Genomic diversity at 22 STR loci (extended CODIS STR) in the population of Rajasthan, India
Introduction
The state of Rajasthan is located in the North-western region of India (Fig. 1). Its western international boundaries are formed by Punjab and Sindh provinces of Pakistan and remaining borders are formed by Indian states like Haryana, Punjab, Uttar Pradesh, Madhya Pradesh and Gujarat (Gupta and Bakshi, 2008) (Fig. S1). Rajasthan was earlier known as “Rajputana” which means “Land of Kings” (Gupta and Bakshi, 2008). Its gene-pool is known as the oldest one across the globe. According to Census 2011, Rajasthan is inhabited by5.66% of the total population of India. Demography of Rajasthan comprises of 68,548,437 people (35,550,997 males and 32,997,440 females) (John, 2011). Migration of people of Rajasthan is reflected in its genetic diversity (Lawson et al., 2012).
In forensic science, DNA analysis has become “the new form of scientific evidence” and has come under public scrutiny. More and more courts have begun to accept DNA-based evidence. DNA technology has taken an unparalleled position in the forensic sciences field for the investigation of paternity and criminal cases across the globe (Kumar et al., 2019). Since 1985, when Peter Gill and Alec Jeffrey first applied DNA technology to forensic problems, to this day, more than 50,000 cases worldwide have been solved by using DNA-based technology. DNA analysis based on autosomal as well as sex chromosome STR is routinely used in forensic casework, population study and medico-legal investigations. Although the advancement of DNA technology in forensic science has been extremely rapid, today we are witnessing a new era of DNA technology that uses automation and miniaturization like Rapid DNA Typing (Shrivastava et al., 2020).
In Combined DNA Index System (CODIS), short tandem repeat loci are required for the forensic DNA Analysis purposes. These core loci have been expanded to 20 STRs by the use of CODIS (Hares, 2015; Moretti et al., 2016). Until 01.01.2017, CODIS prescribed 13 core loci for forensic purposes are CSF1PO, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51 and D21S11, and since 1ST January 2017, seven new markers namely D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433 and D22S1045 are included in the extended CODIS markers. In this study we explore genomic diversity on 20 CODIS markers along with two additional Penta E and Penta D markers in the population of Rajasthan. The allelic diversity and several forensic parameters for 13 CODIS core loci have been already reported for the population of Rajasthan (Kumar et al., 2020) and various states of India (Shrivastava et al., 2015).Therefore, there is utmost need of forensic parameter data based on extended CODIS core loci.
This study provides allelic frequencies and various forensic parameter dataset on extended CODIS core loci for the purpose of forensic inferences in the population of Rajasthan. In order to discover genetic affinity of geographically close Indian populations viz., Central Indian Population, Uttar Pradesh, Balmiki (Punjab), Jharkhand; geographically distinct Indian populations viz., Mahadev Koli (Maharashtra), Kora (Bengal), Maheli (Bengal), Tamil Population (Tamil Nadu) and reported populations of Rajasthan, their pre-existing databases were taken into consideration. Comparison of genomic ancestry of studied population with reported global populations was also performed.
Section snippets
Samples
Blood samples of 595 unrelated randomly selected normal adult individuals were taken for the study with prior written informed consent from the candidates. These samples were from the routine casework performed at DNA division, State Forensic Science Laboratory, Jaipur.
DNA isolation and quantification
DNA was isolated from the blood samples using PrepFiler Express™ kit (Thermo Fisher Scientific, CA, USA-Thermo) with the help of Automate Express (Thermo) according to the recommended protocol of the manufacturers. The
Results and discussion
A total of 267 alleles were observed among all the studied loci in the population of Rajasthan. The highest number of the alleles were observed at locus Penta E (21) whereas the lowest number of the alleles were found at locus TH01 (6). A wide range of allele frequency with a minimum value of 0.001 to a maximum value of 0.425 was observed for the studied population among all the tested loci. Allele 15 of locus D22S1045 was found to be the most frequent allele among all the studied genetic
Conclusion
In conclusion, the genetic DNA data of this study would enrich the existing DNA database in respect of extended CODIS core loci, and therefore, may aid in parentage testing and identification of victims of natural disasters. Furthermore, this investigation revealed that locus Penta-E is the most informative and useful marker for the population of Rajasthan. The population of Rajasthan showed a greater genetic affinity with north-western and central Indian populations than southern and eastern
Ethical approval
The study was approved by Ethics Committee of Banaras Hindu University, Varanasi, India (Ref. No. - I.Sc./ECM-XII/2018-19/06).
Funding
This research received no external funding.
CRediT authorship contribution statement
AK and RK designed the study, AK analyzed the samples, AK, PS and RK (Kumawat) did the statistical analysis of the obtained genetic data. AK and RK (Kumawat) wrote the manuscript. RK, PS and GC reviewed the manuscript. All authors read and approved the final manuscript.
Declaration of competing interest
The authors declare that they do not have any conflict of interest.
Acknowledgment
Authors are thankful to the Director, State Forensic Science Laboratory, Rajasthan for permitting the study.
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Genetic polymorphism of 21 STR markers in the representative sample of Indian population
2021, Gene ReportsCitation Excerpt :Whereas Sahajpal et al. identified Penta E as the most polymorphic and discriminative locus in the North Indian population (Sahajpal et al., 2020). Similarly, Penta E was also found to be the most polymorphic in the North-Western Indian population as reported by Kumar et al. (Kumar et al., 2021a, 2021b). Kumar et al. also identified a similar result where Penta E and TPOX were highly prevalent in the North Indian population specifically in the region of Rajasthan (Kumar et al., 2021a, 2021b).
Population genetic data of 22 autosomal STR loci for the Scheduled Caste population of Rajasthan India
2021, Annals of Human Biology
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