Haplotypes of six miniY-STR loci in the Han population from Sichuan province and the Zhuang population in Guangxi Zhuang autonomous region

Population: The blood samples were provided from 307 unrelated males of the Han population in Sichuan province and 253 unrelated males of the Zhuang population in Guangxi Zhuang Autonomous Region. Sichuan is located in west China and is relatively isolated from other parts of China. Guangxi Zhuang Autonomous Region (Guangxi) is situated in south China (Fig. 1). Over 90% of the inhabitants of this region are Chinese Zhuang. People residing in both areas speak a unique dialect and have a distinct life style.

View Large Image Download to PowerPoint

Fig. 1. Distribution of Han population in Sichuan and Zhuang population in Guangxi in China.

DNA extraction: Genomic DNA was extracted using the Chelex-100 protocol as described by Walsh et al. [1].

Amplification: PCR amplifications were performed using the primers and amplification conditions described in [2], except for modifications of two pairs of primers for amplifications of DYS522 and DYS540 loci (see Table 1).

Table 1. Primer sequences used in the present study and [2]

	Y-STR locus	Primer sequencesa	Primer sequencesb
	DYS522c	5′-AATGGATAGACATAGGTGACAGA-3′	5′-TGGATAGACATAGGTGACAGATGAT-3′
		5′-GACAGAGTCATAAACAGAGGGTT -3′	5′-GTTTCTTGGAACCTCATGGTGGACATC-3′
	DYS540	5′- CCCGGGTCCTATACTCATTATT-3′	5′-CCCGGGTCCTATACTCATTATT-3′
		5′- CAACCTGGGCTACAGAGACA-3′	5′-GTTTCTTCAACCTGGGCTACAGAGACA-3′

a Body type for bases at 3′end of the primer indicates that the bases belong to the repeat region used in the present study. b Body type for bases at 3′end of the primer indicates that the bases belong to the repeat region used in the reference [2]. c Primer sequences used for amplification were also used in sequencing study.

Electrophoresis and typing: A total of 2μl PCR products were analyzed by non-denaturing polyacrylamide gel ectrophoresis (T=6%, C=5%) with discontinuous buffer system and visualized by silver staining.

Quality control: Laboratory internal control standards.

Analysis of data: Haplotypes were estimated by direct counting. The haplotype diversities were calculated according to the formula used by Hou et al. [3]. The Rst coefficients which were used for population comparisons were calculated by using the Arlequin version 3.1 software [4].

Access to the data: Available upon request: woodydanyan@yahoo.com.cn.

Results: See Supplementary Table 2.

Other remarks: The specificity of primers used in reference [2] for DYS522 locus is not specific enough. It cannot amplify products specifically. Therefore, we modified the primers in the present study.

The new primers of DYS522 and DYS540 with specificity were designed on line by primer3 (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3.cgi). The length of amplified products of both DYS522 and DYS540 loci ranged from 150 to 170bp and 118 to 130bp respectively. The latter length is shorter than that reported in the reference [2].

According to our present knowledge, the present study is the first report of the Han and the Zhuang populations database on DYS570, DYS556, DYS576, DYS522, DYS508 and DYS540 in China.They are important forensic parameters.

As compared with the reference [2], two new structures – (TATC)10 at DYS508, (TTAT)9 at DYS540 – were found in two Chinese populations. It confirms the usefulness of these markers for characterizing the population structures and differentiation of different ethnic groups.

For six miniY-STR loci analyzed in both populations we observed a total of 395 different haplotypes, 240 in Han, 189 in Zhuang. Haplotype diversity (HD) indicated that these markers are highly discriminating in both Han (0.9980) and Zhuang (0.9965) ethnic populations (see Supplementary Table 2).

A comparative analysis of the haplotypes between Han population data and Zhuang population data has been done by calculating Rst-value and applying AMOVA (Arlequin3.1 software). The results showed that the haplotypes of the Sichuan Han population are significantly different from those of the Guangxi Zhuang population (Rst=0.06975, p<10–4). The results indicated that the structural characteristics of these haplotypes may also be observed in population genetic studies throughout China. These data have great usefulness for forensic application in these two regions, as well as for population genetics study. Furthermore, they can enrich China's ethnical genetic informational resources.

This paper is writtened according to the recommendations approved by the DNA Commission of the International Society of Forensic Genetics (ISFG) [5] and the guidelines for publication of population data requested by the Journal of Forensic Science International [6].