Genetic polymorphic investigation of 21 autosomal short tandem repeat loci in the Chinese Li ethnic group

Genetic polymorphic investigation of 21 autosomal short tandem repeat loci in the Chinese Li ethnic group

Accepted Manuscript Title: Genetic polymorphic investigation of 21 autosomal short tandem repeat loci in the Chinese Li ethnic group Author: Yadong Gu...

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Accepted Manuscript Title: Genetic polymorphic investigation of 21 autosomal short tandem repeat loci in the Chinese Li ethnic group Author: Yadong Guo Juanjuan Guo Yanfang Liu Xiaoliang Fu PII: DOI: Reference:

S1872-4973(16)30121-1 http://dx.doi.org/doi:10.1016/j.fsigen.2016.07.001 FSIGEN 1548

To appear in:

Forensic Science International: Genetics

Author: Shengzhong Dong Yaxian Zhong Zhihui Wang Kun Geng PII: DOI: Reference:

S1872-4973(16)30121-1 http://dx.doi.org/doi:10.1016/j.fsigen.2016.07.001 FSIGEN 1548

To appear in:

Forensic Science International: Genetics

Author: Lingmei Lan Lagabaiyila Zha Jifeng Cai PII: DOI: Reference:

S1872-4973(16)30121-1 http://dx.doi.org/doi:10.1016/j.fsigen.2016.07.001 FSIGEN 1548

To appear in:

Forensic Science International: Genetics

Received date: Revised date: Accepted date:

31-3-2016 1-7-2016 3-7-2016

Please cite this article as: Lingmei Lan, Lagabaiyila Zha, Jifeng Cai, Genetic polymorphic investigation of 21 autosomal short tandem repeat loci in the Chinese Li ethnic group, Forensic Science International: Genetics http://dx.doi.org/10.1016/j.fsigen.2016.07.001

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Genetic polymorphic investigation of 21 autosomal short tandem repeat loci in the Chinese Li ethnic group Yadong Guoa, Juanjuan Guoa, Yanfang Liua, Xiaoliang Fua, Shengzhong Dongb, Yaxian Zhongb, Zhihui Wangb, Kun Gengb, Lingmei Lana, Lagabaiyila Zhaa, Jifeng Caia* a

Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha 410013, Hunan, P.R.China b School of Basic Medical Sciences, Central South University, Changsha 410013, Hunan, P.R. China *Corresponding author: Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Tongzipo Road 172, Changsha, Hunan 410013, P.R. China. Tel.: +86-731-82650414, Fax: +86-731-82650414 E-mail address: [email protected]

Dear Editor, Some data about autosomal and Y chromosome-specific short tandem repeat (STR) loci in the Chinese Li ethnic group have been published [1,2]. However, to the best of our knowledge, nothing has been documented about the 21 autosomal STR loci of the AGCU 21+1 STR Fluorescence Assay Kit in the Li nationality. Hence, we first investigated the allele frequencies and forensic parameters of 21 STR loci (D1GATA113, D1S1627, D1S1677, D2S1776, D2S441, D3S4529, D4S2408, D5S2500, D6S1017, D6S474, D9S1122, D10S1248, D10S1435, D11S4463, D12ATA63, D14S1434, D17S1301, D18S853, D19S433, D20S482, and D22S1045) in a sample of 504 unrelated healthy individuals from the Chinese Li ethnic group. Hainan Island, the second largest Chinese island after Taiwan, is located in the southernmost part of mainland China. Several ethnic groups live on the island, including Han, Li, Miao, and Hui nationalities. The Li nationality, with a population of about 1.25 million, is the second largest ethnic group, comprising ~17% of the total population on the island. Li ancestors settled on the island around 5000 years ago and gradually migrated southwards to settle in the rainforest-covered mountains from the second century BC onwards [3]. Li people speak the Li language, which belongs to the Sino-Tibetan and Tai-Kadai language families. However, in areas close to the Han nationality and where different ethnicities intermingle, many Li people also speak Chinese. The Li nationality does not have its own characters, so Chinese characters have been adopted gradually after the founding of the People’s Republic of China. Bloodstains were collected from 504 unrelated healthy Chinese Li individuals

(228 males and 276 females) living in Hainan Province, following written informed consent. Genomic DNA was isolated from bloodstains using the Chelex 100 protocol described by Walsh et al [4]. The 21 autosomal STR loci and amelogenin locus were co-amplified on a GeneAmp PCR 9700 thermal cycler (Thermo Fisher Scientific, Waltham, MA) using an AGCU 21+1 STR Fluorescence Assay Kit (AGCU ScienTech Incorporation, Wuxi, Jiangsu, China) [5]. Amplification products were separated by electrophoresis and detected by an Applied Biosystems® 3130xl Genetic Analyzer (Thermo Fisher Scientific). Genotyping was performed by comparison with allele ladders using GeneMapper ID version 3.2 software (Thermo Fisher Scientific). All analyses included the 9947A DNA sample as a positive control and a negative control without DNA. Allele frequencies, exact tests of the Hardy–Weinberg equilibrium (HWE), and forensic parameters were evaluated using a modified PowerStat version 1.2 spreadsheet (Promega, Madison, WI) [6]. Population differentiation between the Li group and other previously published population data was analyzed using Arlequin Version 3.5 software [7]. Nei’s genetic distances between populations were calculated using Gendist in the phylogeny inference package (Phylip) version 3.69 [8]. A neighbor-joining (N-J) phylogenetic tree was built by the Neighbor in Phylip, and was visualized using TreeView software [9]. The current study was approved by the Ethics Committee of Central South University Xiangya School of Medicine (approval code: 201303147). Allele frequencies and forensic parameters of the 21 STR loci studied are shown in Supplementary Table S1. In the Li ethnic group from Hainan Province, a total of

196 alleles and 614 genotypes were observed, with corresponding allele frequencies ranging from 0.001 to 0.506. All 21 STR loci were found to be highly genetically polymorphic, with unique allele numbers for these markers ranging from 6 (D1S1627 locus) to 16 (D19S433 locus). No deviations from HWE were observed at any loci. The observed heterozygosity, matching probability, polymorphism information content, and typical paternity index ranged from 0.571 (D1GATA113 locus) to 0.794 (D1S1627 locus), 0.049 (D19S433 locus) to 0.184 (D1S1627 locus), 0.58 (D1GATA113 locus) to 0.82 (D19S433 locus), and 1.17 (D1GATA113 locus) to 2.42 (D1S1627 locus), respectively. The power of discrimination ranged from 0.816 (D1S1627 locus) to 0.951 (D19S433 locus), and the combined power of discrimination was 0.999999999999999999990467. The power of exclusion ranged from 0.258 (D1GATA113 locus) to 0.587 (D1S1627 locus), and the combined power of exclusion was 0.99998319. Allelic frequencies of the 21 STR loci in the Li group were compared with previously published population data from other ethnic groups and regions in China, and the p values are shown in Supplementary Table S2. After Bonferroni’s correction for multiple testing (p = 0.05/21), the AMVOA results showed that the Li group was significantly different from the Uygur group [10] at 19 loci, and from the Mongolian [11], Hunan Han [12], Guangdong Han [13], Eastern Han [14], Salar [15], Northern Han [16], Ningxia Han [17], Russian [18], Tibetan [19], Bai [20], and Tujia [21] groups at 18, 17, 15, 12, 12, 12, 12, 10, 10, eight, and seven STR loci, respectively. These results show that differences can be found in allele frequency distributions

between populations of different ethnic groups and different linguistic families. The Li group was significantly different from all other 12 populations at D1S1627, D2S441, D2S1776, D6S1017, D12ATA63, and D22S1045 loci. These STR loci showed higher population differentiation than the other loci in the panel, and possess the potential to separate the Li nationality from other ethnic groups. As shown in Supplementary Figure S1, the phylogenetic tree constructed by the N-J method from allele frequencies of 21 STR loci reveals the genetic relationships of the Li group with 12 other Chinese populations. Genetic distances between the populations ranged from 0.0054 to 0.0576 (Supplementary Table S3). Compared with the Li group, the largest genetic distance (0.0576) was observed with the Tibetan group, followed by Russian (0.0541) and Salar (0.0505) groups; whereas the smallest genetic distance was found with the Hunan Han population (0.0184), followed by Uygur (0.0212) and Eastern Han (0.0259) populations. Even the smallest genetic distance between the Li group and the Hunan Han population is larger than those between the other 12 populations for more than half of the pairwises. These results indicate that the Li group residing in Hainan Island possesses unique genetic characteristics that differ from ethic groups in other provinces; this is likely to be caused by their relative geographic isolation. The current paper was written in accordance with guidelines for the publication of population genetic papers in the journal [22,23]. We also strictly adhered to recommendations of the International Society for Forensic Genetics for the analysis of DNA polymorphisms and nomenclature [24].

Acknowledgments This study was supported by the Youth Fund of the National Natural Science Foundation of China (No. 81302615 and 81302621) and the National Natural Science Foundation of China (No. 81373249 and 81571855). March 24, 2016 References [1]

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