Table 1.
Observed size range, genetic diversity statistics and genotyping profile characteristics for 39 microsatellite loci tested on 8 captive Bengal tigers
| Locus ID | Chr. Asn. | Size range (bp) | N | Na | Ne | Ho | HE | PIC | FIS | PID(locus) | PIDSibs (locus) | Main allele peak (height) | Height ratio (1) | Height ratio (2) | Height ratio (3) | Height ratio (4) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 6HDZ0071 | NI | 170 | 8 | 1 | 1.000 | 0.000 | 0.000 | 0 | - | 1.00E + 00 | 1.00E + 00 | 2000 | 1:20 | 1:03 | 0 | 0 |
| 6HDZ0561† | NI | 172-176 | 8 | 3 | 2.415 | 0.750 | 0.586 | 0.52 | −0.217 | 2.38E-01 | 5.16E-01 | 2700 | 1:03 | 1:03 | 1:1.6 | 1:1.4 |
| 6HDZ0641 | NI | 166-170 | 8 | 2 | 1.753 | 0.625 | 0.430 | 0.337 | −0.4 | 4.18E-01 | 6.40E-01 | 800 | 1:2.6 | 1:08 | 1:6 | 1:1.6 |
| 6HDZ0891 | NI | 207-221 | 8 | 3 | 1.910 | 0.625 | 0.477 | 0.427 | −0.25 | 3.23E-01 | 5.93E-01 | 500 | 1:05 | 1:12 | 1:1 | 1:02 |
| 6HDZ1701† | NI | 216-226 | 8 | 3 | 2.723 | 0.875* | 0.633 | 0.556 | −0.324 | 2.12E-01 | 4.87E-01 | 6200 | 1:7.5 | 1:6.2 | 1:6.2 | 1.24 |
| 6HDZ3171 | NI | 192-206 | 8 | 2 | 1.882 | 0.750 | 0.469 | 0.359 | −0.555 | 3.92E-01 | 6.14E-01 | 10000 | 1:05 | 1:2.5 | 1:5.2 | 1:02 |
| 6HDZ7001 | NI | 141-143 | 8 | 2 | 1.600 | 0.500 | 0.375 | 0.305 | −0.272 | 4.61E-01 | 6.78E-01 | 800 | 1:2.6 | 1:04 | 1:1.6 | 1.1 |
| 6HDZ8171 | NI | 238-242 | 8 | 2 | 1.969 | 0.625 | 0.492 | 0.371 | −0.206 | 3.79E-01 | 5.99E-01 | 1000 | 1:05 | 1:10 | 1:2.5 | 1:1.4 |
| Fca0082 | A1 | 130-134 | 8 | 3 | 2.032 | 0.625 | 0.508 | 0.428 | −0.166 | 3.22E-01 | 5.77E-01 | 2300 | 1:03 | 1:1.1 | 1:1.8 | 1:1.5 |
| Fca1262 | B1 | 124-150 | 8 | 4 | 1.969 | 0.625 | 0.492 | 0.458 | −0.206 | 2.92E-01 | 5.77E-01 | 4600 | 1:2.3 | 1:18 | 0 | 1:1.5 |
| Fca2722 | A3 | 112-122 | 8 | 3 | 1.684 | 0.500 | 0.406 | 0.371 | −0.166 | 3.88E-01 | 6.44E-01 | 950 | 1:2.4 | 1:5.2 | 0 | 1:1.2 |
| Fca3042† | A2 | 125-141 | 8 | 3 | 2.462 | 0.750 | 0.594 | 0.511 | −0.2 | 2.48E-01 | 5.15E-01 | 5800 | 1:2 | 1:6.4 | 1:7.8 | 1:1.2 |
| Fca5062† | F2 | 206-220 | 8 | 3 | 2.844 | 0.625 | 0.648 | 0.575 | 0.102 | 1.97E-01 | 4.75E-01 | 6800 | 1:3.4 | 1:4.5 | 1:34 | 1:2.2 |
| Fca6282† | D2/E3 | 106-110 | 8 | 3 | 2.723 | 0.500 | 0.633 | 0.556 | 0.272 | 2.12E-01 | 4.87E-01 | 1900 | 1:19 | 1:12.6 | 1:9.5 | 1:1.5 |
| Ple233† | NI | 152-168 | 8 | 4 | 2.844 | 0.750 | 0.648 | 0.592 | −0.09 | 1.80E-01 | 4.71E-01 | 8000 | 1:04 | 0.097 | 1:16 | 1:1.4 |
| Ple513 | NI | 172-176 | 8 | 2 | 1.600 | 0.500 | 0.375 | 0.305 | −0.272 | 4.61E-01 | 6.78E-01 | 3800 | 1:2.7 | 1:09.5 | 1:7.6 | 1:1.3 |
| Ple553 | NI | 148 | 8 | 1 | 1.000 | 0.000 | 0.000 | 0 | - | 1.00E + 00 | 1.00E + 00 | 8200 | 1:4.7 | 1:02.5 | 1:82 | 0 |
| Ple573† | NI | 141-155 | 8 | 5 | 2.977 | 0.750 | 0.664 | 0.618 | −0.063 | 1.59E-01 | 4.58E-01 | 6200 | 1:6.2 | 1:10 | 1:25 | 1:1.6 |
| PUN824† | NI | 100-122 | 8 | 7 | 4.923 | 0.750 | 0.797 | 0.77 | 0.125 | 6.85E-02 | 3.69E-01 | 1690 | 1:2.6 | 1:15.6 | 1:5.6 | 1:1 |
| PUN1004† | NI | 78-100 | 8 | 6 | 3.765 | 0.625 | 0.734 | 0.702 | 0.2135 | 1.03E-01 | 4.09E-01 | 1030 | 1:4 | 1:17.1 | 0 | 1:1.9 |
| PUN1244† | NI | 88-106 | 8 | 6 | 4.129 | 0.750 | 0.758 | 0.723 | 0.0769 | 9.31E-02 | 3.94E-01 | 1140 | 1:3 | 1:09.5 | 1:2.1 | 1:1.9 |
| PUN1324† | NI | 117-121 | 8 | 3 | 2.977 | 1.000 | 0.664 | 0.59 | −0.4545 | 1.87E-01 | 4.65E-01 | 2900 | 1:3.7 | 1:06.6 | 1:1.4 | 1:1.4 |
| PUN2254 | NI | 178-184 | 8 | 3 | 1.471 | 0.375 | 0.320 | 0.294 | −0.1053 | 4.88E-01 | 7.12E-01 | 1450 | 1:3.4 | 1:07.8 | 1:1.8 | 1:1.5 |
| PUN2294 | NI | 106-120 | 8 | 3 | 2.169 | 0.625 | 0.539 | 0.447 | −0.0938 | 3.05E-01 | 5.57E-01 | 1520 | 1:3.3 | 1:10.8 | 1:3.5 | 1:1.87 |
| PUN3274 | NI | 84-90 | 8 | 2 | 1.882 | 0.250 | 0.469 | 0.359 | 0.5172 | 3.92E-01 | 6.14E-01 | 6345 | 1:3 | 1:15.9 | 1:5.2 | 1:1.5 |
| Mean (based only on polymorphic di-nucleotide loci, n = 23) | 3.347 | 2.465 | 0.641 | 0.552 | 0.485 | −0.118 | ||||||||||
| F412† | D2 | 170-188 | 8 | 4 | 2.977 | 0.625 | 0.664 | 0.616 | 0.125 | 1.61E-01 | 4.58E-01 | 5500 | 1:5 | 1:2.8 | 0 | 1:1.3 |
| F422 | A1 | 207-231 | 8 | 3 | 1.662 | 0.500 | 0.398 | 0.354 | −0.191 | 4.06E-01 | 6.52E-01 | 7000 | 1:23 | 1:14 | 0 | 1:1.5 |
| F532 | A1 | 128-152 | 8 | 4 | 2.169 | 0.750 | 0.539 | 0.483 | −0.333 | 2.68E-01 | 5.48E-01 | 4000 | 1:16 | 1:08 | 0 | 1.4 |
| F852† | B1 | 156-176 | 8 | 3 | 2.612 | 0.375* | 0.617 | 0.544 | 0.447 | 2.20E-01 | 4.96E-01 | 1000 | 1:11 | 1:05 | 0 | 1:01 |
| F1242† | E1 | 258-286 | 8 | 4 | 3.368 | 0.625 | 0.703 | 0.644 | 0.176 | 1.48E-01 | 4.35E-01 | 9000 | 1:22.5 | 1:18 | 1:09 | 1:1.1 |
| Fca3912 | B3 | 216-224 | 8 | 2 | 1.438 | 0.375 | 0.305 | 0.258 | −0.166 | 5.30E-01 | 7.30E-01 | 3200 | 1:5.3 | 1:32 | 1:4.5 | 1:02 |
| Fca441† | D3 | 148-160 | 8 | 4 | 2.723 | 0.750 | 0.633 | 0.57 | −0.12 | 1.97E-01 | 4.83E-01 | 5500 | 1:11 | 1:27.5 | 1:18 | 1:1.3 |
| Fca4532 | A1 | 198 | 8 | 1 | 1.000 | 0.000 | 0.000 | 0 | - | 1.00E + 00 | 1.00E + 00 | 9000 | 1:9 | 1:09 | 0 | 0 |
| Fca7232 | A1 | 295-315 | 8 | 2 | 2.000 | 1.000* | 0.500 | 0.375 | −1 | 3.75E-01 | 5.94E-01 | 3000 | 1:15 | 1:06 | 1:7.5 | 1:1.5 |
| Fca7312 | B1 | 278 | 8 | 1 | 1.000 | 0.000 | 0.000 | 0 | - | 1.00E + 00 | 1.00E + 00 | 8200 | 1:41 | 1:08.2 | 1:27 | 0 |
| Fca7332 | B2 | 119-123 | 8 | 2 | 1.753 | 0.375 | 0.430 | 0.337 | 0.192 | 4.18E-01 | 6.40E-01 | 1300 | 1:8.6 | 1:04.3 | 1:2.8 | 1:01 |
| Fca7402 | C1 | 290-302 | 8 | 4 | 1.969 | 0.625 | 0.492 | 0.458 | −0.206 | 2.92E-01 | 5.77E-01 | 7800 | 1:2.6 | 1:09.7 | 0 | 1:1.1 |
| Fca7422† | D4 | 152-176 | 8 | 4 | 2.844 | 0.500 | 0.648 | 0.592 | 0.291 | 1.80E-01 | 4.71E-01 | 7100 | 1:7.1 | 1:04.7 | 1:7.1 | 1:14 |
| Fca7492 | F2 | 103 | 8 | 1 | 1.000 | 0.000 | 0.000 | 0 | - | 1.00E + 00 | 1.00E + 00 | 4400 | 1:14.6 | 1:04.4 | 1:22 | 0 |
| Mean (based on only polymorphic tetra-nucleotide loci, n = 11) | 3.272 | 2.319 | 0.590 | 0.539 | 0.475 | −0.071 | ||||||||||
| Mean (based only on overall polymorphic loci, n = 34) | 3.323 | 2.418 | 0.625 | 0.548 | 0.482 | −0.103 | ||||||||||
| Mean (based only on suggested panel of polymorphic loci, n = 16) | 4.062 | 3.081 | 0.687 | 0.664 | 0.604 | 0.022 |
†Locus recommended for panel of 16 microsatellite loci.
Chr. Asn., chromosomal assignment of locus in species of origin; NI, no information; T, tetranucleotide repeat; D, dinucleotide repeat; bp, base pairs; Na, number of alleles; Ne, number of effective alleles; HO, observed heterozygosity; HE, PIC, polymorphic information content; expected heterozygosity; PID (locus), probability of identity between unrelated individuals; PID Sibs (locus), probability of identity between siblings; Height ratio 1, first stutter peak/main allele peak; Height ratio 2, minus A peak/main allele peak; Height ratio 3, plus A peak/main allele peak; Height ratio 4, heterozygote allele peak/main allele peak; PIC, polymorphic information content; FIS, inbreeding coefficients. 1Williamson et al. (2002); 2Menotti-Raymond et al. (1999 2005); 3Singh et al. (2002); 4Janecka et al. (2008); *significance of Hardy-Weinberg test (*P < 0.05).