Han (n = 214; 108 males and 106 females)

Allele

D3S1358

Allele

FGA

Allele

D21S11

Allele

D19S433

Allele

D18S51

Allele

D2S1338

Allele

D5S818

14

0.0467

16

0.0023

16

0.0047

11

0.0023

10

0.0023

16

0.0187

7

0.0304

15

0.3341

18

0.0140

28

0.0607

12

0.0491

12

0.0467

17

0.0841

9

0.0701

16

0.3248

19

0.0607

28.2

0.0140

12.2

0.0070

13

0.2009

18

0.0771

10

0.2126

17

0.2220

20

0.0491

29

0.2336

13

0.2921

14

0.1939

19

0.1916

11

0.3014

18

0.0607

20.2

0.0023

30

0.2570

13.2

0.0304

15

0.1706

20

0.1192

12

0.2243

19

0.0093

21

0.0864

30.2

0.0164

14

0.2360

16

0.1145

21

0.0164

13

0.1472

20

0.0023

21.2

0.0047

30.3

0.0047

14.2

0.1215

17

0.0935

22

0.0514

14

0.0117

Allele

D13S317

22

0.1379

31

0.0981

15

0.0607

18

0.0374

23

0.2033

15

0.0023

8

0.2570

23

0.2593

31.2

0.0911

15.2

0.1472

19

0.0584

24

0.1706

9

0.1449

23.2

0.0070

31.3

0.0023

16

0.0093

20

0.0444

25

0.0584

10

0.1262

24

0.1776

32

0.0304

16.2

0.0397

21

0.0117

26

0.0070

11

0.2453

24.2

0.0164

32.2

0.1308

17

0.0023

22

0.0117

27

0.0023

12

0.1729

25

0.1168

33

0.0023

17.2

0.0023

23

0.0023

Allele

TH01

13

0.0537

25.2

0.0047

33.2

0.0467

Allele

D8S1179

24

0.0070

6

0.1075

Allele

D7S820

26

0.0491

34.2

0.0047

8

0.0023

25

0.0047

7

0.2570

7

0.0047

27

0.0117

35.2

0.0023

9

0.0023

Allele

CSF1PO

8

0.0444

8

0.1449

Allele

D16S539

Allele

vWA

10

0.1168

7

0.0070

9

0.5070

9

0.0701

8

0.0093

14

0.2360

11

0.1005

9

0.0374

9.3

0.0444

9.1

0.0047

9

0.2407

15

0.0164

12

0.0888

10

0.2547

10

0.0397

10

0.1659

10

0.1449

16

0.1799

13

0.2196

11

0.1963

Allele

TPOX

10.1

0.0047

11

0.2617

17

0.2523

14

0.1846

12

0.4065

8

0.5210

11

0.3107

12

0.1963

18

0.1729

15

0.1519

13

0.0771

9

0.1192

12

0.2430

13

0.1238

19

0.1308

16

0.1121

14

0.0117

10

0.0234

13

0.0467

14

0.0210

20

0.0093

17

0.0187

15

0.0047

11

0.3154

14

0.0047

15

0.0023

21

0.0023

18

0.0023

23

0.0047

12

0.0210

Interpopulation differentiations based on the 15 overlapping autosomal STRs

Fst statistics is one of the most widely used measures for genetic differentiation and plays a central role in genetic studies [11]. Reference populations including Hui [12,13], Uygur [14, 15], Eastern Han (from Zhejiang, China) [16, 17], Salar [18, 19], Miao [20, 21], Tibetan [22, 23], Yi [21, 24], Shandong Han [25, 26], Korean [27, 28], Bangladeshis [29, 30], Serbian [31, 32], Xibe [33, 34], Dong [21, 35], Maonan [21, 36], Moroccan [37, 38], Croatian [39, 40], Nepalese [41, 42], Jilin Han [43, 44] and Liaoning Han [45, 46] were used for population genetic analysis based on the same of autosomal STRs or Y-STR loci, respectively. The pairwise Fst and p values based on 15 STR loci between Southern Shaanxi Han population and other 19 populations were shown in Supplmentary Table 1. The statistically significant differences (p<0.05/15=0.0033 after Bonferroni correction) were found between the Southern Shaanxi Han population and Serbian, Moroccan, Croatian, Miao, Shandong Han, Yi, Bangladeshis, Nepalese, Uygur and Dong populations at 11, 11, 10, 4, 3, 2, 2, 2, 1 and 1 loci, respectively. And then there was no significant difference obtained between Southern Shaanxi Han population and Eastern Han, Liaoning Han, Jilin Han, Hui, Salar, Tibetan, Xibe, Maonan and Korean populations, which indicated there were relatively close genetic distances among them.

Principal component analysis based on the 15 overlapping autosomal STRs

The principal component analysis (PCA) was performed among the Southern Shaanxi Han population and other 19 populations using the allelic frequencies of the 15 overlapping autosomal STR loci. The PCA result was shown in Figure 1. The first and second components accounted for 44.00 and 12.73% of the total variance, respectively; and the cumulative contribution of them was 56.73%, which was over half of the total variance. According to Figure 1, Southern Shaanxi Han was located in left part, close to Eastern Han, Liaoning Han and Jilin Han population. Moroccan, Croatian and Serbian gathered in the right edge of the plot, which were relatively far away from Southern Shaanxi Han.

Principal component analysis based on the 15 overlapping autosomal STR loci of Southern Shaanxi Han population and 19 reference populations.

Figure 1: Principal component analysis based on the 15 overlapping autosomal STR loci of Southern Shaanxi Han population and 19 reference populations.

Phylogenetic analysis based on the 15 overlapping autosomal STRs

The neighbor-joining tree (NJ tree) of the Southern Shaanxi Han and other 19 populations based on allelic frequencies of 15 overlapping autosomal STR loci was shown in Figure 2. In the NJ tree, the Southern Shaanxi Han population was also observed to be close with the Eastern Han and Jilin Han population. However, Serbian, Croatian and Moroccan populations were located furthest away from Southern Shaanxi Han population. The phylogenetic result was consistent with the results of above-mentioned PCA.

The neighbor-joining tree based on the 15 overlapping autosomal STR loci of Southern Shaanxi Han population and 19 reference populations.

Figure 2: The neighbor-joining tree based on the 15 overlapping autosomal STR loci of Southern Shaanxi Han population and 19 reference populations.

Allelic frequencies and haplotypic diversities of the 10 Y-STR loci

Allelic frequencies and Gene diversity (GD) values of the 10 Y-STR loci in 108 Southern Shaanxi Han male individuals were shown in Table 4, the allelic frequencies ranged from 0.0093 to 0.7407. GD values of all the loci were higher than 0.5 with the exceptions of DYS391 (0.4010) and DYS438 (0.3813) loci. The highest GD value was obtained at loci DYS385a, b with a value of 0.9983. The discriminatory capacity (DC) and haplotypic diversities (HD) values of the 10 Y-STR loci were 0.9259 and 0.9983, respectively. Haplotypic results of the 10 Y-STR loci were shown in Supplmentary Table 2. One hundred different haplotypes were obtained, 94 of which were unique. We compared the 10 Y-STR haplotype data with the haplotype database in YHRD (http://www.yhrd.org) (Released March 01, 2017). Forty-one haplotypes detected in the Southern Shaanxi Han population were found with no matches in 131889 Haplotypes. Sixty-three haplotypes were found with matches in 31445 East Asian-Sino-Tibetan-Chinese and 17 haplotypes were found with matches in 3248 East Asian-Sino-Tibetan-Tibeto-Burman.

Table 4: Allele frequencies and Gene diversities (GD) for the 10 Y-STR loci in Southern Shaanxi Han (n = 108)

Allele

DYS635

DYS456

DYS458

DYS391

DYS392

DYS390

DYS393

DYS438

DYS385a,b

8

0.0185

10,12

0.0093

13,17

0.0093

9

0.0185

10,17

0.0185

13,18

0.0926

10

0.7407

0.0093

0.7593

11,11

0.0370

13,19

0.0278

11

0.2315

0.1481

0.2130

11,12

0.0278

13,20

0.0093

12

0.0093

0.1481

0.5556

0.0093

11,13

0.0093

13,21

0.0278

13

0.0093

0.0093

0.3519

0.2593

11,16

0.0185

13,26

0.0093

14

0.2685

0.0185

0.2685

0.1111

11,17

0.0370

14,17

0.0185

15

0.4815

0.1296

0.0741

0.0741

11,18

0.0093

14,18

0.0185

15

0.0093

11,19

0.0370

14,19

0.0093

16

0.1574

0.1852

12,12

0.0370

14,21

0.0093

17

0.0741

0.2778

12,14

0.0093

14,22

0.0093

18

0.0093

0.2222

12,15

0.0093

15,17

0.0093

19

0.1389

0.1111

12,16

0.0741

15,19

0.0093

20

0.2778

0.0185

0.0093

12,17

0.0185

15,20

0.0093

21

0.2778

0.0093

12,19

0.0926

15,22

0.0093

22

0.2037

0.0093

0.0093

12,20

0.0741

18,19

0.0093

23

0.0556

0.5093

13,13

0.1204

24

0.0370

0.2407

13,14

0.0370

25

0.0093

0.2222

13,15

0.0093

26

0.0093

13,16

0.0278

GD

0.7876

0.6719

0.8165

0.4010

0.7617

0.6390

0.6120

0.3813

0.9983

GD, gene diversity.

Multidimensional scaling analysis based on the 10 Y- STRs

The multidimensional scaling analysis (MDS) analysis was performed among the Southern Shaanxi Han population and 19 other populations based on Rst values at the 10 overlapping Y-STR loci in order to address population relationships, and the result was shown in Figure 3. According to the figure, Southern Shaanxi Han was located in right part, closest to Eastern Han population, Liaoning Han and Jilin Han. The result was similar to the above results of population genetic analyses based on the 15 overlapping autosomal STR loci.

Multidimensional scaling analysis plot of the 20 populations based on the 10 overlapping Y-STR loci.

Figure 3: Multidimensional scaling analysis plot of the 20 populations based on the 10 overlapping Y-STR loci.

Phylogenetic analysis based on the 10 Y-STRs

As shown in Figure 4, the genetic relationships of the studied Southern Shaanxi Han and other 19 populations at the 10 overlapping Y-STRs were analyzed by the phylogenetic tree. In the NJ tree, the Southern Shaanxi Han population was also clustered close with the Eastern Han, Liaoning Han, Korean, Shandong Han and Xibe populations. Moreover, Croatian, Serbian, Moroccan and Yi populations were located furthest to Southern Shaanxi Han population. The phylogenetic result was similar to MDS result.

The neighbor-joining tree based on the 10 overlapping Y-STR loci of Southern Shaanxi Han population and 19 reference populations.

Figure 4: The neighbor-joining tree based on the 10 overlapping Y-STR loci of Southern Shaanxi Han population and 19 reference populations.

Southern Shaanxi Han speak Chinese, which belongs to Sino-Tibetan. Although settling in different areas, Southern Shaanxi Han and Eastern Han have a relatively close genetic relationship. However, for populations from other continents or races, such as Serbian, Moroccan, and Croatian, the genetic relationships with Southern Shaanxi Han would be quite distant because of their different origins and genetic structures. At present, there is little research on Southern Shaanxi Han population; more population genetic studies would help us get a better understanding of this population genetic backgroud in the future.

MATERIALS AND METHODS

Sample collection and DNA extraction

We collected 214 blood samples (108 males and 106 females) from unrelated healthy Han individuals living in the south of Shaanxi province (Southern Shaanxi), China. All the samples were collected according to the criteria for selection as follows: their ancestors within three generations should be unrelated individuals and members of Han ethnic group, with no migration. All volunteers without diseases signed informed consents. The present study followed the human rights and the ethical principle of Xinjiang Medical University and approved by institutional ethics committee, Xinjiang medical university, China. Genomic DNA was extracted using the Chelex-100 method as described by Walsh et al [47].

Multiplex amplification and STR genotyping

The 25 STR loci (D3S1358, D13S317, D7S820, D16S539, D19S433, DYS635, DYS456, TPOX, TH01, D2S1338, CSF1PO, DYS385a,b, DYS458, DYS391, vWA, D5S818, FGA, DYS392, DYS390, D8S1179, D21S11, D18S51, DYS393 and DYS438) and Amelogenin locus were co-amplified in a new single multiplex reaction in a 25μL PCR reaction volume using the Expressmarker 16+10Y fluorescence amplification reagents (AGCU ScienTech Incorporation, Wuxi, Jiangsu, China), according to the manufacturer’s instructions. DNA samples were amplified on a GeneAmp PCR System 9700 Thermal Cycler (Applied Biosystems, Foster City, CA, USA) following the manufacturer’s instructions.

Electrophoresis was performed using an ABI 3130 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). Fragment sizing was supported using the AGCU Marker SIZ-500 (AGCU ScienTech Incorporation, Wuxi, Jiangsu, China) internal size standard and allelic ladder as basis for comparison. Alleles were identified using the GeneMapper® ID V3.2 (Applied Biosystems, Foster City, CA, USA). The 9948 cell-line (Promega, Madison, WI, USA) DNA was also genotyped using the reagent as control.

Statistical analysis

Fifteen autosomal STRs were statistically analyzed as follows. We calculated the allelic frequencies and tested the Hardy-Weinberg equilibrium using the modified powerstat v1.2 spreadsheet [48]. The linkage disequilibrium of autosomal STRs was analyzed by Genepop v4.0.10 (http://genepop.curtin.edu.au/). The pairwise Fst and p values between the studied Han population and reference populations at 15 overlapping autosomal STR loci were estimated by the program ARLEQUIN v3.1 (http://cmpg.unibe.ch/software/arlequin3). Principal component analysis was performed with MVSP 3.1 (http://www.kovcomp.com) based on allelic frequencies of 15 overlapping autosomal STR loci, which was used to explore the extent of correlation genetic relationships. Neighbor-joining tree based on allelic frequencies of 15 overlapping autosomal STR loci were calculated using the Phylip-3.69 Software (http://evolution.gs.washington.edu/phylip.html). Based on the 10 overlapping Y-STR loci, another NJ tree was obtained by Phylip-3.69 Software (http://evolution.gs.washington. edu/phylip.html). Multidimensional scaling analysis of Y-STR based on Rst values was constructed by statistical software SPSS version 13.0 (SPSS Inc., Chicago, IL). Gene diversity and haplotype diversity were calculated using Nei's formula [49].

CONCLUSION

In summary, the results demonstrated high genetic diversities of the 15 autosomal STR loci and 10 Y-STR loci in the Southern Shaanxi Han population and the studied polymorphic markers were suitable for forensic DNA cases, which could offer a new tool for forensic investigation. In this study, 15 autosome and 10 Y chromosome STR loci were amplified by the multi-color fluorescence technique in a single PCR reaction, and genotyping profile of both autosomal STR and Y chromosome STR loci could be obtained simultaneously. This made it possible for forensic geneticists to get the information of personal identification, gender determination and pedigree investigation in one step, which is a time, labor and cost saving strategy. The results of population differentiation, principal component analysis, multidimensional scaling analysis and phylogenic analysis indicated the Southern Shaanxi Han population had closer genetic relationship with the Eastern Han population and more distant relationships with populations from other races. The present data which combined autosomal STR loci and Y-STR loci will be useful for the enrichment of Chinese genetic information resources and provide valuable forensic data for forensic DNA cases.

Abbreviations

HWE, Hardy-Weinberg equilibrium; LD, linkage disequilibrium; MP, matching probability; PD, power of discrimination; PIC, polymorphism information content; PE, probability of exclusion; TPI, typical paternity index; Ho, observed heterozygosity; He, expected heterozygosity; p, probability values of exact tests for Hardy–Weinberg equilibrium; NJ tree, neighbor-joining tree; PCA, principal component analysis; GD, Gene diversity; HD, haplotype diversity; DC, discriminatory capacity; MDS, Multidimensional scaling analysis.

Authors’ contributions

B.Z. and L.Z. designed the study. X.J., T.M. and J.L. provided human blood samples. Y.W., Y.G. and H.M. conducted the data processing and performed statistical analyses. Y.L. and J.C. wrote the main manuscript text. All authors reviewed the manuscript.

ACKNOWLEDGMENTS

This project was supported by the National Natural Science Foundation of China (NSFC, No. 81525015 and 81460286). The authors would like to thank Jiangwei Yan for helping us to analysis data.

CONFLICTS OF INTEREST

The authors state that they have no conflicts of interest.

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