Genetic analysis of 15 mtDNA SNP loci in Chinese Yi ethnic group using SNaPshot minisequencing

SNaPshot minisequencing is a rapid and robust methodology based on a single base extension with a labeled ddNTP. The present study detected 15 selected SNPs in the mitochondrial DNA (mtDNA) control and coding regions by minisequencing methodology using SNaPshot for forensic purpose. The samples were...

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Bibliographic Details
Published in:Gene 2016-01, Vol.576 (1), p.105-108
Main Authors: Hu, Chun-Ting, Yan, Jiang-Wei, Chen, Feng, Zhang, Qing-Xia, Wang, Hong-Dan, Yin, Cai-Yong, Fan, Han-Ting, Hu, Ling-Li, Shen, Chun-Mei, Meng, Hao-Tian, Zhang, Yu-Dang, Wang, Hui, Zhu, Bo-Feng
Format: Article
Language:English
Subjects:
Asian Continental Ancestry Group
China
DNA, Mitochondrial - genetics
Female
Genetic distance
Genetic Loci
Humans
Male
Mitochondrial DNA
Polymorphism, Single Nucleotide
Sequence Analysis, DNA - methods
Single nucleotide polymorphism
SNaPshot
Yi ethnic group
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Summary:SNaPshot minisequencing is a rapid and robust methodology based on a single base extension with a labeled ddNTP. The present study detected 15 selected SNPs in the mitochondrial DNA (mtDNA) control and coding regions by minisequencing methodology using SNaPshot for forensic purpose. The samples were collected from 99 unrelated individuals of the Yi ethnic minority group in Yunnan Province. We have predominantly found high-frequency transitions (91.7%) and a significantly lower frequency of transversions (8.3%). The nt152, 489, 8701, 10,398, 16,183, and 16,362 loci were highly polymorphic, while the nt231, 473 and 581 loci were not polymorphic in the studied population. Based on these 15 SNPs, a total of 28 mtDNA haplotypes were defined in 99 individuals with the haplotype diversity of 0.9136. Also, we compared the mtDNA sequences of Yi group and other 9 populations worldwide and drew a Neighbor-Joining tree based on the shared 12 mtDNA SNP loci, which demonstrated a close relationship between Yi and Bai groups. In conclusion, the analysis of the 15 selected SNPs increases considerably the discrimination power of mtDNA. Moreover, the SNaPshot minisequencing method could quickly detect mtDNA SNPs, and is economical and sensitive. The set of selected 15 SNPs is highly informative and is capable for anthropology genetic analysis. •SNaPshot minisequencing was applied to type SNPin this study.•15 SNPs were typed in 99 unrelated individuals from Chinese Yi group.•Totally 28 mtDNA haplotypes were defined with the haplotype diversity of 0.9136.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2015.09.071