12 Y-STRs haplotypes in Chinese Naxi ethnic minority group

Forensic Science International 174 (2008) 244–248 www.elsevier.com/locate/forsciint

Announcement of population data

12 Y-STRs haplotypes in Chinese Naxi ethnic minority group Na Xin a,b, Teng Chen a,b,*, Bing Yu a,b, Shengbin Li a,b b

a Department of Forensic Science, Medical College of Xi’an Jiaotong University, Xi’an 710061, PR China Ministry of Education, Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Xi’an Shaanxi 710061, PR China

Received 14 September 2006; received in revised form 21 March 2007; accepted 28 March 2007 Available online 25 May 2007

Abstract Twelve Y-STRs loci including minimal haplotypes (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, and DYS385a,b) and three additional loci, namely DYS437, DYS438 and DYS439 were co-amplified in 138 healthy unrelated males of Chinese Naxi ethnic minority group using the PowerPlex1 Y System. A total of 113 haplotypes were identified, among which 103 were unique, and 6, 2, 1 and 1 were found in 2, 4, 5 and 10 individuals, respectively. The haplotype diversity for 12 Y-STRs loci was 0.9923.The results from the present study can be used in forensic application and population genetics in the region, and can enrich Chinese ethnical genetic informational resources. # 2007 Elsevier Ireland Ltd. All rights reserved. Keywords: Y-chromosomal STR; Haplotype; Chinese Naxi ethnic minority group; PowerPlex1 Y System

Population: Whole EDTA blood samples were randomly collected from 138 unrelated, healthy, male individuals of Chinese Naxi population living in Lijiang Naxi Autonomous County, Yunnan Province of China. Their ancestors lived in the region for at least three generations. The Naxi ethnic group, with a population of 308,839 (year of 2000), most of whom live in the concentrated communities in the Lijiang Naxi Autonomous County in Yunnan Province, the rest being scattered in Weixi, Zhongdian, Ninglang, Deqin, Yongsheng, Heqing, Jianchuan and Lanping counties in Yunnan Province, and in Yanyuan, Yanbian and Muli counties in Sichuan Province. A small number of them live in Mangkang County of Tibet Autonomous Region. The Naxi areas, traversed by rivers such as the Jinsha, Lancang and Yalong, and the Yunling, Xueshan and Yulong mountain ranges, have a complicated terrain. The Naxi language belongs to the Chinese–Tibetan language family. More than 1000 years ago, the Naxi people had already created pictographic characters called the ‘‘Dongba’’ script and a syllabic writing known as the ‘‘Geba’’ script. With these scripts they recorded a lot of beautiful folklore, legends, poems and religious classics. Most Naxi

* Corresponding author at: Key Laboratory of Environment and Genes Related to Diseases, Department of Forensic Science, Xi’an Jiaotong University of Medicine, 76 Yanta West Road, Xi’an Shaanxi 710061, PR China. Tel.: +86 29 82657977. E-mail address: [email protected] (T. Chen). 0379-0738/$ – see front matter # 2007 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.forsciint.2007.03.021

people are followers of the ‘‘Dongba’’ religion, which is a form of Shamanism. DNA extraction: Genomic DNA was extracted using the Chelex-100 method. [1]. PCR: PCR for 12 Y-chromosomal STRs was performed in fluorescence-based multiplex reaction using PowerPlex1 Y System kit (Promega, USA). The amplification system was 8 ml in total which contained 0.8 ml of Gold ST$R 10 Buffer, 0.8 ml of PowerPlex1 Y 10 Primer Pair Mix, 0.20 ml of Ampli TaqGold1 DNA Polymerase (5 U/ml), 5.6 ml of deionized water and 0.6 ml of Genomic DNA (approximately 1 ng). According to the manufacturer’s protocols of the kit, thermal cycling conditions were conducted using GeneAmp PCR system 9700 (PE Applied Biosystems). Typing: Electrophoresis and typing were performed on ABI 377 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA) and GeneScan3.7 software (Applied Biosystems, USA). The genotyping of the PCR products at each of 12 STR loci was carried out based on the sequenced allelic ladder using PowerTyperTM Y Macro (Promega, USA). The alleles of all loci were named according to the number of repeat units present, as recommended by the DNA Commission of the International Society of Forensic Genetics [2]. Results: The haplotype distributions and gene diversity values of Chinese Naxi population are shown in Table 1. The Rst values obtained in the comparison between populations are shown in Table 2. Location of studied population is shown by Fig. 1.

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Table 1 Y-STR haplotypes in 138 unrelated male individuals of Chinese Naxi ethnic minority group Haplotypes

DYS19

DYS389I

DYS389II

DYS390

DYS391

DYS392

DYS393

DYS437

DYS438

DYS439

DYS385a,b

h1 h2 h3 h4 h5 h6 h7 h8 h9 h10 h11 h12 h13 h14 h15 h16 h17 h18 h19 h20 h21 h22 h23 h24 h25 h26 h27 h28 h29 h30 h31 h32 h33 h34 h35 h36 h37 h38 h39 h40 h41 h42 h43 h44 h45 h46 h47 h48 h49 h50 h51 h52 h53 h54 h55 h56 h57 h58 h59 h60 h61 h62 h63 h64

13 13 13 13 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15

12 13 13 13 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 13 13 13 13 13 13 13 13 13 14 14 14 14 14 14 14 15 12 12 12 12 12 12 12 12 12 12 12 12 12 13 13 13 13 13 13 13 13 13 13 13 13 13 13

31 29 29 29 28 28 28 28 28 28 28 28 28 29 29 29 30 30 30 28 28 28 28 29 29 29 29 29 29 28 29 30 30 30 30 32 31 28 28 28 28 28 28 28 29 29 29 30 30 31 28 28 28 28 28 28 29 29 29 29 29 29 29 29

24 23 23 23 22 23 23 24 24 24 25 25 25 24 24 24 23 23 24 24 24 24 25 22 23 23 23 23 24 22 23 23 23 23 24 23 23 24 24 24 24 27 27 27 23 23 25 23 23 24 24 25 25 25 25 25 23 23 23 25 25 25 25 25

10 10 10 10 11 10 10 10 10 11 10 10 10 10 10 10 10 11 10 10 10 10 10 11 10 10 10 11 10 10 11 11 11 11 10 10 11 10 10 10 11 10 10 10 10 11 10 10 10 11 10 10 10 10 10 10 10 10 10 10 10 10 10 11

8 11 11 11 14 14 15 14 14 13 14 14 14 11 13 14 14 14 14 13 14 14 13 14 11 11 14 14 13 14 14 13 14 14 14 11 14 10 11 13 13 13 13 13 12 14 7 12 12 14 13 13 13 13 13 13 11 12 13 7 7 7 12 7

12 10 14 15 13 12 12 12 12 12 12 12 12 12 12 12 13 13 13 12 12 12 14 13 13 14 13 11 12 14 13 13 13 14 13 15 14 12 12 10 13 12 12 12 12 13 14 12 12 13 14 12 14 14 14 14 15 13 13 13 13 13 14 13

14 14 14 14 14 15 14 15 15 16 15 15 15 14 15 15 14 14 14 15 16 16 14 14 15 14 14 15 15 14 14 14 14 14 14 14 14 14 14 14 14 15 15 15 15 14 14 15 15 14 14 14 14 14 14 14 14 13 14 14 14 14 14 14

8 10 10 10 10 11 11 8 11 11 11 11 11 10 11 11 10 10 11 11 11 11 10 10 9 10 10 10 12 10 11 11 11 11 11 10 11 10 10 10 11 10 10 11 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 8 10 11 10 11

12 12 12 12 12 11 11 12 12 12 12 12 14 10 12 12 13 11 11 12 12 12 11 12 12 12 12 11 12 12 11 11 11 11 11 11 11 11 11 11 11 12 12 12 14 11 12 12 13 12 11 12 11 12 12 12 12 11 11 11 11 12 13 12

11,12 14,14 14,14 14,14 12,12 13,19 13,18 13,13 14,19 13,19 13,17 13,19 13,19 14,14 19,20 13,13 13,14 11,12 17,18 13,19 13,19 13,20 11,14 12,12 13,17 14,14 13,13 13,18 13,18 12,13 11,12 11,12 11,12 11,12 17,18 12,19 11,12 16,17 15,16 21,22 12,16 13,21 13,23 19,23 12,16 13,13 15,17 12,18 18,23 17,18 15,17 21,22 15,17 15,16 15,17 16,17 11,21 13,19 17,18 11,11 11,11 11,11 15,17 11,11

N 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 4 5 1 1 1 1 1 1 1 1 1

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Table 1 (Continued ) Haplotypes

DYS19

DYS389I

DYS389II

DYS390

DYS391

DYS392

DYS393

DYS437

DYS438

DYS439

DYS385a,b

N

h65 h66 h67 h68 h69 h70 h71 h72 h73 h74 h75 h76 h77 h78 h79 h80 h81 h82 h83 h84 h85 h86 h87 h88 h89 h90 h91 h92 h93 h94 h95 h96 h97 h98 h99 h100 h101 h102 h103 h104 h105 h106 h107 h108 h109 h110 h111 h112 h113 D

15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17 0.6276

13 13 13 13 13 13 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 10 12 12 12 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 14 14 12 0.6574

29 29 30 30 30 30 29 29 30 30 30 30 30 31 31 31 31 31 31 31 32 32 32 26 28 28 28 28 29 29 29 29 29 29 29 29 29 29 29 29 29 29 29 30 31 30 30 31 29 0.7538

25 25 24 25 25 25 23 25 23 23 25 25 25 22 23 23 24 25 25 25 23 25 25 23 23 24 25 25 23 24 24 24 25 25 25 25 25 25 25 25 25 25 25 25 24 23 24 23 26 0.6686

11 11 10 10 11 11 10 10 10 11 10 10 11 10 11 11 10 10 10 10 11 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11 11 11 11 11 11 11 11 11 10 11 11 11 10 0.4265

13 13 13 7 7 13 11 13 13 12 7 7 13 11 14 14 7 7 7 7 14 7 7 13 11 13 13 13 11 7 11 13 12 13 13 13 13 13 13 13 13 13 14 13 13 14 13 12 13 0.7443

14 14 13 13 13 13 15 14 13 13 13 13 14 15 13 13 13 13 13 14 13 13 13 12 14 12 12 14 10 12 15 14 14 10 10 10 14 14 14 14 14 14 14 14 12 13 14 13 12 0.7163

14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 13 14 14 14 14 15 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 15 14 14 14 14 0.3101

10 10 10 11 11 10 10 10 10 11 11 11 10 10 10 10 11 11 11 11 10 11 11 10 10 10 10 10 10 11 10 10 10 10 10 10 10 10 10 10 10 11 10 10 10 10 10 10 10 0.5065

12 13 11 12 13 12 13 12 13 11 11 12 13 12 11 11 12 12 12 12 11 12 12 11 12 12 11 13 12 11 11 10 13 12 12 13 11 12 12 13 14 12 12 13 12 11 12 11 11 0.5930

17,18 17,19 14,18 11,11 11,11 15,17 11,21 15,17 11,18 15,18 11,12 11,11 13,19 11,11 11,12 12,12 11,12 11,11 11,12 11,11 12,12 11,11 11,12 14,19 11,15 13,20 17,25 15,17 16,17 11,17 11,16 13,18 17,18 17,18 18,19 17,18 17,18 17,18 23,24 17,19 16,18 23,24 17,18 17,18 12,21 12,12 13,18 15,18 14,17 0.9393

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 10 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1

N: number of individuals observed for each haplotypes; D: diversity value of 12 Y-STR loci.

Data analysis: Haplotype frequencies were estimated by direct counting method. Haplotype and gene diversities were estimated according to Nei [3]. A comparative analysis between these haplotype data and previously published data was carried out by the analysis of molecular variance (AMOVA) test [4] implemented by Arlequin software, V.2000 [5]. Quality control: Laboratory internal control standards and kit controls. Access to data: All data are accessible from corresponding author through e-mail.

Other remarks: In the study, out of a total of 138 male individuals, 113 showed different haplotypes, of which 103 haplotypes were unique, while 10 haplotypes occurred more than once. The overall haplotype diversity value for 12 Y-STR loci was 0.9923. The most frequent haplotype h82 (15-14-3125-10-7-13-11,11-14-11-12) of this population was found in 10 individuals (7.25%). We searched these haplotypes in the YHRD database (www.yhrd.org) (last updated 21/3/2007) and found no matches with these 10 frequent haplotypes of this population and other population. Consider just the ‘‘minimal

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Fig. 1. A map showing location of studied Naxi population in China.

haplotypes’’ included in the YHRD, h32 (14-14-30-23-11-1313-11,12) matched only one Swedish sample found in an Eurasian metapopulation of 31,592 haplotypes in a set of 247 populations. DYS385a,b locus showed the highest level of polymorphism (gene diversity: 0.9393), DYS437 the lowest (0.3101), and the other loci varied between 0.4265 and 0.7538. We compared the haplotypes observed among the Naxi population with previously published data for the same set of Y-STR loci and found that Naxi population has significant differences from Japanese population (Rst = 0.00115, p < 0.0001) [6], Basque population (Rst = 0.00802, p < 0.0001) [7], and slightly significant with Tunisian population (Rst = 0.00219, p = 0.03604  0.0201)[8]. There were no significant differences between the studied population and some neighboring populations including Korean [9], Chinese Han populations [10–12], Chinese Mongol, Uigur, and Yi populations [13–15]. Research results will form a foundation for future studies in forensic application and population Table 2 The Rst values obtained in the comparison between Naxi population and other populations population

Rst value

P-value

Japanese Basque Tunisian Korean Han population in Tianjin Minnan Han Chinese Chaoshan Han Chinese Chinese Mongol ethnic group Chinese Uigur ethnic group Chinese Yi ethnic group

0.00115 0.00802 0.00219 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

0.00000  0.0000 0.00000  0.0000 0.03604  0.0201 0.58559  0.0654 0.96396  0.0196 0.98198  0.0096 0.99099  0.0030 0.99099  0.0030 0.99099  0.0030 0.95495  0.0151

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