Panel of polymorphic heterologous microsatellite loci to genotype critically endangered Bengal tiger: a pilot study

Mishra, Sudhanshu; Singh, Sujeet Kumar; Munjal, Ashok Kumar; Aspi, Jouni; Goyal, Surendra Prakash

doi:10.1186/2193-1801-3-4

SpringerPlus

Table 1 Observed size range, genetic diversity statistics and genotyping profile characteristics for 39 microsatellite loci tested on 8 captive Bengal tigers

From: Panel of polymorphic heterologous microsatellite loci to genotype critically endangered Bengal tiger: a pilot study

Locus ID	Chr. Asn.	Size range (bp)	N	Na	Ne	Ho	H_E	PIC	F_IS	P_ID(locus)	P_IDSibs (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
6HDZ056^1†	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
6HDZ170^1†	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
Fca304^2†	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
Fca506^2†	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
Fca628^2†	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
Ple23^3†	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
Ple57^3†	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
PUN82^4†	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
PUN100^4†	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
PUN124^4†	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
PUN132^4†	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
F41^2†	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
F85^2†	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
F124^2†	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
Fca742^2†	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; H_O, observed heterozygosity; H_E, PIC, polymorphic information content; expected heterozygosity; P_ID (locus), probability of identity between unrelated individuals; P_ID 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; F_IS, 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).

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