Forensic Science International 128 (2002) 190–195

Announcement of population data

Genomic diversity at 15 fluorescent labeled short tandem
repeat loci in few important populations of
State of Uttar Pradesh, India
M. Tandon, R. Trivedi, V.K. Kashyap*
DNA Typing Unit, Central Forensic Science Laboratory, Ministry of Home Affairs, Government of India,
30 Gorachand Road, Kolkata 700014, India
Received 30 May 2002; accepted 31 May 2002

Abstract

Genomic diversity at 15 short tandem repeat loci is studied in four major endogamous populations of Uttar Pradesh (UP),
India. The studied populations included Thakur, Khatri, Kurmi and Jat; all of whom belong to Hindi speaking linguistic group of
UP State of India. All the STR loci of Powerplex 16TM System have been found highly significant in showing genomic diversity
among the addressed populations. Homozygosity test values for all the 15 loci in studied population range between 0.053 and
0.999, following Hardy–Weinberg equilibrium. Distribution of allele pattern at fluorescent labeled 13 tetranucleotide repeat loci
and two pentanucleotide repeat loci of Powerplex 16TM System portrays that these markers are highly polymorphic, and thus,
suitable in human identity testing and human genetic studies.

Keywords: UP populations; Short tandem repeat; Genomic diversity; Tetranucleotide loci; Pentanucleotide loci

Population information: The studied populations are DNA extraction: From blood of 191 unrelated indivi-
distributed all over the Uttar Pradesh (UP) and practice very duals by phenol chloroform method [1].
high degree of endogamy [5]. The participants included in PCR and typing: The PCR reaction was done with 2 ng
study were only from UP. template DNA following manufacturer’s instructions for
typing Powerplex 16TM loci [2] and genotypes of the multi-
(i) Thakurs (Rajputs) are a heterogeneous community of
plexed products were detected on Long RangerTM gel using
traditional warriors, rulers and land holders. Popula-
ABI Prism1 377 automated DNA Sequencer.
tion size is 5 million approximately in UP.
Analysis of data: The data were analyzed using DNATYPE
(ii) Khatris are predominant community of north-west
program [3]. Power of discrimination has been calculated [4].
India mostly engaged in business and are money-
Results: Presented in Tables 1–4.
lenders in rural areas. Population size is 10 million
Quality control: Laboratory internal control standards
approximately in UP.
and Kit controls.
(iii) Kurmis are a widely distributed community having 11
Access of data: Via electronic mail from communicating
main endogamous divisions. They are landowning and
author.
agricultural community. Population size is 4 million
Other remarks: All the studied loci are observed highly
approximately in UP.
polymorphic in the studied population groups (Tables 1–4).
(iv) Jats are a peasant community of north-west India
Statistical evaluations of homozygosity test, exact test and
whose economy centers round agriculture but some of
likelihood ratio test shows that all the studied populations
them are also self-employed. Population size is 8.5
follow the Hardy–Weinberg equilibrium. The most frequent
million approximately in UP.
and least frequent alleles are calculated and are mentioned
*
Corresponding author. Tel.: þ91-33-284-1753; in Table 5. The data is addition to database of allele frequen-
fax: þ91-33-284-1753. cies of polymorphic loci of other studied Indian populations
E-mail address: vkk2k@hotmail.com (V.K. Kashyap). [6–13] and found consistent with them. The present study

0379-0738/02/$ – see front matter

PII: S 0 3 7 9 - 0 7 3 8 ( 0 2 ) 0 0 1 9 3 - 7
 M. Tandon et al. / Forensic Science International 128 (2002) 190–195 191

Table 1
Allele frequencies and HWE statistical analysis for 15 STR loci in Jat (N ¼ 48) population of Uttar Pradesh
Allele D3S1358 THO1 D21S11 TPOX D18S51 PENTAE vWA D8S1179 FGA D5S818 D13S317 D7S820 D16S539 CSF1PO PENTAD

5 – – – – – 0.141 – – – – – – – – –
6 – 0.232 – – – – – – – – – 0.012 – – –
7 – 0.195 – 0.048 – 0.098 – – – 0.010 0.010 0.095 – 0.011 –
8 – 0.146 – 0.369 – 0.011 – – – 0.135 0.250 0.250 0.128 0.021 0.022
9 – 0.318 – 0.167 – – – 0.011 – 0.031 0.083 0.083 0.085 0.021 0.185
9.3 – 0.109 – – – – – – – – – – – – –
10 – – – 0.095 0.022 0.110 0.022 0.178 – 0.063 0.115 0.095 0.128 0.191 0.207
11 – – – 0.286 – 0.163 0.011 0.078 – 0.427 0.156 0.286 0.319 0.298 0.239
12 – – – 0.035 0.054 0.110 0.022 0.089 – 0.313 0.271 0.179 0.191 0.351 0.185
13 0.011 – – – 0.120 0.110 0.010 0.133 – 0.021 0.094 – 0.117 0.043 0.087
13.2 – – – – – – – – – 0.000 – – – –
14 0.022 – – – 0.210 0.011 0.130 0.267 – – 0.021 – 0.032 0.064 0.065
15 0.228 – – – 0.360 0.065 0.109 0.211 – – – – – – 0.011
16 0.338 – – – 0.065 0.098 0.250 0.033 0.013 – – – – – –
17 0.163 – – – 0.065 0.022 0.272 – 0.013 – – – – – –
18 0.206 – – – 0.011 0.022 0.141 – 0.028 – – – – – –
19 0.021 – – – 0.043 0.006 0.022 – 0.083 – – – – – –
19.2 – – – – – – – – 0.013 – – – – – –
20 0.011 – – – 0.011 – 0.011 – 0.083 – – – – –
21 – – – – – 0.033 – – 0.181 – – – – – –
21.2 – – – – – – – – 0.028 – – – – – –
22 – – – – – – – – 0.097 – – – – – –
22.2 – – – – – – – – 0.028 – – – – – –
23 – – – – 0.006 – – – 0.223 – – – – – –
23.2 – – – – – – – – 0.028 – – – – – –
24 – – – – – – – – 0.069 – – – – – –
24.2 – – – – – – – – 0.013 – – – – – –
25 – – – – 0.011 – – – 0.097 – – – – – –
26 – – 0.011 – 0.022 – – – – – – – – – –
27 – – 0.011 – – – – – – – – – – – –
28 – – 0.202 – – – – – – – – – – – –
29 – – 0.234 – – – – – – – – – – – –
30 – – 0.181 – – – – – – – – – – – –
31 – – 0.053 – – – – – – – – – – – –
31.2 – – 0.117 – – – – – – – – – – – –
32 – – 0.011 – – – – – – – – – – – –
32.2 – – 0.128 – – – – – – – – – – – –
33.2 – – 0.043 – – – – – – – – – – – –
35 – – 0.009 – – – – – – – – – – – –
HT 0.295 0.148 0.970 0.167 0.985 0.981 0.821 0.521 0.993 0.878 0.278 0.144 0.883 0.460 0.380
ET 0.043 0.161 0.395 0.108 0.116 0.603 0.050 0.262 0.034 0.702 0.093 0.049 0.895 0.292 0.352
LR 0.02 0.253 0.542 0.144 0.124 0.549 0.060 0.434 0.071 0.651 0.145 0.086 0.962 0.090 0.218
PD 0.764 0.774 0.820 0.742 0.789 0.892 0.814 0.820 0.876 0.696 0.810 0.784 0.807 0.745 0.820

N: number of individuals typed; HT: HWE homozygosity test; ET: exact test; LR: likelihood ratio; PD: power of discrimination.

Table 2
Allele frequencies and HWE statistical analysis for 15 STR loci in Kurmi (N ¼ 51) population of Uttar Pradesh
Allele D3S1358 THO1 D21S11 TPOX D18S51 PENTAE vWA D8S1179 FGA D5S818 D13S317 D7S820 D16S539 CSF1PO PENTAD

5 – 0.034 – – – 0.009 – – – – – – – – –
6 – 0.250 – – – 0.019 – 0.010 – – – – – – –
7 – 0.102 – – – – – – – – 0.019 – – – 0.020
8 – 0.262 – 0.340 – – – – – 0.144 0.163 0.297 0.088 – –
9 – 0.239 – 0.120 – – – 0.010 – 0.019 0.087 0.159 0.118 0.010 0.340
9.3 – 0.068 – – – – – – – – – – – – –
10 – 0.045 – 0.070 0.020 0.049 0.010 0.170 – 0.029 0.067 0.159 0.088 0.220 0.160
11 – – – 0.400 0.059 0.167 – 0.110 – 0.288 0.395 0.215 0.315 0.250 0.130
12 – – – 0.070 0.039 0.137 – 0.120 – 0.425 0.163 0.159 0.118 0.410 0.090
13 0.009 – – – 0.127 0.118 – 0.070 – 0.086 0.087 0.011 0.235 0.090 0.160
13.2 – – – – – – – – – – – – – 0.000 –
192 M. Tandon et al. / Forensic Science International 128 (2002) 190–195

Table 2 (Continued )
Allele D3S1358 THO1 D21S11 TPOX D18S51 PENTAE vWA D8S1179 FGA D5S818 D13S317 D7S820 D16S539 CSF1PO PENTAD

14 0.019 – – – 0.235 0.059 0.088 0.230 0.011 0.009 0.019 – 0.019 0.020 0.070
15 0.414 – – – 0.157 0.039 0.157 0.140 – – – – 0.019 – 0.030
16 0.231 – – – 0.098 0.147 0.225 0.070 – – – – – – –
17 0.183 – – – 0.147 0.118 0.295 0.050 – – – – – – –
18 0.135 – – – 0.02 0.049 0.176 0.020 – – – – – – –
18.2 – – – – – – – – 0.111 – – – – – –
19 0.009 – – – 0.029 0.029 0.049 – 0.044 – – – – – –
20 – – – – – 0.019 – – 0.144 – – – – – –
21 – – – – 0.010 0.019 – – 0.146 – – – – – –
21.2 – – – – – – – – 0.022 – – – – – –
22 – – – – – – – – 0.100 – – – – – –
22.2 – – – – – – – – 0.011 – – – – – –
23 – – – – 0.010 0.009 – – 0.133 – – – – – –
23.2 – – – – – 0.009 – – 0.078 – – – – – –
24 – – – – 0.010 – – – 0.122 – – – – – –
25 – – – – 0.019 – – – 0.056 – – – – – –
26 – – 0.009 – – – – – 0.022 – – – – – –
27 – – – – 0.020 – – – –
28 – – 0.163 – – – – – – – – – – – –
28.2 – – 0.019 – – – – – – – – – – – –
29 – – 0.221 – – – – – – – – – – – –
30 – – 0.048 – – – – – – – – – – – –
30.2 – – 0.067 – – – – – – – – – – – –
31 – – 0.067 – – – – – – – – – – – –
31.2 – – 0.173 – – – – – – – – – – – –
32.2 – – 0.058 – – – – – – – – – – – –
33 – – 0.009 – – – – – – – – – – – –
33.2 – – 0.105 – – – – – – – – – – – –
34 – – 0.004 – – – – – – – – – – – –
35 – – 0.019 – – – – – – – – – – – –
36 – – 0.009 – – – – – – – – – – – –
36.2 – – 0.019 – – – – – – – – – – – –
HT 0.430 0.055 0.784 0.054 0.860 0.974 0.114 0.099 0.301 0.108 0.501 0.271 0.105 0.492 0.081
ET 0.250 0.020 0.003 0.010 0.144 0.088 0.062 0.002 0.010 0.040 0.182 0.148 0.065 0.308 0.032
LR 0.100 0.031 0.000 0.052 0.094 0.040 0.059 0.001 0.002 0.010 0.412 0.245 0.037 0290 0.032
PD 0.722 0.657 0.869 0.700 0.880 0.893 0.727 0.859 0.884 0.699 0.770 0.790 0.801 0.712 0.790

N: number of individuals typed; HT: HWE homozygosity test; ET: exact test; LR: likelihood ratio; PD: power of discrimination.

Table 3
Allele frequencies and HWE statistical analysis for 15 STR loci in Thakur (N ¼ 45) population of Uttar Pradesh
Allele D3S1358 THO1 D21S11 TPOX D18S51 PENTAE vWA D8S1179 FGA D5S818 D13S317 D7S820 D16S539 CSF1PO PENTAD

4 – 0.011 – – – – – – – – – – – – –
5 – 0.035 – – – 0.041 – – – – – – – – –
6 – 0.221 – 0.031 – – – – – – – 0.014
7 – 0.116 – 0.064 – 0.054 – 0.010 – 0.022 0.022 0.014
8 – 0.256 – 0.340 – – – 0.056 – 0.293 0.141 0.114 0.070 0.033 0.041
9 – 0.221 – 0.128 0.012 0.068 – 0.089 – 0.087 0.033 0.043 0.116 0.044 0.149
9.3 – 0.070 – – – – – – – – – – – – –
10 0.035 – 0.128 0.012 0.081 0.204 0.067 – 0.087 0.109 0.300 0.093 0.233 0.216
11 – 0.035 – 0.256 0.024 0.108 0.020 0.078 – 0.207 0.207 0.258 0.291 0.311 0.216
12 – – – 0.032 0.060 0.095 – 0.111 – 0.185 0.174 0.114 0.186 0.280 0.068
13 0.027 – – 0.021 0.143 0.081 0.040 0.200 – 0.109 0.163 0.129 0.173 – 0.203
13.2 – – – – – – – – – – 0.000 – – 0.044 –
14 0.108 – – – 0.274 0.081 0.040 0.200 – 0.010 0.141 0.014 0.070 0.033 0.014
15 0.234 – – – 0.071 0.108 0.082 0.089 – – 0.010 – – 0.022 0.041
16 0.189 – – – 0.095 0.095 0.122 0.056 0.010 – – – – – 0.041
17 0.230 – – – 0.060 0.041 0.196 0.033 0.061 – – – – – 0.014
18 0.162 – – – 0.024 0.041 0.184 0.011 0.020 – – – – – –
18.2 – – – – – – – – 0.061 – – – – – –
19 0.050 – – – 0.071 0.014 0.061 – 0.030 – – – – – –
 M. Tandon et al. / Forensic Science International 128 (2002) 190–195 193

Table 3 (Continued )
Allele D3S1358 THO1 D21S11 TPOX D18S51 PENTAE vWA D8S1179 FGA D5S818 D13S317 D7S820 D16S539 CSF1PO PENTAD

19.2 – – – – – – – – 0.010 – – – – – –
20 – – – – 0.036 0.010 0.031 – 0.061 – – – – –
20.2 – – – – – – – – 0.010 – – – – – –
21 – – – – 0.024 – 0.010 – 0.177 – – – – – –
21.2 – – – – – – – – 0.051 – – – – – –
22 – – – – – 0.014 0.010 – 0.143 – – – – – –
22.2 – – – – – – – – 0.020 – – – – – –
23 – – – – 0.012 0.014 – – 0.061 – – – – – –
24 – – 0.012 – 0.010 0.054 – – 0.051 – – – – – –
25 – – 0.070 – 0.012 – – – 0.081 – – – – – –
25.2 – – – – – – – – 0.031 – – – – – –
26 – – 0.047 – 0.060 – – – 0.082 – – – – – –
26.2 – – – – – – – – 0.010 – – – – – –
27 – – 0.047 – – – – – 0.020 – – – – – –
28 – – 0.070 – – – – – 0.010 – – – – – –
28.2 – – 0.035 – – – – – – – – – – – –
29 – – 0.210 – – – – – – – – – – – –
29.2 – – 0.023 – – – – – – – – – – – –
30 – – 0.093 – – – – – – – – – – – –
30.2 – – 0.035 – – – – – – – – – – – –
31 – – 0.047 – – – – – – – – – – – –
31.2 – – 0.081 – – – – – – – – – – – –
32 – – 0.023 – – – – – – – – – – – –
32.2 – – 0.058 – – – – – – – – – – – –
33 – – 0.047 – – – – – – – – – – – –
33.2 – – 0.023 – – – – – – – – – – – –
34 – – 0.012 – – – – – – – – – – – –
35 – – 0.047 – – – – – – – – – – – –
37 – – 0.023 – – – – – – – – – – – –
HT 0.086 0.710 0.998 0.111 0.971 0.996 0.772 0.904 0.999 0.238 0.271 0.933 0.446 0.302 0.717
ET 0.071 0.503 0.005 0.020 0.077 0.203 0.043 0.541 0.010 0.040 0.017 0.432 0.618 0.073 0.159
LR 0.073 0.439 0.004 0.020 0.071 0.223 0.150 0.698 0.009 0.099 0.099 0.672 0.655 0.074 0.237
PD 0.815 0.815 0.893 0.780 0.871 0.923 0.856 0.874 0.915 0.809 0.847 0.798 0.819 0.764 0.833

N: number of individuals typed; HT: HWE homozygosity test; ET: exact test; LR: likelihood ratio; PD: power of discrimination.

Table 4
Allele frequencies and HWE statistical analysis for 15 STR loci in Khatri (N ¼ 47) population of Uttar Pradesh
Allele D3S1358 THO1 D21S11 TPOX D18S51 PENTAE vWA D8S1179 FGA D5S818 D13S317 D7S820 D16S539 CSF1PO PENTAD

5 – 0.021 – – – 0.032 – – – – – – – – –
6 – 0.319 – – – – – – – – – – – – –
7 – 0.159 – 0.063 – 0.074 – – – – 0.011 – – – –
8 – 0.138 – 0.300 – 0.043 – – – 0.202 0.138 0.119 0.080 – 0.023
9 – 0.202 – 0.200 – 0.043 – – – 0.234 0.053 0.143 0.125 0.044 0.216
9.3 – 0.096 – – – – – – – – – – – – –
10 – 0.011 – 0.100 0.022 0.085 0.110 0.145 – 0.043 0.085 0.238 0.114 0.178 0.160
11 – 0.021 – 0.213 0.011 0.149 0.024 0.079 – 0.277 0.287 0.310 0.295 0.290 0.284
12 0.033 – – 0.063 0.033 0.053 0.012 0.184 – 0.170 0.266 0.131 0.182 0.300 0.148
13 0.022 – – 0.061 0.087 0.085 0.024 0.197 – 0.064 0.053 0.059 0.159 0.144 0.068
14 0.100 – – – 0.218 0.160 0.122 0.184 – 0.010 0.096 – 0.045 0.044 0.091
15 0.290 – – – 0.196 0.043 0.098 0.118 – – 0.011 – – – 0.010
16 0.233 – – – 0.076 0.064 0.159 0.079 – – – – – – –
17 0.178 – – – 0.163 0.053 0.220 0.013 0.100 – – – – – –
18 0.122 – – – 0.087 0.053 0.171 – 0.071 – – – – – –
19 0.022 – – – 0.043 0.032 0.061 – 0.029 – – – – – –
19.2 – – – – – – – – 0.086 – – – – – –
20 – – – – 0.022 0.021 – – 0.071 – – – – – –
21 – – – – 0.022 0.011 – – 0.143 – – – – – –
21.2 – – – – – – – – 0.014 – – – – – –
22 – – – – 0.011 – – – 0.086 – – – – – –
22.2 – – – – – – – – 0.029 – – – – – –
194 M. Tandon et al. / Forensic Science International 128 (2002) 190–195

Table 4 (Continued )
Allele D3S1358 THO1 D21S11 TPOX D18S51 PENTAE vWA D8S1179 FGA D5S818 D13S317 D7S820 D16S539 CSF1PO PENTAD

23 – – – – – – – – 0.129 – – – – – –
23.2 – – – – – – – – 0.029 – – – – – –
24 – – 0.011 – 0.009 – – – 0.142 – – – – – –
24.2 – – – – – – – – 0.014 – – – – – –
25 – – 0.022 – – – – – 0.057 – – – – – –
27 – – 0.033 – – – – – – – – – – – –
28 – – 0.098 – – – – – – – – – – – –
28.2 – – 0.022 – – – – – – – – – – – –
29 – – 0.142 – – – – – – – – – – – –
29.2 – – 0.011 – – – – – – – – – – – –
30 – – 0.163 – – – – – – – – – – – –
30.2 – – 0.043 – – – – – – – – – – – –
31 – – 0.076 – – – – – – – – – – – –
31.2 – – 0.174 – – – – – – – – – – – –
32 – – 0.022 – – – – – – – – – – – –
32.2 – – 0.120 – – – – – – – – – – – –
33 – – 0.011 – – – – – – – – – – – –
33.2 – – 0.033 – – – – – – – – – – – –
34 – – 0.022 – – – – – – – – – – – –
HT 0.093 0.753 0.999 0.656 0.999 0.609 0.264 0.203 0.428 0.692 0.507 0.093 0.181 0.644 0.013
ET 0.019 0.470 0.922 0.584 0.757 0.008 0.060 0.127 0.109 0.025 0.095 0.217 0.128 0.723 0.149
LR 0.025 0.054 0.882 0.786 0.796 0.001 0.060 0.198 0.187 0.027 0.172 0.138 0.267 0.725 0.053
PD 0.803 0.802 0.887 0.803 0.862 0.913 0.855 0.845 0.902 0.793 0.806 0.792 0.818 0.770 0.812

N: number of individuals typed; HT: HWE homozygosity test; ET: exact test; LR: likelihood ratio; PD: power of discrimination.

Table 5
Most frequent and least frequent allele for 15 STR loci in four important populations of Uttar Pradesh
Population Allele Loci

D3S1358 THO1 D21S11 TPOX D18S51 PENTA E vWA D8S1179 FGA D5S818 D13S317 D7S820 D16S539 CSF1PO PENTA D

Jat Most frequent 16 9 29 8 15 11 17 14 23 11 12 11 11 12 11

Least frequent 13, 20 9.3 35 12 23 19 13 16 16, 17, 7 7 6 14 7 15
24.2
Kurmi Most frequent 15 8 29 11 14 16 17 14 21 12 11 8 11 11 10, 13
Least frequent 13, 19 5 33, 36 10, 21, 23, 23, 23.2 10 6, 9 14, 22.2 14 7, 14 13 14, 15 9 7
12 24
Thakur Most frequent 15 8 29 8 14 15 10 13, 14 21 8 11 10 11 11 10, 11
Least frequent 13 4 24, 34 13 24 20 21, 22 17 16, 19.2, 14 15 6, 7, 14 8, 14 15 17
20.2, 26.2,
28
Khatri Most frequent 15 9 31.2 8 14 14 17 13 21 11 11 11 11 12 11
Least frequent 13, 19 10 29.2, 33 13 24 21 12 17 21.2, 24.2 14 7, 15 13 14 9, 14 15

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