Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations

Du, Weian; Feng, Chunlei; Yao, Ting; Cheng, Xiangdong; Huang, Hongyan; Wu, Weibin; Zhu, Linnan; Qiao, Honghua; Liu, Chao; Chen, Ling

doi:10.7717/peerj.6861

Cited by 9 publications

(3 citation statements)

References 29 publications

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“…The insertion allele frequency differences between loci are huge, which are even more than one order of magnitude. We observed the same results from other East Asian populations (Du et al, 2019;He et al, 2019a,b). On the contrary, the allele frequency distribution is relatively balanced in European and American populations (Kis et al, 2012;Saiz et al, 2014), indicating that the panel of 30 InDels is informative for population substructure dissection and ancestral information inference at the continental level.…”

Section: Linkage Disequilibrium Forensic Parameters and Allele Freqsupporting

confidence: 92%

Forensic Features and Population Genetic Structure of Dong, Yi, Han, and Chuanqing Human Populations in Southwest China Inferred From Insertion/Deletion Markers

Liu

Zhang

et al. 2020

Front. Genet.

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Guizhou province in southwest China has abundant genetic and cultural diversities, but the forensic features and genetic structure of Guizhou populations remain poorly understood due to the sparse sampling of present-day populations. Here, we present 30 insertion/deletion polymorphisms (InDels) data of 591 human individuals collected from four populations, Dong, Yi, Han, and Chuanqing residing in Guizhou. We calculated the forensic parameters of 30 InDel loci and found that this panel meets the efficiency of forensic personal identification based on the high combined power of discrimination, but it could only be used as a complementary tool in the parentage testing because of the lower combined probability of exclusion values. The studied populations are genetically closer related to geographically adjacent or linguistically related populations in southern China, such as the Tai-Kadai and Hmong-Mien speaking groups. The unrecognized ethnic Chuanqing people show an additional genetic affinity with Han Chinese, highlighting the role of possible military immigrations in their origin.

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Section: Linkage Disequilibrium Forensic Parameters and Allele Freqsupporting

confidence: 92%

Forensic Features and Population Genetic Structure of Dong, Yi, Han, and Chuanqing Human Populations in Southwest China Inferred From Insertion/Deletion Markers

Liu

Zhang

et al. 2020

Front. Genet.

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“…All the allelic frequency data of 30 InDel markers from 100 populations, including African, (Northern and Southern) American, European, and Asian, were collected as the dataset f. Since the genotype data could not be found in some populations in their reports, we sorted out the genotype data from 52 populations as the dataset g, including an African, 3 European, 7 American, 41 Asian populations, and Guizhou Sui (Fondevila et al, 2012;Friis et al, 2012;Kis et al, 2012;Larue et al, 2012;Akhteruzzaman et al, 2013;Carvalho and Pinheiro, 2013;da silva et al, 2013;Martin et al, 2013;Kim et al, 2014;Ferreira Palha et al, 2015;Hefke et al, 2015;Meng et al, 2015;Guo et al, 2016Guo et al, , 2018Martinez-Cortes et al, 2016;Mei et al, 2016;Du et al, 2017Du et al, , 2019Kong et al, 2017;Li et al, 2018Li et al, , 2019Ma et al, 2018;Chen et al, 2019;He et al, 2019a,c;Jian et al, 2019;Liu Y. et al, 2020). The genome-wide SNP data of the Sui population were merged with the reference dataset including 1240 k, Human Origin, and so on (Patterson et al, 2012;Lipson et al, 2018;Mccoll et al, 2018;Liu D. et al, 2020;Ning et al, 2020;Yang et al, 2020;Wang C. C. et al, 2021) to generate two combined datasets covering 189,177 and 71,989 SNPs for subsequent analyses.…”

Section: Reference Datasets and Data Mergingmentioning

confidence: 99%

Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms

Yang

Ren

et al. 2022

Front. Ecol. Evol.

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Insertion-deletion (Indel) serves as one of the important markers in forensic personal identification and parentage testing, especially for cases with degraded samples. However, the genetic diversity and forensic features in ethnolinguistically diverse southwestern Chinese populations remain to be explored. Sui, one Tai-Kadai-speaking population residing in Guizhou, has a complex genetic history based on linguistic, historic, and anthropological evidence. In this study, we genotyped 30 Indels from 511 Guizhou Sui individuals and obtained approximately 700,000 genome-wide single-nucleotide polymorphisms (SNPs) in 15 representative Sui individuals to comprehensively characterize the genetic diversity, forensic characteristics, and genomic landscape of Guizhou Sui people. The estimated forensic statistically allele frequency spectrum and parameters demonstrated that this Indels panel was polymorphic and informative in Tai-Kadai populations in southern China. Results of principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed that Guizhou Sui had a close genetic relationship with geographically close Tai-Kadai and Hmong-Mien people. Furthermore, genomic analysis based on the Fst and f4-statistics further suggested the genetic affinity within southern Chinese Tai-Kadai-speaking populations and a close relationship with geographically adjoining Guizhou populations. Admixture models based on the ADMIXTURE, f4, three-way qpAdm, and ALDER results demonstrated the interaction between the common ancestor for Tai-Kadai/Austronesian, Hmong-Mien, and Austroasiatic speaking populations played a significant role in the formation of modern Tai-Kadai people. We observed a sex-biased influence in Sui people by finding that the dominant Y chromosomal type was a Hmong-Mien specific lineage O2a2a1a2a1a2-N5 but the mtDNA lineages were commonly found in Tai-Kadai populations. The additional southward expansion of millet farmers in the Yellow River Basin has impacted the gene pool of southern populations including Tai-Kadai. The whole-genome sequencing in the future will shed more light on the finer genetic profile of Guizhou populations.

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“…Hence, InDels are considered to be ideal forensic markers and have attracted attentions from forensic researchers worldwide ( Sheng et al, 2018 ). InDels have been increasingly explored and used in forensic genetics and biogeographical ancestry inferences, and much more extensive forensic and population genetic studies are ongoing ( Bastos-Rodrigues et al, 2006 ; Larue et al, 2014 ; Du et al, 2019 ; He et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic Structure and Forensic Feature of 38 X-Chromosome InDels in the Henan Han Chinese Population

Zhang

Zhu

et al. 2022

Front. Genet.

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Insertion/deletion (InDel) polymorphisms, as ideal forensic markers, show useful characteristics of both SNPs and STRs, such as low mutation rate, short amplicon size and general applicability of genotyping platform, and have been used in human identification, population genetics and biogeographic research in recent years. X-chromosome genetic markers are significant in population genetic studies and indispensable complements in some complex forensic cases. However, the population genetic studies of X-chromosome InDel polymorphisms (X-InDels) still need to be explored. In this study, the forensic utility of a novel panel including 38 X-InDel markers was evaluated in a sample of Han population from Henan province in China. It is observed that the heterozygosities ranged from 0.0054 to 0.6133, and the combined discrimination power was 1–9.18 × 10−17 for males and 1–7.22 × 10−12 for females respectively. The mean exclusion chance in trios and duos were 0.999999319 and 0.999802969 respectively. Multiple biostatistics methods, such as principal component analysis, genetic distances analysis, phylogenetic reconstruction, and structure analysis was used to reveal the genetic relationships among the studied Henan Han group and other 26 reference groups from 1,000 Genomes Project. As expected, the Henan Han population was clustered with East Asian populations, and the most intimate genetic relationships existed in three Han Chinese populations from Henan, Beijing and South China, and showed significant differences compared with other continental groups. These results confirmed the suitability of the 38 X-InDel markers both in individual identification and parentage testing in Han Chinese population, and simultaneously showed the potential application in population genetics.

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Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations

Cited by 9 publications

References 29 publications

Forensic Features and Population Genetic Structure of Dong, Yi, Han, and Chuanqing Human Populations in Southwest China Inferred From Insertion/Deletion Markers

Forensic Features and Population Genetic Structure of Dong, Yi, Han, and Chuanqing Human Populations in Southwest China Inferred From Insertion/Deletion Markers

Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms

Genetic Structure and Forensic Feature of 38 X-Chromosome InDels in the Henan Han Chinese Population

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