J Forensic Sci, January 2006, Vol. 51, No. 1 doi:10.1111/j.1556-4029.2005.00036.x Available online at: www.blackwell-synergy.com FOR THE RECORD Anamika Singh,1 M.Sc.; R. Trivedi,1 Ph.D.; and V. K. Kashyap,1,2 Ph.D. Genetic Polymorphism at 15 Tetrameric Short Tandem Repeat Loci in Four Aboriginal Tribal Populations of Bengal POPULATIONS: This study reports the genetic polymorphism observed at 15 short tandem repeat loci D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433, and FGA in four aboriginal populations of Bengal. The analysis was performed to decipher the suitability of CODIS as well as six other highly polymorphic and unlinked markers in Forensic Testing. Studied populations include four tribes: Karmali, Kora, Maheli, and Lodha. KEYWORDS: forensic science, DNA typing, population genetics, D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433, FGA, polymorphism, short tandem repeat, Australoid, tribe, Bengal, allele frequency, power of discrimination, power of exclusion All the four studied tribal groups are Australoids. Karmali belong to the traditional blacksmith community. Kora is another tribal community from eastern India that comprises earth-workers and well-diggers. Although the Kora as well as Karmali belong to the Australoid Racial family, they use an Indo-Aryan language ‘‘Khotta’’ for communication (1). Maheli were mainly associated with Indigo cultivation, and their name means bamboo, which signifies their involvement with the bamboo work. They speak the Indoaryan language, Sadri (1). Lodha derive its name from the word ‘‘Lubdhak’’ meaning ‘‘Forest robbers’’ (1). They use the Austro-Asiatic language called ‘‘Lodha’’ for communication. They are mainly concentrated in the west Midnapore district of Chhotanagpur area and were considered a criminal tribe until the revocation of the Criminal Tribe Act. Among the varied occupations, hunting and food-gathering are still their principal sources of livelihood. This study carries great significance, as they are unique due to their association with crime in the past. Besides, no microsatellite study has ever been performed on these populations. Blood samples were collected randomly from different rural areas of Bankura, Midnapur (east and west), and Burdwan districts of Bengal. Genomic DNA was isolated through the organic method of extraction (2). The quantitation of DNA was carried out using the Quantiblot kit (PE Applied Biosystems, Foster City, CA), and PCR amplification of the mentioned short tandem repeat (STR) loci was performed using the AmpF‘STRs IdentifilerTM Multiplex system (PE Applied Biosystems) following the manufacturer’s manual (3). Analysis was carried out on a 4% polyacrylamide gel using an ABI Prism 377 Automated DNA Sequencer machine (PE Applied Biosystems), and genotype classification was carried out by comparison with allelic ladders provided with the Identifiler kit (3). The forensic utility of these markers was evaluated by calculating the allele frequency, likelihood ratio test (LR), exact test (ET), observed heterozygosity (h), and probability of homozygosity (HP) using DNA Type software (4,5) (Tables 1–4). Keeping in view the criteria mentioned in NRC (National Research Council) Report II (6), the power of discrimination (PD) and the power of exclusion (PE) were also computed for those microsatellite markers in these populations (Tables 5 and 6). In the studied populations, the average PD computed is 0.766, whereas the average PE is 0.545. Among the 15 STR studied, loci the highest PD was observed at the D2S1338 locus in Karmali (0.877) population. These 15 STR markers are found to be highly polymorphic in the populations, and they meet Hardy–Weinberg expectations except D19S433 in Karmali and TPOX in Lodha. This work is intended to supplement the ever-increasing information on the Indian population database (7–11) throughout the world. The complete dataset is available at the institute’s website (http://humstr.ndacdb.org) and can also be obtained from the authors upon request. 1 DNA Typing Unit, Central Forensic Science Laboratory, Kolkata 700014, India. 2 Present address: National Institute of Biologicals, A-32, Sector 62, Institutional Area, Noida-201307, India. Acknowledgments Copyright r 2005 by American Academy of Forensic Sciences The study was supported by a grant from BPR&D, MHA, Government of India. 183 184 JOURNAL OF FORENSIC SCIENCES TABLE 1––Genetic polymorphism at fifteen STR loci in Lodha (N 5 198) of Bengal. Allele D5S818 6 7 8 9 9.3 10 11 11.2 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17 18 19 20 21 21.2 22 22.2 23 24 25 26 27 28 29 30 30.2 31 31.2 32.2 33.2 35.2 ET LR h HP FGA D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 vWA TPOX D18S51 0.005 0.046 0.005 0.005 0.126 0.313 0.030 0.126 0.394 0.192 0.035 0.162 0.268 0.303 0.147 0.101 0.106 0.020 0.076 0.146 0.066 0.667 0.045 0.091 0.081 0.136 0.086 0.177 0.222 0.167 0.434 0.091 0.328 0.465 0.202 0.273 0.091 0.131 0.025 0.076 0.217 0.005 0.202 0.304 0.081 0.098 0.025 0.438 0.108 0.010 0.020 0.120 0.170 0.010 0.180 0.010 0.090 0.210 0.150 0.040 0.355 0.322 0.748 0.748 0.030 0.020 0.850 1.00 0.052 0.339 0.333 0.005 0.005 0.199 0.026 0.174 0.01 0.245 0.077 0.107 0.112 0.026 0.015 0.01 0.020 0.314 0.081 0.020 0.005 0.04 0.288 0.030 0.126 0.100 0.435 0.010 0.232 0.005 0.086 0.040 0.330 0.310 0.200 0.030 0.071 0.005 0.086 0.222 0.131 0.121 0.432 0.435 0.818 0.612 0.121 0.051 0.207 0.136 0.081 0.096 0.162 0.121 0.015 0.010 0.109 0.057 0.909 0.194 0.341 0.293 0.768 0.821 0.378 0.459 0.636 0.285 0.948 0.95 0.68 0.812 0.431 0.243 0.556 0.504 0.113 0.316 0.626 0.024 0.578 0.403 0.788 0.809 0.148 0.073 0.859 0.185 0.566 0.587 0.857 0.62 0.700 0.770 0.820 0.090 0.002 0.002 0.596 0.043 0.318 0.364 0.717 0.809 STR, short tandem repeat; N, number of chromosomes; h, observed heterozygosity; ET, exact test; LR, likelihood ratio test; HP, probability of homozygosity. TABLE 2—Genetic polymorphism at fifteen STR loci in Kora (N 5 118) of Bengal. Allele D5S818 6 7 8 9 9.3 10 11 12 13 13.2 14 14.2 15 15.2 16 16.2 17 18 19 FGA D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 vWA TPOX D18S51 0.025 0.161 0.390 0.297 0.127 0.127 0.136 0.102 0.034 0.025 0.034 0.246 0.068 0.034 0.195 0.280 0.212 0.203 0.500 0.263 0.093 0.102 0.093 0.551 0.161 0.254 0.076 0.263 0.280 0.076 0.008 0.356 0.203 0.085 0.339 0.068 0.042 0.085 0.110 0.203 0.246 0.017 0.068 0.398 0.195 0.144 0.017 0.068 0.271 0.305 0.008 0.051 0.407 0.009 0.178 0.025 0.136 0.127 0.017 0.042 0.051 0.102 0.28 0.110 0.297 0.017 0.025 0.051 0.076 0.238 0.263 0.059 0.127 0.381 0.127 0.314 0.203 0.059 0.051 0.017 0.009 SINGH ET AL. . GENETIC POLYMORPHISM IN TRIBES OF BENGAL 185 TABLE 2— Continued. Allele D5S818 FGA 20 21 21.2 22 22.2 23 24 24.2 25 26 28 29 30 31 31.2 32 32.2 33.2 ET LR h HP 0.136 0.102 0.043 0.203 0.008 0.178 0.136 0.008 0.110 0.017 0.454 0.243 0.763 0.439 0.204 0.125 0.932 0.125 D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 vWA TPOX D18S51 0.093 0.059 0.059 0.093 0.068 0.025 0.170 0.120 0.160 0.898 0.097 0.127 0.178 0.144 0.042 0.280 0.025 0.153 0.051 0.693 0.509 0.899 0.138 0.195 0.292 0.661 0.038 0.946 0.947 0.678 0.528 0.643 0.473 0.814 0.202 0.352 0.474 0.610 0.600 0.584 0.497 0.797 0.579 0.141 0.048 0.848 0.133 0.001 0.002 0.780 0.127 0.522 0.396 0.814 0.359 0.025 0.020 0.780 0.983 0.872 0.804 0.780 0.418 0.338 0.372 0.763 0.924 STR, short tandem repeat; N, number of chromosomes; h, observed heterozygosity; ET, exact test; LR, likelihood ratio test; HP, probability of homozygosity. TABLE 3—Genetic polymorphism at fifteen STR loci in Karmali (N 5 102) of Bengal. Allele D5S818 6 7 8 9 9.3 10 11 11.2 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30.2 31 32.2 33.2 ET LR h HP FGA D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 vWA TPOX D18S51 0.098 0.019 0.029 0.029 0.010 0.422 0.049 0.039 0.216 0.049 0.108 0.529 0.098 0.010 0.186 0.078 0.020 0.186 0.010 0.167 0.147 0.049 0.137 0.520 0.206 0.353 0.118 0.088 0.098 0.225 0.127 0.216 0.108 0.314 0.127 0.333 0.324 0.039 0.167 0.490 0.265 0.186 0.039 0.137 0.029 0.088 0.020 0.069 0.019 0.079 0.020 0.275 0.020 0.176 0.225 0.020 0.284 0.059 0.176 0.088 0.137 0.049 0.029 0.049 0.039 0.078 0.265 0.118 0.255 0.118 0.108 0.039 0.019 0.910 0.897 0.823 0.114 0.275 0.232 0.784 0.539 0.366 0.183 0.882 0.298 0.010 0.010 0.039 0.304 0.265 0.02 0.098 0.245 0.009 0.344 0.253 0.784 0.753 0.544 0.717 0.823 0.135 0.310 0.189 0.745 0.369 0.006 0.008 0.764 0.270 0.088 0.059 0.186 0.157 0.039 0.059 0.079 0.137 0.137 0.059 0.357 0.708 0.588 0.359 0.588 0.581 0.765 0.817 0.834 0.850 0.902 0.053 0.104 0.064 0.902 0.589 0.078 0.029 0.187 0.069 0.088 0.049 0.157 0.186 0.029 0.020 0.049 0.002 0.0045 0.784 0.041 0.029 0.176 0.167 0.186 0.324 0.078 0.010 0.216 0.225 0.078 0.010 0.020 0.147 0.226 0.127 0.010 0.184 0.178 0.902 0.143 0.869 0.833 0.647 0.835 0.873 0.770 0.882 0.075 STR, short tandem repeat; N, number of chromosomes; h, observed heterozygosity; ET, exact test; LR, likelihood ratio test; HP, probability of homozygosity. 186 JOURNAL OF FORENSIC SCIENCES TABLE 4—Genetic polymorphism at fifteen STR loci in Maheli (N 5 98) of Bengal. Allele D5S818 6 7 8 9 9.3 10 11 11.2 12 12.2 13 13.2 14 14.2 15 15.2 16 16.2 17 18 19 20 21 22 22.2 23 24 25 26 28 29 30 31 31.2 32.2 ET LR h HP FGA D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 vWA TPOX D18S51 0.133 0.255 0.214 0.286 0.112 0.010 0.061 0.214 0.041 0.020 0.306 0.061 0.061 0.082 0.143 0.214 0.092 0.408 0.245 0.235 0.092 0.143 0.214 0.276 0.194 0.286 0.347 0.020 0.224 0.398 0.010 0.174 0.173 0.112 0.102 0.031 0.072 0.020 0.061 0.143 0.020 0.153 0.041 0.010 0.224 0.337 0.245 0.082 0.296 0.031 0.122 0.041 0.082 0.020 0.184 0.276 0.092 0.020 0.225 0.102 0.061 0.020 0.943 0.828 0.837 0.153 0.146 0.074 0.878 0.267 0.630 0.554 0.867 0.421 0.010 0.010 0.010 0.164 0.010 0.204 0.031 0.082 0.082 0.306 0.061 0.020 0.031 0.051 0.082 0.265 0.112 0.143 0.051 0.010 0.204 0.347 0.020 0.153 0.194 0.082 0.357 0.051 0.061 0.357 0.122 0.255 0.194 0.061 0.051 0.031 0.031 0.163 0.051 0.072 0.010 0.010 0.010 0.071 0.398 0.184 0.061 0.041 0.225 0.544 0.570 0.816 0.263 0.306 0.123 0.061 0.126 0.674 0.074 0.301 0.369 0.755 0.547 0.210 0.062 0.816 0.831 0.673 0.478 0.898 0.042 0.022 0.030 0.796 0.933 0.848 0.914 0.755 0.896 0.041 0.027 0.918 0.182 0.385 0.366 0.878 0.287 0.716 0.572 0.796 0.523 0.93 0.889 0.714 0.818 0.484 0.554 0.735 0.359 STR, short tandem repeat; N, number of chromosomes; h, observed heterozygosity; ET, exact test; LR, likelihood ratio test; HP, probability of homozygosity. TABLE 5—Power of discrimination and power of exclusion values at fifteen STR loci in Lodha, Kora, Karmali, and Maheli tribes of Bengal. Lodha Allele D5S818 FGA D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 D2S1338 D19S433 vWA TPOX D18S51 Kora Karmali PD PE PD PE PD PE 0.723 0.847 0.836 0.864 0.777 0.686 0.691 0.522 0.727 0.777 0.805 0.838 0.744 0.690 0.727 0.506 0.689 0.633 0.814 0.541 0.336 0.398 0.241 0.323 0.577 0.713 0.709 0.633 0.286 0.455 0.717 0.864 0.814 0.824 0.773 0.638 0.74 0.643 0.766 0.764 0.85 0.762 0.780 0.733 0.757 0.455 0.722 0.626 0.646 0.551 0.34 0.494 0.345 0.538 0.535 0.695 0.532 0.563 0.481 0.523 0.724 0.817 0.818 0.765 0.73 0.687 0.824 0.65 0.778 0.792 0.877 0.877 0.824 0.660 0.779 0.506 0.629 0.580 0.504 0.561 0.454 0.606 0.557 0.600 0.533 0.695 0.635 0.522 0.475 0.578 STR, short tandem repeat; PD, power of discrimination; PE, power of exclusion. SINGH ET AL. TABLE 6—Average power of exclusion and discrimination at 15 STR loci in Lodha, Kora, Karmali, and Maheli of Bengal. Lodha Kora Karmali Maheli Average PD Average PE 0.750 0.761 0.773 0.779 0.523 0.536 0.558 0.562 STR, short tandem repeat; PD, power of discrimination; PE, power of exclusion. References 1. Singh KS. India’s communities. National series. People of India. Oxford, UK: Oxford University Press; 1998. 2. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning. A laboratory manual. 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 1989. 3. Applied Biosystems. Applied Biosystems AmpF‘STRs IdentifilerTM PCR amplification kit user’s manual, instruction for use of products, Foster City, CA: Applied Biosystems. 4. Chakraborty R, Zhong Y. Statistical power of an exact test of Hardy– Weinberg proportions of genotype data at a multi-allelic locus. Hum Hered 1994;44:1–9. 5. Guo SW, Thompson EA. Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 1992;48:361–72. . GENETIC POLYMORPHISM IN TRIBES OF BENGAL 187 6. Budowle B, Monson KL, Wooley JR. The reliability of statistical estimates in forensic DNA typing. In: Billings PR, editor. DNA identification. New York: Cold Spring Harbor Press; 1992:79–90. 7. Sarkar N, Kashyap VK. Genetic diversity at two pentanucleotide STR and thirteen tetranucleotide STR loci by multiplex PCR in four predominant population groups of Central India. Forensic Sci Int 2002;128: 196–201. 8. Sahoo S, Kashyap VK. Genetic variation at fifteen autosamal microsatellite loci in three highly endogamous tribal population of Orissa, India. Forensic Sci Int 2002;130:189–93. 9. Gaikwad S, Kashyap VK. Genetic diversity in four tribal groups of Western India: a survey of Polymorphism in 15 STR loci and their application in human identification. Forensic Sci Int 2003;134:225–31. 10. Sitalaximi T, Trivedi R, Kashyap VK. Autosomal microsatellite profile of three socially diverse ethnic Tamil populations of India. J Forensic Sci 2003;48(1):211–4. 11. Neeta S, Kashyap VK. Allelic variation at 15 microsatellite loci in one important Australoid and two Indocaucasoid groups of Chhattisgarh, India. J Forensic Sci 2004;49(1):184–8. Additional information and reprint requests: Anamika Singh, M.Sc. National Institute of Biologicals A-32, Sector 62 Institutional Area Noida-201307 India E-mail: vkk2k@hotmail.com and anamikasingh22@rediffmail.com