научная статья по теме MATERNAL AND PATERNAL DIVERSITY IN XINJIANG KAZAKH POPULATION FROM CHINA Биология

Текст научной статьи на тему «MATERNAL AND PATERNAL DIVERSITY IN XINJIANG KAZAKH POPULATION FROM CHINA»

ГЕНЕТИКА, 2014, том 50, № 11, с. 1374-1385

ГЕНЕТИКА ЧЕЛОВЕКА

УДК 575.17:599.9

MATERNAL AND PATERNAL DIVERSITY IN XINJIANG KAZAKH

POPULATION FROM CHINA

© 2014 W. Shan1, Zh. Ren1, W. Wu2, H. Hao2, A. Abulimiti1, K. Chen1, F. Zhang1, Z. Ma1, X. Zheng13,4

1 Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China e-mail: mzhxju@xju.edu.cn 2 Institute of Forensic Science of Zhejiang, Zhejiang, China 3 Departments of Pathology, The University of Western Ontario, London, N6A5A5 Canada

e-mail: xzheng26@uwo.ca 4 Lawson Institute of Health Research, London, Canada Received December 30, 2013

The ancient silk road of China passed through Xinjiang and facilitated gene exchanges from the East and the West which impacted on the genetic variation and structure of the nomadic Kazakh population residing there. In order to understand the nature of this genetic variation, 151 Xinjiang Kazakh samples were obtained from four main Kazakh groups and were analyzed using mtDNA and Y-chromosome markers.The Xinjiang Kazakh population is heterogeneous, showing the coexistence of matrilineal lineages with different origins. No genetic differentiation of mtDNA is observed among the four different regional Xinjiang Kazakh populations in Xinjiang by AMOVA and Networks. The genetic diversity of Y-STR loci is higher in Xinjiang Kazakhs (0.968 ± 0.014) than the Kazakhs from Kazakhstan (0.629 ± 0.071) and Russia (0.835 ± 0.020). East Eurasians make a more than 50% contribution to the maternal and paternal lineages of Xinjiang Kazakhs. There is more gene flow from West Eurasian into the maternal lineages of Xinjiang Kazakh than to the Kazakhs from Russia and Kazakhstan. Moreover, mtDNA and Y-STR displayed high polymorphism in Xinjiang Kazakhs (the haplotype diversity and power of discrimination were 0.990 ± 0.003, 0.9137 for mtDNA HVS and 0.968 ± ± 0.014, 0.9489 for Y-STR system, respectively), suggesting they would be very useful and important markers for forensic analysis and population genetic studies.

DOI: 10.7868/S0016675814110149

The Kazakhs are a Turkic speaking nomadic population. They first emerged as a political unit during the 15 th century CE in the region that is now southern Kazakhstan [1, 2]. During the 19th and into the 20th centuries, Kazakhs migrated throughout Xinjiang, China, and eventually spread north around the Altai Mountains in western Mongolia and southern Russia. Previous studies have suggested that these Kazakhs contain a mixture of people [2, 3]. Due to this complex population history including migration(s) and a seasonal nomadic life-style, Kazakhs display gene flow from the East and West Eurasian population, dominated by East Eurasian haplogroups demonstrated by the mitochondria DNA (mtDNA) control region sequence information [4]. Studies have also demonstrated that there are notable differences in maternal and paternal genetic systems between different geographic Altaian Kazakh populations [2, 4—5]. However, these studies mainly focused on Russia and Kazakhstan Kazakh populations. Xinjiang Kazakhs have been studied employing limited data sets (45 subjects) from one location (Urumqi, Xinjiang) and using maternal inherited mtDNA marker only [6], which has provided an incomplete picture of human phylogeography for this population.

Xinjiang Province, located in northwest China (Fig. 1), is famous for being home to part of the ancient Silk Road linking the East and the West. The Kazakh in Xinjiang can trace their origins to the populations residing in Central Asia more than 2000 years ago [7]. Most of them reside in four regions: Altay (the north end ofXinjiang), Yili, Tacheng and Bole. During the early part of the 20th century, some Kazakhs moved eastward to Urumqi and its surrounding areas [7]. Due to political and historical reasons, unceasing migration events occurred among the Kazakhs resulting in a mixture ofmultiple cultures and genetics [7, 8]. Using a powerful molecular tool for population genetic studies [9— 12], we characterized the mtDNA control region and Y-chromosome short tandem repeats (Y-STR) in Kazakh people from Xinjiang to elucidate their genetic diversity and relationship with other populations.

MATERIALS AND METHODS

Sample collection and DNA preparation

A total of 151 blood samples were collected from unrelated, healthy Kazakh individuals residing in Xin-

jiang, China (Fig. 1). Among these samples, 26 samples were collected from donors living in Altay (ALT), 12 in Yili (YL), 103 in Bole (BL), 10 in central and eastern Xinjiang (including Urumqi, Changji and Ku-mol, named WC in this study), respectively. Due to an uneven and small number of male samples, the four subpopulations were pooled and handled as a whole in 17 Y-STR study of 76 Kazakh males from Xinjiang China. For each individual it was confirmed there had been no intermarriage with other populations for more than three generations. Oral informed consent was obtained from all participants. The study was approved by the Ethical Committee of the Xinjiang University. Total DNA was extracted and purified from whole blood using a commercial DNA extraction kit (Qiagen, Beijing).

Russia

Kazakhstan , B

% % % \ % \ •a C. 'b A •c ,d Kyrgyzstan Mongolia

* Tajikistan Xinjiang Afghanistan China

mtDNA sequencing and Y-chromosome genotyping

The hyper variable segments I and II (HVS I and II) of the mtDNA control region were amplified by PCR. DNA sequencing was conducted by Sangon Biotech (Shanghai) Co., Ltd. after being purified using Qiagen DNA product purification KIT (Qiagen, Beijing). Y-STR genotyping was conducted using AmpFLSTR® YFiler™ PCR Amplification Kits (Applied Biosystems), at the following loci: DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS 393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.

Data analysis

mtDNA sequences (GenBank accession numbers: KC155427—KC155577) were aligned and compared with the revised Cambridge Sequence using Clustal X software [13, 14]. Haplotypes of mtDNA were assigned using Mitotool online (www.mitotool.org), the phylotree website (www.phylotree.org) and the standards outlined by papers [6, 15, 16]. The frequencies of haplotypes of 17 Y-STR loci were calculated by direct counting. Gene diversity, haplotype diversity, pairwise difference, FST values and analysis of molecular variance (AMOVA) were calculated and performed with Arlequin [17]. Taking Mongolians and Caucasians as parental populations, the admixture estimation was performed by the Weighted Least Squares (WLS) Method using the Statistical Package for the Social Sciences (SPSS) 19 software. Furthermore, median-joining networks [18] based on mtDNA HVS and Y-STR haplotypes were drawn by NETWORK 4.6.1.1 software (www.Fluxus-engineering.Come/sharenet.htm) respectively. Multidimensional scaling (MDS) plots of mtDNA were created by SPSS 19. MDS plots ofY-STR were produced using SPSS 19 and the population analysis tool of the YHRD (www.yhrd.org) [19]. Loci DYS385a and DYS385b were excluded from all analyses due to the possibility of ambiguous assignment of the alleles to these loci. The haplogroup of Y-STR was predicted by Haplo-group Predictor website (www.hprg.com/hapest5/in-dex.html).

Fig. 1. Geographic locations of Kazakh samples in this study. A: XJKAZ (Kazakhs from Xinjiang China): a: ALT (Altay), b: BL (Bole), c: YL (Yili), d: WC (Urumqi, Changji and Kumul); B: RKAZ (Kazakhs from Russia) [2, 4]; C: HKAZ (Kazakhs from Kazakhstan) [2, 4].

RESULTS AND DISCUSSION

Mitochondrial DNA diversity and genetic variation in Xinjiang Kazakhs

A total of 115 different mtDNA haplotypes were observed in the 151 unrelated Xinjiang Kazakh individuals. The haplotype diversity was 0.990 ± 0.003 (Table 1), which was very similar to that of Kazakhstan Kazakhs (0.990 ± 0.006) and Russian Kazakhs (0.997 ± ± 0.001) [4]. The nucleotide diversity of mtDNA in Xinjiang Kazakhs was 0.017 ± 0.009 and the pairwise difference was 5.838 ± 2.805 (Table 1). The power of discrimination based on mtDNA HVS was 0.9137. Compared to the other three Xinjiang Kazakhs settlements (ALT, YL and WC), BL showed relatively lower gene diversity (0.984 ± 0.006), nucleotide diversity (0.016 ± 0.009) and pairwise differences (5.612 ± ± 2.716) (Table 1).

The 115 mtDNA haplotypes of Xinjiang Kazakhs were further assigned into 15 haplogroups according to Yao et al. [6] and their frequencies were calculated (see Supplementary Table 1). Similar to previous studies [6, 20], every known East Eurasian specific haplo-groups (A, C, D, F, G, M7, M8, N9, and Z) and West Eurasian specific haplogroups (HV, H, J, T, R, and W) were present in Xinjiang Kazakhs, in which East Eurasian haplogroup was predominant (60.3%). In this study, the sample numbers and sample locations were expanded and the proportion of western Eurasian-specific haplogroups (39.1%) was higher in Xinjiang Kazakhs compared to that reported inYao's previous study (30.2%) [6].

BL, YL, ALT and WC samples shared the same haplogroups such as A, C, D, H, M and U, while some haplogroups were location specific. For example, Z, D, M8, M9, N10, and W were specific for BL. D2 and

Table 1. mtDNA HVS summary statistics of Xinjiang Kazakhs

Index Total ALT BL YL WC

Number of samples 151 26 103 12 10

Number of haplotypes 115 25 73 12 10

Number of Unique haplotypes 104 21 66 10 7

Haplotype diversity 0.990 ± 0.003 0.997 ± 0.012 0.984 ± 0.006 1.000 ± 0.034 1.000 ± 0.045

Pairwise differences 5.838 ± 2.805 6.037 ± 2.971 5.612 ± 2.716 6.000 ± 3.077 6.378 ± 3.302

Nucleotide diversity 0.017 ± 0.009 0.017 ± 0.009 0.016 ± 0.009 0.017 ± 0.001 0.018 ± 0.011

Tajima's D -2.040 -1.856 -2.036 -1.353 -1.460

P-value 0.000 0.030 0.000 0.080 0.090

Fu's Fs -25.083 -22.555 -25.277 -7.216 -4.959

P-value 0.000 0.000 0.000 0.000 0.010

M7 were special for WC. U and F were limited to YL and ALT, respectively. The u

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