Abstract
Northeastern Thailand comprises one-third of the country and is home to various populations, with Lao Isan constituting the majority, while others are considered minority groups. Previous studies on forensic short tandem repeats (STRs) in Thailand predominantly focused on autosomal STRs but there was a paucity of X-STRs, exclusively reported from the North and Central regions of the country. In this study, we have newly established a 12 X-STRs from a total of 896 samples from Northeastern Thailand, encompassing Lao Isan as the major group in the region, alongside nine minor populations (Khmer, Mon, Nyahkur, Bru, Kuy, Phutai, Kalueang, Nyaw, and Saek). Across all ten populations, the combined powers of discrimination in both genders were high and the combined mean exclusion chance (MEC) indices calculated for deficiency, normal trio and duo cases were also high (> 0.99999). DXS10148 emerged as the most informative marker, while DXS7423 was identified as the least informative. Genetic comparison based on X-STRs frequency supported genetic distinction of cerain minor groups such as Kuy, Saek and Nyahkur from other northeastern Thai groups as well as genetic differences according to the geographic region of Thai groups (Northeast, North and Central). In sum, the overall results on population genetics are in agreement with earlier reports on other genetic systems, indicating the informativeness of X-STRs for use in anthropological genetics studies. From a forensic perspective, despite the limitations of small sample sizes for minority groups, the present results contribute to filling the gap in the reference X-STRs database of the major group Lao Isan, providing valuable frequency data for forensic applications in Thailand and neighboring countries.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
Raw genotypes of 12 X-STRs of females and males are shown in Online Resource 1, (ESM_1).
References
Almarri MA, Lootah RA (2018) Allelic and haplotype diversity of 12 X-STRs in the United Arab Emirates. Forensic Sci Int Genet 33:e4–e6. https://doi.org/10.1016/j.fsigen.2017.12.013
Ardlie KG, Kruglyak L, Seielstad M (2002) Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 3:299–309. https://doi.org/10.1038/nrg777
Asamura H, Sakai H, Kobayashi K, Ota M, Fukushima H (2006) Mini X-STR multiplex system population study in Japan and application to degraded DNA analysis. Int J Legal Med 120:174–181. https://doi.org/10.1007/s00414-005-0074-6
Baeta M, Núñez C, Aznar JM, Sosa C, Casalod Y, Bolea M, Gonzlez-Andrade F, de Pancorbo MM, Martnez-Jarreta B (2013) Analysis of 10 X-STRs in three population groups from Ecuador. Forensic Sci Int Genet 7:e19-20. https://doi.org/10.1016/j.fsigen.2012.08.004
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
Changmai P, Jaisamut K, Kampuansai J, Kutanan W, Altınışık NE, Flegontova O, Inta A, Yüncü E, Boonthai W, Pamjav H, Reich D, Flegontov P (2022) Indian genetic heritage in Southeast Asian populations. PLoS Genet 18:e1010036. https://doi.org/10.1371/journal.pgen.1010036
Chantakot P, Pittayaporn P, Srithongdaeng K, Srithawong S, Kutanan W (2017) Genetic divergence of Austroasiatic speaking groups in the Northeast of Thailand: a case study on Northern Khmer and Kuy. Chiang Mai J Sci 44:1279–1294
Desmarais D, Zhong Y, Chakraborty R, Perreault C, Busque L (1998) Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA). J Forensic Sci 43:1046–1049
Diegoli TM (2015) Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 18:140–151. https://doi.org/10.1016/j.fsigen.2015.03.013
Eberhard DM, Simons GF, Fennig CD (2020) Ethnologue: languages of the World, 23rd edn. SIL International, Dallas
Elakkary S, Hoffmeister-Ullerich S, Schulze C, Seif E, Sheta A, Hering S, Edelmann J, Augustin C (2014) Genetic polymorphisms of twelve X-STRs of the investigator Argus X-12 kit and additional six X-STR centromere region loci in an Egyptian population sample. Forensic Sci Int Genet 11:26–30. https://doi.org/10.1016/j.fsigen.2014.02.007
Excoffier L, Lischer L (2010) Arlequin software 3.5.: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
Garcia FM, Bessa BGO, dos Santos EVW, Pereira JDP, Alves LNR, Vianna LA, Casotti MC, Trabach RSR, Stange VS, Meira DD, Louro ID (2022) Forensic applications of markers present on the X chromosome. Genes 13:1597. https://doi.org/10.3390/genes13091597
Gomes I, Pinto N, Antão-Sousa S, Gomes V, Gusmão L, Amorim A (2020) Twenty years later: a comprehensive review of the X chromosome use in forensic genetics. Front Genet 11:926. https://doi.org/10.3389/fgene.2020.00926
Guo J, Ji J, He G, Ren Z, Zhang H, Wang Q, Zhang H, Wang Q, Yang M, Nabijiang Y, Zhang Z, Zhang J, Huang J, Wang CC (2019) Genetic structure and forensic characterization of 19 X-chromosomal STR loci in Guizhou Sui population. Ann Hum Biol 46:246–253. https://doi.org/10.1080/03014460.2019.1623911
Higham C (2014) Early mainland Southeast Asia: from first humans to Angkor. River Books, Bangkok
Illescas MJ, Pérez A, Aznar JM, Valverde L, Cardoso S, Algorta J, de Pancorbo MM (2012) Population genetic data for 10 X-STR loci in autochthonous Basques from Navarre (Spain). Forensic Sci Int Genet 6(5):e146-148. https://doi.org/10.1016/j.fsigen.2012.02.014
Inturri S, Menegon S, Amoroso A, Torre C, Robino C (2011) Linkage and linkage disequilibrium analysis of X-STRs in Italian families. Forensic Sci Int Genet 5:152–154. https://doi.org/10.1016/j.fsigen.2010.10.012
Khacha-ananda S, Mahawong P (2020) Genetic analysis of 12 X-short tandem repeats loci in a northern Thai population. Med Sci Law 1:34–43. https://doi.org/10.1177/0025802420965000
Kishida T, Wang W, Fukuda M, Tamaki Y (1997) Duplex PCR of the Y-27H39 and HPRT loci with reference to Japanese population data on the HPRT locus. Jpn J Legal Med 51(2):67–69
Krüger J, Fuhrmann W, Lichte KH, Steffens C (1968) On the utilization of erythrocyte acid phosphatase polymorphism in paternity evaluation. Dtsch Z Gesamte Gerichtl Med 64(2):127–146
Kutanan W, Ghirotto S, Bertorelle G, Srithawong S, Srithongdaeng K, Pontham KD (2014) Geography has more influence than language on maternal genetic structure of various northeastern Thai ethnicities. J Hum Genet 59(9):512–520. https://doi.org/10.1038/jhg.2014.64
Kutanan W, Kampuansai J, Srikummool M, Kangwanpong D, Ghirotto S, Brunelli A, Stoneking M (2017) Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages. Hum Genet 136(1):85–98. https://doi.org/10.1007/s00439-016-1742-y
Kutanan W, Kampuansai J, Brunelli A, Ghirotto S, Pittayaporn P, Ruangchai S, Schröder R, Macholdt E, Srikummoo M, Kangwanpong D, Arias L, Stoneking M (2018) New insights from Thailand into the maternal genetic history of Mainland Southeast Asia. Eur J Hum Genet 26(6):898–911. https://doi.org/10.1038/s41431-018-0113-7
Kutanan W, Kampuansai J, Srikummool M, Brunelli A, Ghirotto S, Arias L, Macholdt E, Hübner A, Schröder R, Stoneking M (2019) Contrasting paternal and maternal genetic histories of Thai and Lao populations. Mol Biol Evol 36(7):1490–1506. https://doi.org/10.1093/molbev/msz083
Kutanan W, Liu D, Kampuansai J, Srikummool M, Srithawong S, Shoocongdej R, Sangkhano S, Ruangchai S, Pittayaporn P, Arias L, Stoneking M (2021) Reconstructing the human genetic history of Mainland Southeast Asia: insights from genome-wide data from Thailand and Laos. Mol Biol Evol 38(8):3459–3477. https://doi.org/10.1093/molbev/msab124
Lang Y, Guo F, Niu Q (2019) StatsX v20: the interactive graphical software for population statistics on X-STR. Int J Legal Med 133(1):39–44. https://doi.org/10.1007/s00414-018-1824-6
Li C, Ma T, Zhao S, Zhang S, Xu J, Zhao Z et al (2011) Development of 11 X-STR loci typing system and genetic analysis in Tibetan and Northern Han populations from China. Int J Legal Med 125(5):753–756. https://doi.org/10.1007/s00414-011-0592-3
Liu QL, Lv DJ, Sun HY, Lu HL, Wu XL, Wu XY (2007) Development and forensic application of a pentaplex X-STR loci typing system. Yi Chuan 29:1459–1462 (PMID: 18065380)
Messaoudi SA, Babu SR, Alsaleh AB, Albajjah M, Alsnan N (2019) Genetic diversity and haplotypic structure of a Saudi population sample using Investigator Argus X-12 amplification kit. bioRxiv [Preprit]. https://www.biorxiv.org/content/https://doi.org/10.1101/760819v3
Mishra PP (2010) The history of Thailand. ABC-CLIO/Greenwood, Santa Barbara
Myers RL (2005) The Isan saga: the inhabitants of rural northeast Thailand and their struggle for identity, equality and acceptance (1964–2004). Master’s thesis, San Diego State University, San Diego
Nei M, Roychoudhury AK (1974) Sampling variances of heterozygosity and genetic distance. Genetics 76(2):379–390
Pepinski W, Niemcunowicz-Janica A, Skawronska M, Koc-Zorawska E, Janica J, Berent J, Soltyszewski I (2007) X-chromosomal polymorphism data for the ethnic minority of Polish Tatars and the religious minority of Old Believers residing in northeastern Poland. Forensic Sci Int Genet 1(2):212–214. https://doi.org/10.1016/j.fsigen.2007.01.007
Pereira V, Gusmão L, Valente C, Pereira R, Carneiro J, Gomes I, Morling N, Amorim A, Prata MJ (2012) Refining the genetic portrait of Portuguese Roma through X-chromosomal markers. Am J Phys Anthropol 148(3):389–394. https://doi.org/10.1002/ajpa.22061
Perera N, Galhena G, Ranawaka G (2021) X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations. Sci Rep 11:1. https://doi.org/10.1038/s41598-021-92314-9
Poulsen L, Tomas C, Drobnič K, Ivanova V, Mogensen HS, Kondili A, Miniati P, Bunokiene D, Jankauskiene J, Pereira V, Morling N (2016) NGMSElect™ and Investigator(®) Argus X-12 analysis in population samples from Albania, Iraq, Lithuania, Slovenia, and Turkey. Forensic Sci Int Genet 22:110–112. https://doi.org/10.1016/j.fsigen.2016.02.004
Robino C, Giolitti A, Gino S, Torre C (2006) Development of two multiplex PCR systems for the analysis of 12 X-chromosomal STR loci in a northwestern Italian population sample. Int J Legal Med 120:315–318. https://doi.org/10.1007/s00414-006-0115-9
Salvador JM, Apaga DLT, Delfin FC, Calacal GC, Dennis SE, De Ungria MCA (2018) Filipino DNA variation at 12 X-chromosome short tandem repeat markers. Forensic Sci Int Genet 36:e8–e12. https://doi.org/10.1016/j.fsigen.2018.06.008
Schaffner SF (2004) The X chromosome in population genetics. Nat Rev Genet 5:43–51. https://doi.org/10.1038/nrg1247
Schliesinger J (2000) Ethnic groups of Thailand: non-Tai-speaking peoples. White Lotus Press, Bangkok
Schliesinger J (2001) Tai Group of Thailand: introduction and overview. White Lotus Press, Bangkok
Schliesinger J (2003) Ethnic groups of Laos: profiles of Austro-Thai-speaking peoples. White Lotus Press, Bangkok
Shin SH, Yu JS, Park SW, Min GS, Chung KW (2005) Genetic analysis of 18 X-linked short tandem repeat markers in Korean population. Forensic Sci Int 147:35–41. https://doi.org/10.1016/j.forsciint.2004.04.012
Shrivastava P, Jain T, Gupta U, Trivedi VB (2015) Genetic polymorphism study on 12 X STR loci of investigator Argus X STR kit in Bhil tribal population of Madhya Pradesh, India. Leg Med (tokyo, Japan). 17(3):214–217. https://doi.org/10.1016/j.legalmed.2014.11.004
Srithawong S, Srikummool M, Pittayaporn P, Ghirotto S, Chantawannakul P, Sun J, Eisenberg A, Chakraborty R, Kutanan W (2015) Genetic and linguistic correlation of the Kra-Dai-speaking groups in Thailand. J Hum Genet 60(7):371–380. https://doi.org/10.1038/jhg.2015.32
Srithawong S, Muisuk K, Srikummool M, Mahasirikul N, Triyarach S, Sriprasert K, Kutanan W (2020) Genetic structure of the ethnic Lao groups from mainland Southeast Asia revealed by forensic microsatellites. Ann Hum Genet 84(5):357–369. https://doi.org/10.1111/ahg.12379
Srithawong S, Muisuk K, Srikummool M, Kampuansai J, Pittayaporn P, Ruangchai S, Liu D, Kutanan W (2021) Close genetic relationship between central Thai and Mon people in Thailand revealed by autosomal microsatellites. Int J Legal Med 135(2):445–448. https://doi.org/10.1007/s00414-020-02290-4
Sufian A, Hosen MI, Fatema K, Hossain T, Hasan MM, Mazumder AK, Akhteruzzaman S (2017) Genetic diversity study on 12 X-STR loci of investigator® Argus X STR kit in Bangladeshi population. Int J Legal Med 131(4):963–965. https://doi.org/10.1007/s00414-016-1513-2
Takezaki N, Nei M, Tamura K (2014) POPTREEW: webersion of POPTREE for constructing population trees from allele frequency data and computing some other quantities. Mol Biol Evol 31(6):1622–1624. https://doi.org/10.1093/molbev/msu093
Tao R, Zhang J, Bian Y, Dong R, Liu X, Jin C, Zhu R, Zhang S, Li C (2018) Investigation of 12 X-STR loci in Mongolian and Eastern Han populations of China with comparison to other populations. Sci Rep 98(1):4287. https://doi.org/10.1038/s41598-018-22665-3
Tetzlaff S, Wegener R, Lindner I (2012) Population genetic investigation of eight X-chromosomal short tandem repeat loci from a northeast German sample. Forensic Sci Int Genet 6:e155-156. https://doi.org/10.1016/j.fsigen.2012.03.007
Than KZ, Muisuk K, Woravatin W, Suwannapoom C, Srikummool M, Srithawong S, Lorphengsy S, Kutanan W (2022) Genetic structure and forensic utility of 23 autosomal STRs of the ethnic Lao Groups From Laos and Thailand. Front Genet 13:954586. https://doi.org/10.3389/fgene.2022.954586
Uchigasaki S, Tie J, Takahashi D (2013) Genetic analysis of twelve X-chromosomal STRs in Japanese and Chinese populations. Mol Biol Rep 40(4):3193–3196. https://doi.org/10.1007/s11033-012-2394-1
Vongpaisarnsin K, Boonlert A, Rasmeepaisarn K, Dangkao P (2016) Genetic variation study of 12 X chromosomal STR in central Thailand population. Int J Leg Med 130:1497–1499. https://doi.org/10.1007/s00414-016-1363-y
Xing J, Adnan A, Rakha A, Kasim K, Noor A, Xuan J, Zhang X, Yao J, McNevin D, Wang B (2019) Genetic analysis of 12 X-STRs for forensic purposes in Liaoning Manchu population from China. Gene 683:153–158. https://doi.org/10.1016/j.gene.2018.10.020
Yang X, Zhang X, Zhu J, Chen L, Liu C, Feng X, Chen L, Wang H, Liu C (2017) Genetic analysis of 19 X chromosome STR loci for forensic purposes in four Chinese ethnic groups. Sci Rep 7:42782. https://doi.org/10.1038/srep42782
Zeng X, Ren Z, Chen J, Lv D, Tong D, Chen H, Sun HY (2011) Genetic polymorphisms of twelve X-chromosomal STR loci in Chinese Han population from Guangdong Province. Forensic Sci Int Genet 5(4):e114-116. https://doi.org/10.1016/j.fsigen.2011.03.005
Acknowledgements
We would like to thank all volunteers for donating their biological samples. This work has received scholarship under the Post-Doctoral Training Program from Khon Kaen University, Thailand (PD-2564-10). W.K. was also supported by Global and Frontier Research University Fund, Naresuan University (Grant number: R2566C051).
Author information
Authors and Affiliations
Contributions
Suparat Srithawong, Kanha Muisuk, Nonglak Prakhun and Wibhu Kutanan collected the samples. Suparat Srithawong, Kanha Muisuk and Nonglak Prakhun extracted DNA and performed genotyping. Suparat Srithawong designed the project, analyzed data and drafted the manuscript. Nisarat Tungpairojwong and Wibhu Kutanan designed the project, drafted and edited the manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Ethical approval
The rights of participants and their identity have been protected during the whole process of this research. All experiments were performed in accordance with relevant guidelines and regulations based on the experimental protocol on human subjects which was approved by the Khon Kaen University Ethic Committee (Protocol No. HE642161).
Additional information
Communicated by Boon Peng Hoh.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Srithawong, S., Muisuk, K., Prakhun, N. et al. Forensic efficiency and genetic polymorphisms of 12 X-chromosomal STR loci in Northeastern Thai populations. Mol Genet Genomics 299, 42 (2024). https://doi.org/10.1007/s00438-024-02134-5
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00438-024-02134-5