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Chai S, Li S, Zhu R, Luo L, Chen K, Lei Y, Wan W, Hu X, Liu S, Chen P. Forensic efficiency and population genetic construction of Guizhou Gelao minority from Southwest China revealed by a panel of 23 autosomal STR loci. Forensic Sci Res 2024; 9:owad058. [PMID: 38651135 PMCID: PMC11034531 DOI: 10.1093/fsr/owad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/16/2023] [Indexed: 04/25/2024] Open
Abstract
Short tandem repeats (STRs) are the most common genetic markers in forensic and human population genetics due to their high polymorphism, rapid detection, and reliable genotyping. To adapt the rapid growth of forensic DNA database and solve problems in disputed cases, a panel of 23 autosomal STR loci with high discriminating ability was constructed recently. The Tai-Kadai-speaking Gelao is the most ancient indigenous minority in Guizhou province, however, the forensic efficiency and population genetic structure remain poorly explored. Here, 490 Guizhou Gelao individuals from Southwest China were genotyped with the panel of 23 STRs using the Huaxia Platinum Kit. A total of 265 alleles were screened. The combined discrimination power and the combined probability of paternity were 0.9999 and 0.9999, respectively. This indicated the 23 loci had higher discrimination power in Guizhou Gelao and could be applied to forensic practice. Comprehensive population structures with reference populations from China and abroad using the neighbour-joining phylogenetic tree (N-J tree), multidimensional scaling, principal component analysis and heatmap demonstrated that Guizhou Gelao was genetically closer to Guizhou Han than other populations. Moreover, our results showed that a complex phylogenetic model was influenced by ethnic, geographic, and linguistic factors. Key points The first batch of genetic data for 23 autosomal STRs in 490 Geolao individuals from Guizhou was provided.The 23 STR panel can afford high genetic polymorphisms and discrimination power and can be efficiently applied to forensic practice in Guizhou Gelao population.A complex phylogenetic model influenced by ethnic, geographic, and linguistic factors was uncovered.
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Affiliation(s)
- Siyu Chai
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Shanghai, China
- Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
| | - Shuhua Li
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Guizhou, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Guizhou, China
- Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
| | - Ruxin Zhu
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Shanghai, China
| | - Li Luo
- Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
- School of forensic medicine, Shanxi Medical University, Taiyuan, China
| | - Kaiqin Chen
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Guizhou, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Guizhou, China
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Shanghai, China
| | - Yinlei Lei
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Guizhou, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Guizhou, China
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Shanghai, China
| | - Weihong Wan
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Guizhou, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Guizhou, China
| | - Xijie Hu
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Guizhou, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Guizhou, China
| | - Shiquan Liu
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Pengyu Chen
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Guizhou, China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Guizhou, China
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Shanghai, China
- Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Guizhou, China
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Fu ZY, Sa KJ, Park H, Jang SJ, Kim YJ, Lee JK. Utilization of Novel Perilla SSR Markers to Assess the Genetic Diversity of Native Perilla Germplasm Accessions Collected from South Korea. PLANTS (BASEL, SWITZERLAND) 2022; 11:2974. [PMID: 36365424 PMCID: PMC9659169 DOI: 10.3390/plants11212974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The Perilla crop is highly regarded in South Korea, both as a health food and traditional food. However, there is still a lack of Perilla SSR primer sets (PSPSs) for studying genetic variation among accessions of cultivated and weedy types of Perilla crop (CWTPC) from South Korea. In this study, 30 PSPSs were newly developed based on transcriptome contigs in P. frutescens, and 17 of these PSPSs were used to study the genetic diversity, phylogenetic relationships and structure population among 90 accessions of the CWTPC collected from South Korea. A total of 100 alleles were detected from selected 17 PSPSs, with an average of 5.9 alleles per locus. The gene diversity (GD) ranged from 0.164 to 0.831, with an average of 0.549. The average GD values from the cultivated var. frutescens, weedy var. frutescens, and weedy var. crispa, were 0.331, 0.588, and 0.389 respectively. In addition, most variance shown by Perilla SSR markers was within a population (73%). An analysis of the population structure and phylogenetic relationships showed that the genetic relationship among accessions of the weedy var. frutescens and weedy var. crispa is closer than that for the accessions of the cultivated var. frutescens. Based on association analysis between 17 PSPSs and three seed traits in 90 Perilla accessions, we detected 11 PSPSs that together were associated with the seed size and seed hardness traits. Therefore, the newly developed PSPSs will be useful for analyzing genetic variation among accessions of the CWTPC, association mapping, and selection of important morphological traits in Perilla crop breeding programs.
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Affiliation(s)
- Zhen Yu Fu
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Kyu Jin Sa
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Hyeon Park
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Korea
| | - So Jung Jang
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Korea
| | - Yeon Joon Kim
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Ju Kyong Lee
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Korea
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Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs. Genes (Basel) 2022; 13:genes13081363. [PMID: 36011274 PMCID: PMC9407086 DOI: 10.3390/genes13081363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation.
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