Y-chromosomal STRs haplotypes in the Taiwanese Paiwan population
The distribution of Y-chromosomal short tandem repeat (Y-STR) haplotypes was determined in a population of Taiwanese Paiwan aboriginals. Using 17 Y-STR markers, a total of 135 haplotypes were observed, 102 of which were unique. The overall haplotype diversity for the 17 Y-STR loci tested was 0.9922 and the discrimination capacity was 0.6490. In addition, three novel intermediate alleles at the DYS448 locus were also found.
KeywordsY chromosome Paiwan Y-STR DYS19 Yfiler Haplotype
Materials and methods
After obtaining consent, buccal swab samples were collected from 208 unrelated male Paiwan volunteers residing in the southern mountainous regions of Taiwan. Genomic DNA was extracted and purified using the Genomic DNA Extraction Kit (Yeastern Company, Taipei County, Taiwan, ROC.), and DNA concentrations were determined with the 7300 real-time PCR system using the Quantifiler™ Y Human Male DNA Quantification Kit (Applied Biosystems, Foster City, CA, USA).
Target DNA (0.1 ng/μL) was amplified by PCR, using the AmpFlSTR® YFiler™ PCR Amplification Kit (Applied Biosystems), at the following loci: DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4. The efficacy of the kit was determined by the identification of a 9-marker European minimal haplotype (minHt, the haplotype set of DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) and an 11-marker SWGDAM (Scientific Working Group on DNA Analysis Methods) core set (minHt plus DYS438 and DYS439). Amplification was performed in 25 μL reactions containing 10 μL target DNA, 5 μL primer set, 9.2 μL PCR reaction mix and 0.8 μL DNA polymerase using a GeneAmp PCR System 9700 (Applied Biosystems) under the following conditions: 95°C for 11 min, followed by 30 cycles at 94°C for 1 min, 61°C for 1 min and 72°C for 1 min, with a final extension step at 60°C for 80 min. Electrophoresis of the PCR products, together with GeneScan-500 Internal Lane Size Standard (LIZ-500) to determine the base-pair sizes, was performed on the ABI Prism® 3100 Avant Genetic Analyzer (Applied Biosystems). GeneMapper ID Software Version 3.1 (Applied Biosystems) was used in order to determine the allelic repeats by applying YFiler Allelic Ladder. Alleles were named as suggested by the DNA Commission of the International Society of Forensic Genetics .
Allelic frequencies were estimated by direct counting. Gene diversity and haplotype diversity were calculated according to Nei . Comparisons among populations were computed by an analysis of molecular variance (AMOVA) test. Pairwise values of Φ st, an analogue of F st that takes the evolutionary distance between individual haplotypes into account [17, 18], were calculated to measure genetic distances between minimal 9-locus haplotypes of the Paiwan and the published data from ten other populations [19, 20, 21, 22, 23, 24, 25, 26, 27] from the region (n = 2112) with the statistical significance determined by a permutation test (10,000 replicates). We used an implementation of AMOVA provided at the YHRD website . The DYS389I allele length was obtained by subtracting the shorter allele from the longer allele at DYS389I/II. To illustrate the relationship between populations based on pairwise Φ st, an MDS plot was created by using the “Population analysis” tools of the YHRD . A median-joining network  based on 12-locus Y-STR haplotypes (omitting the complex repeats) was calculated using the NETWORK 2.0b software (available online, www.fluxus-engineering.come/sharenet.htm).
Results and discussion
While the national Y-STR database for the Taiwanese populations is growing with currently 1183 haplotypes (refer to www.yhrd.org, National databases, Taiwan) the heterogeneous populations structure must strictly be observed by construction of separate database branches for major and minor subpopulations.
We would like to thank the National Science Council of R.O.C. for supporting the study and appreciate the Pingtung County Government, the Pingtung County Public Health Bureau, and the Majja and Manjhou Township Health Centers for collecting samples.
This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
- 2.Government Information Office of ROC (2009) The Republic of China yearbook 2008. Government Information Office Press, TaipeiGoogle Scholar
- 12.Hsieh HM, Shen RK, Yuen TY et al (2003) Screening of Y-chromosome STR loci in Taiwanese populations. Forensic Sci J 2:69–76Google Scholar
- 16.Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
- 24.Lessig R, Willuweit S, Krawczak M et al (2003) Asian online Y-STR Haplotype Reference Database. Leg Med (Tokyo) 5:160–163Google Scholar
- 31.Chai CK (1967) Taiwan aborigines: A genetic study of tribal variations. Harvard University Press, CambridgeGoogle Scholar