Polymorphism at fifteen

Forensic Science International 126 (2002) 267±271

Announcement of population data

Polymorphism at ®fteen hypervariable microsatellite loci in four populations of Maharashtra, India S. Gaikwad, V.K. Kashyap* DNA Typing Unit, Central Forensic Science Laboratory, Ministry of Home Affairs, Government of India, 30 Gorachand Road, Kolkata 700014, India Received 20 March 2002; received in revised form 25 March 2002; accepted 25 March 2002

Abstract Polymorphism at 15 microsatellite loci was studied in four predominant, endogamous populations of Maharashtra state in India. The studied populations included Marathas, Desasth Brahmins, Chitpavan Brahmins and Dhangars; all of whom belong to Marathi speaking linguistic group of India. The distribution of allele pattern at 13 tetranucleotide repeat and two pentanucleotide repeat of Powerplex 16TM System portrays that these markers are highly polymorphic and thus, informative in human identi®cation and understanding diversity in the addressed populations. Keywords: Maharashtra populations; Microsatellite polymorphism; Powerplex 16TM

General information on the studied populations of Maharashtra: These population groups are distributed all over Maharashtra state and practice very high degree of endogamy.

(iv) Dhangars are peasants (agricultural community) engaged in crop cultivation. Population size is 2.5 million approximately.

(i) Marathas are Ksatriyas (warriors) belonging to legendary cluster of 96 sub-ethnic division raised during the Great King Shivaji's regime. Population size is 3 million approximately. (ii) Desasth brahmins are Rigvedi brahmin, distributed all over Maharashtra. They are the most predominant and ancient group of Maharashtra forming a population size of 2 million approximately. (iiii) Chitpavan Brahmins, spread all over the coastal region (Konkan) of the state, resemble barbers of Egypt with their conspicuous light-eye and light-hair features. Population size is 2 million approximately. The two brahmin groups studied belong to a section of Dravidian brahmins.

DNA extraction: DNA was extracted from blood of 356 unrelated individuals by phenol chloroform method [1]. PCR and typing: The PCR reaction was done with 2 ng template DNA following manufacturer's instructions [2] and genotypes of the multiplex products were detected on long ranger gel using ABI prism 377 Automated DNA Sequencer. Analysis of data: Hardy±Weinberg Expectation test, exact test and likelihood ratio test were carried out using DNA TYPE software for understanding the informativeness of studied genetic markers in human identi®cation and diversity in populations [3±7]. Results: Presented in Tables 1±15. All the microsatellite loci studied were found to be highly polymorphic and informative in these populations.

* Corresponding author. Tel.: ‡91-33-284-1753; fax: ‡91-33-284-1753. E-mail addresses: [email protected], [email protected] (V.K. Kashyap).

0379-0738/02/$ ± see front matter PII: S 0 3 7 9 - 0 7 3 8 ( 0 2 ) 0 0 0 9 0 - 7

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Table 1 Genetic variation at microsatellite locusÐVWA for four population groups of Maharashtra

Table 3 Genetic variation at microsatellite locusÐTPOX for four population groups of Maharashtra

Allele frequencies

Allele frequencies

Allele class

Maratha (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

10 12 13 14 15 16 17 18 19 20 P ET LR

0.005 0.005 0.000 0.195 0.035 0.280 0.255 0.175 0.045 0.005 0.993 0.773 0.901

0.005 0.000 0.010 0.165 0.065 0.255 0.255 0.170 0.050 0.025 0.454 0.093 0.178

0.000 0.000 0.000 0.096 0.095 0.191 0.287 0.243 0.073 0.015 0.452 0.305 0.478

0.000 0.000 0.007 0.150 0.050 0.200 0.450 0.114 0.028 0.000 0.170 0.476 0.372

6 7 8 9 10 11 12 13 14 P ET LR

0.000 0.005 0.226 0.113 0.097 0.468 0.059 0.021 0.011 0.099 0.392 0.481

0.000 0.015 0.390 0.116 0.096 0.323 0.035 0.025 0.000 0.205 0.470 0.585

0.000 0.016 0.306 0.081 0.073 0.444 0.024 0.048 0.008 0.628 0.111 0.210

0.034 0.017 0.237 0.169 0.093 0.280 0.127 0.042 0.000 0.008 0.585 0.297

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio. Table 4 Genetic variation at microsatellite locusÐD3S1358 for four population groups of Maharashtra Allele frequencies

Table 2 Genetic variation at microsatellite locusÐD8S1179 for four population groups of Maharashtra Allele frequencies Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

7 8 9 10 11 12 13 14 15 16 17 18 P ET LR

0.005 0.010 0.000 0.156 0.063 0.083 0.141 0.188 0.250 0.073 0.031 0.000 0.344 0.169 0.148

0.005 0.005 0.005 0.194 0.071 0.056 0.122 0.220 0.211 0.066 0.025 0.020 0.950 0.493 0.517

0.000 0.008 0.000 0.205 0.083 0.098 0.136 0.167 0.182 0.068 0.023 0.030 0.396 0.241 0.219

0.017 0.033 0.042 0.183 0.117 0.092 0.067 0.167 0.192 0.059 0.017 0.017 0.091 0.000 0.003

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

13 14 15 16 17 18 19 20 P ET LR

0.015 0.020 0.362 0.267 0.257 0.074 0.005 0.000 0.461 0.897 0.192

0.014 0.080 0.297 0.326 0.193 0.090 0.000 0.000 0.845 0.944 0.895

0.000 0.022 0.221 0.316 0.302 0.132 0.007 0.000 0.051 0.016 0.013

0.006 0.032 0.234 0.286 0.260 0.104 0.065 0.013 0.202 0.021 0.045

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio. Table 5 Genetic variation at microsatellite locusÐFGA for four population groups of Maharashtra Allele frequencies Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

16 17 18 18.2 19

0.000 0.000 0.017 0.012 0.023

0.000 0.010 0.000 0.000 0.071

0.000 0.000 0.018 0.000 0.123

0.009 0.028 0.019 0.000 0.028

S. Gaikwad, V.K. Kashyap / Forensic Science International 126 (2002) 267±271 Table 5 (Continued )

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Table 7 Genetic variation at microsatellite locusÐD5S818 for four population groups of Maharashtra

Allele frequencies Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

19.2 20 20.2 21 21.2 22 22.2 23 23.2 24 24.2 25 25.2 26 27 28 29 30 31 31.2 43.2 44.2 45.2 P ET LR

0.000 0.081 0.012 0.081 0.012 0.198 0.017 0.116 0.017 0.122 0.035 0.105 0.035 0.047 0.012 0.017 0.006 0.000 0.006 0.017 0.000 0.006 0.006 0.999 0.293 0.165

0.000 0.164 0.010 0.139 0.005 0.107 0.005 0.149 0.015 0.102 0.010 0.102 0.005 0.051 0.020 0.010 0.000 0.005 0.000 0.010 0.010 0.000 0.000 0.999 0.820 0.338

0.017 0.106 0.000 0.035 0.070 0.167 0.017 0.097 0.009 0.175 0.009 0.131 0.000 0.017 0.000 0.009 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.949 0.016 0.045

0.009 0.074 0.009 0.111 0.037 0.074 0.019 0.083 0.037 0.130 0.028 0.046 0.111 0.074 0.065 0.000 0.000 0.009 0.000 0.000 0.000 0.000 0.000 0.997 0.149 0.332

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

Table 6 Genetic variation at microsatellite locusÐTHO1 for four population groups of Maharashtra Allele frequencies Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

4 5 6 7 8 9 9.3 10 11 13.3 P ET LR

0.005 0.015 0.353 0.132 0.127 0.294 0.074 0.000 0.000 0.000 0.339 0.179 0.176

0.000 0.004 0.290 0.159 0.168 0.248 0.112 0.014 0.000 0.005 0.634 0.330 0.268

0.000 0.000 0.265 0.103 0.140 0.375 0.103 0.007 0.007 0.000 0.667 0.400 0.436

0.000 0.000 0.151 0.057 0.089 0.633 0.057 0.006 0.000 0.006 0.372 0.020 0.085

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

Allele frequencies Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

8 9 10 11 12 13 14 P ET LR

0.000 0.029 0.123 0.392 0.328 0.123 0.005 0.425 0.375 0.300

0.009 0.042 0.145 0.360 0.290 0.131 0.023 0.461 0.501 0.343

0.000 0.044 0.169 0.294 0.287 0.199 0.007 0.455 0.272 0.358

0.000 0.032 0.221 0.329 0.247 0.165 0.006 0.588 0.413 0.480

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

Table 8 Genetic variation at microsatellite locusÐD21S11 for four population groups of Maharashtra Allele frequencies Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

25 25.2 26 27 28 28.2 29 29.2 30 30.2 31 31.2 32 32.2 33 33.2 34 34.2 35 35.2 37 P ET LR

0.000 0.000 0.000 0.015 0.112 0.015 0.181 0.000 0.108 0.020 0.064 0.132 0.010 0.235 0.010 0.073 0.005 0.005 0.000 0.005 0.010 0.994 0.145 0.118

0.000 0.000 0.005 0.023 0.154 0.000 0.168 0.000 0.192 0.014 0.051 0.131 0.000 0.192 0.000 0.056 0.000 0.000 0.005 0.000 0.009 0.531 0.561 0.301

0.000 0.000 0.000 0.007 0.125 0.000 0.184 0.015 0.279 0.022 0.052 0.140 0.007 0.103 0.000 0.059 0.000 0.007 0.000 0.000 0.000 0.867 0.116 0.176

0.006 0.006 0.006 0.019 0.095 0.000 0.177 0.026 0.222 0.013 0.006 0.108 0.000 0.228 0.013 0.063 0.000 0.006 0.000 0.000 0.006 0.996 0.010 0.011

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

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Table 9 Genetic variation at microsatellite locusÐD7S820 for four population groups of Maharashtra

Table 11 Genetic variation at microsatellite locusÐD13S317 for four population groups of Maharashtra

Allele frequencies

Allele frequencies

Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

6 7 8 9 10 11 12 13 14 P ET LR

0.000 0.040 0.213 0.064 0.178 0.267 0.213 0.015 0.010 0.119 0.671 0.396

0.005 0.033 0.215 0.079 0.224 0.224 0.168 0.047 0.005 0.299 0.122 0.067

0.000 0.051 0.221 0.059 0.236 0.235 0.176 0.022 0.000 0.315 0.219 0.342

0.000 0.026 0.250 0.102 0.212 0.218 0.173 0.019 0.000 0.362 0.406 0.360

7 8 9 10 11 12 13 14 15 P ET LR

0.020 0.206 0.103 0.073 0.245 0.260 0.054 0.034 0.005 0.288 0.068 0.116

0.000 0.236 0.118 0.118 0.217 0.170 0.127 0.014 0.000 0.364 0.261 0.410

0.000 0.213 0.111 0.088 0.287 0.221 0.073 0.007 0.000 0.184 0.065 0.128

0.019 0.183 0.127 0.127 0.272 0.222 0.044 0.006 0.000 0.274 0.142 0.133

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

Table 12 Genetic variation at microsatellite locusÐPENTA E for four population groups of Maharashtra Table 10 Genetic variation at microsatellite locusÐD18S51 for four population groups of Maharashtra Allele frequencies Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

10 11 12 13 13.2 14 15 16 17 18 19 20 21 22 23 24 P ET LR

0.005 0.020 0.064 0.134 0.000 0.030 0.208 0.109 0.089 0.010 0.049 0.044 0.025 0.010 0.005 0.000 0.959 0.773 0.921

0.010 0.024 0.077 0.144 0.000 0.217 0.163 0.149 0.092 0.034 0.029 0.038 0.014 0.009 0.000 0.000 0.953 0.810 0.824

0.007 0.007 0.082 0.082 0.000 0.239 0.262 0.105 0.075 0.045 0.022 0.022 0.007 0.030 0.000 0.015 0.980 0.299 0.256

0.006 0.006 0.091 0.156 0.006 0.247 0.156 0.104 0.065 0.052 0.059 0.006 0.026 0.000 0.020 0.000 0.441 0.255 0.059

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

Allele frequencies Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 P ET LR

0.062 0.011 0.101 0.011 0.023 0.073 0.152 0.219 0.056 0.028 0.079 0.090 0.039 0.034 0.011 0.011 0.000 0.000 0.000 0.000 0.043 0.210 0.551

0.095 0.000 0.067 0.010 0.005 0.067 0.138 0.086 0.071 0.081 0.124 0.124 0.033 0.052 0.028 0.005 0.009 0.000 0.005 0.000 0.786 0.010 0.034

0.086 0.007 0.085 0.007 0.007 0.039 0.092 0.054 0.139 0.054 0.100 0.108 0.077 0.031 0.015 0.039 0.039 0.007 0.007 0.007 0.999 0.591 0.512

0.033 0.000 0.091 0.006 0.019 0.058 0.104 0.084 0.097 0.045 0.071 0.175 0.071 0.065 0.033 0.039 0.006 0.000 0.000 0.000 0.631 0.158 0.076

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

S. Gaikwad, V.K. Kashyap / Forensic Science International 126 (2002) 267±271

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Table 13 Genetic variation at microsatellite locusÐD16S539 for four population groups of Maharashtra

Table 15 Genetic variation at microsatellite locusÐPENTA D for four population groups of Maharashtra

Allele frequencies

Allele frequencies

Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 107)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

5 8 9 10 11 12 13 14 P ET LR

0.000 0.094 0.153 0.149 0.228 0.238 0.114 0.024 0.760 0.854 0.859

0.005 0.093 0.117 0.140 0.308 0.229 0.089 0.019 0.925 0.827 0.902

0.000 0.088 0.125 0.081 0.382 0.191 0.118 0.015 0.381 0.329 0.416

0.006 0.095 0.196 0.120 0.209 0.184 0.152 0.038 0.449 0.423 0.409

5 6 7 8 9 10 11 12 13 14 15 16 17 P ET LR

0.005 0.000 0.010 0.015 0.181 0.278 0.227 0.116 0.096 0.056 0.005 0.000 0.010 0.936 0.727 0.829

0.000 0.000 0.005 0.014 0.229 0.182 0.243 0.149 0.075 0.065 0.014 0.014 0.010 0.955 0.598 0.671

0.000 0.015 0.000 0.015 0.149 0.202 0.186 0.172 0.119 0.082 0.030 0.000 0.030 0.036 0.003 0.616

0.000 0.006 0.025 0.032 0.139 0.158 0.298 0.158 0.101 0.051 0.013 0.013 0.006 0.486 0.019 0.012

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

Table 14 Genetic variation at microsatellite locusÐCSF1PO for four population groups of Maharashtra Allele frequencies Allele class

Marathas (N ˆ 102)

Desasth brahmin (N ˆ 10)

Chitpavan brahmin (N ˆ 67)

Dhangar (N ˆ 80)

7 8 9 10 11 12 13 14 15 P ET LR

0.000 0.010 0.030 0.260 0.240 0.390 0.035 0.025 0.010 0.233 0.572 0.214

0.000 0.005 0.033 0.205 0.271 0.397 0.075 0.014 0.000 0.163 0.014 0.037

0.000 0.000 0.037 0.216 0.254 0.396 0.090 0.007 0.000 0.189 0.044 0.090

0.013 0.006 0.025 0.165 0.335 0.335 0.089 0.019 0.013 0.067 0.275 0.013

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

Quality control: Laboratory internal control standards and kit controls. Access of data: Data are access via electronic mail from communicating author.

N: number of individuals typed; P: HWE homozygosity test; ET: exact test; LR: likelihood ratio.

Acknowledgements The work was carried out from ®nancial assistance under a plan project of CFSL, Kolkata. References [1] J. Sambrook, E.F. Fritsch, T. Maniatis, Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor New York, 1989. [2] Powerplex 16TM Kit User Manual, Promega Corp., USA, 2000. [3] R. Chakraborty, Y. Zhong, DNA TYPE Software, CHG University of Texas. [4] V.K. Kashyap, N. Sarkar, R. Trivedi, Allele frequencies for STR loci of the Powerplex 16TM multiplex system in ®ve endogamous populations of India, For. Sci. Int., 2001, in press. [5] S. Sahoo, V.K. Kashyap, Allele Frequency of data for Powerplex 16TM loci in four major population of Orissa, India, J. For. Sci., 2002, in press. [6] R. Rajkumar, V.K. Kashyap, Distribution of alleles of ®fteen STR loci of the Powerplex 16TM multiplex in four predominant population groups of South India, For. Sci. Int., 2002, in press. [7] R. Ashma, V.K. Kashyap, Genetic study of 15 important STR loci among four major ethnic groups of Bihar, India. J. For. Sci., 2002, in press.