Genetic polymorphism of 19 autosomal STR loci in the Yi ethnic minority of Liangshan Yi autonomous prefecture from Sichuan province in China

The Yi is one of fifty-six ethnic populations and one of the most ancient ethnic groups in China. The Liangshan Yi Autonomous Prefecture (LYAP) in Sichuan Province has the single largest Yi community in China. To establish a Yi population database in the LYAP of Sichuan in China, a Goldeneye™ DNA Identification System 20A Kit with 19 autosomal STRs (short tandem repeats) was used. As a result, the total discrimination power (TDP) and the cumulative probability of exclusion (CPE) for these STRs in 1016 unrelated individuals were 0.999999999999999999999897 and 0.9999999597, respectively. Totals of 273 alleles for 19 STRs and 8–22 alleles for each locus were found. The allelic frequencies ranged from 0.0005 to 0.5084. The forensic parameter averages of these STRs were as follows: observed heterozygosity (Hobs) of 78.44%, expected heterozygosity (Hexp) of 79.89%, discrimination power (DP) of 92.66%, and probability of exclusion (PE) of 57.68%. Penta E presented the highest levels of Hobs and DP, whereas TPOX showed the lowest Hobs and DP values. Nei’s standard genetic distance matrix among 31 populations found that the nearest genetic distance to the Yi population was the Sichuan Han (0.0056). Altogether, we first reported the forensic parameters and allele frequencies of 19 autosomal STRs of the Yi group in Liangshan. These 19 STR makers could provide highly informative polymorphisms for individual identification, paternity testing and genetic population analyses.

. Due to the rich history and complex ethnic makeups in China, it is necessary to study allele frequency for autosomal STRs in different geographic areas and different ethnic groups including Yi Chinese in the LYAP. However, the genetic polymorphisms for autosomal STR loci of the Yi minority in the LYAP are unclear, and the genetic relationships of populations between the Yi minority and other populations are unknown. It is necessary to use autosomal STRs to fill the gap among Y-STRs and X-STRs of this Yi minority. Thus, in this study we focus on establishing a Yi population database from the LYAP in China by using the Goldeneye™ DNA Identification System 20A Kit, which includes 19 autosomal STRs.

Results
Linkage disequilibrium, forensic parameters and allele frequencies. We first performed a linkage disequilibrium (LD) analysis of 19 autosomal STR loci in the Yi group in LYAP. For the LD test, only 3 pairs (Supplementary Table S1) of loci showed significant LD after Bonferroni correction (p = 0.05/171 ≈ 0.0003), indicating that most loci were statistically independent. These few pairs in linkage disequilibrium may be due to random sampling errors because the pairs were located on different autosomal chromosomes or chromosome arms. The forensic parameters, allelic frequencies and p-values of exact tests for Hardy-Weinberg equilibrium (HWE) of 19 autosomal STR loci in the Yi group in Liangshan are presented in Table 1 and Supplementary  Table S2. In the present study, eighteen of the 19 STR loci were observed to show HWE after Bonferroni correction (p = 0.05/19 ≈ 0.0026), and only the D21S11 locus was a significant HWE departure. Individual migration or genetic exchange may be a possible explanation for this deviation. The total discrimination power (TDP) and the cumulative probability of exclusion (CPE) of the 19 STRs in 1016 unrelated individuals were 0.999999999999999999999897 and 0.9999999597, respectively.
A total of 273 alleles for 19 STRs with corresponding allelic frequencies from 0.0005 to 0.5084 were noticed, and 8-22 alleles for each locus were found (Supplementary Table S2     In this study, by recruiting 1016 unrelated individuals, the total discrimination power (TDP) and the cumulative probability of exclusion (CPE) for 19 STRs were found to be 0.999999999999999999999897 and 0.9999999597, respectively. Totals of 273 alleles for 19 STRs and 8-22 alleles for each locus were found. The observed heterozygosity (H obs ) was 78.44%, the expected heterozygosity (H exp ) was 79.89%, the discrimination power (DP) was 92.66%, and the probability of exclusion (PE) was 57.68%. Penta E presented the highest levels of H obs (0.8917) and DP (0.9839), whereas TPOX showed the lowest H obs of 0.6230 and DP of 0.8154. Nei's standard genetic distance matrix among 31 populations found that the nearest genetic distance to the Yi population was the Sichuan Han (0.0056), followed by the Anhui Han (0.0058) and Guangdong Han (0.0059). Nei's standard genetic distance of the Yi population in Sichuan Province to the Yi population in Yunnan Province was 0.0189, showing the 24th nearest genetic distance. Surprisingly, Yunnan Miao showed an obvious distant relationship from other groups, which was consistent with other analyses 11 , showing far distance to Filipinos from the Philippines. Altogether, the NJ phylogenetic tree and MDS corresponded with the cultural, historical, and geographical distribution of the studied majority groups.
The In conclusion, our work was the first to report the forensic parameters and allele frequencies of 19 autosomal STR markers of the Yi group in Liangshan, China, and the population genetic relationships between the Yi minority and 30 other neighbouring populations. These 19 STR makers could provide highly informative polymorphisms for individual identification, paternity testing and genetic population analyses.

Methods
Sample collections and genomic DNA isolation. Bloods from 1016 unrelated healthy Yi individuals were recruited from Xichang City and its surrounding areas of the LYAP, Sichuan Province, P. R. China. Chelex-100 protocol was used to extract DNA 12,13 . The study was approved by the institutional review boards of Southwest Medical University. Informed consent from participants and ethical approval from the Committee of Southwest Medical University were obtained. All experiments were performed in accordance with relevant guidelines and regulations. PCR amplification and STR genotyping. In