Characterization of 29 polymorphic microsatellite markers developed by genomic screening of Sumatran rhinoceros (Dicerorhinus sumatrensis)

Brandt, Jessica R.; Saidah, Sinta H.; Zhao, Kai; Ishida, Yasuko; Apriyana, Isabella; Ryder, Oliver A.; Ramono, Widodo; Sudoyo, Herawati; Suryadi, Helena; Van Coeverden de Groot, Peter J.; Roca, Alfred L.

doi:10.1186/s13104-021-05522-x

Table 2 Characterization of 29 microsatellite markers in Sumatran rhinoceros

From: Characterization of 29 polymorphic microsatellite markers developed by genomic screening of Sumatran rhinoceros (Dicerorhinus sumatrensis)

Locus	Primer Sequence (5′–3′)	A	Size Range (bp)	H_E	H_O	F_IS	P_ID	P_ID(sib)
	Highly recommended
Disu033	F: TCTGGATACCTGAGGCTTGAC	2	152–164	0.53	0.00	1.00	0.41	0.63
Disu033	R: ACTGGCATCACTTCTTTCCC	2	152–164	0.53	0.00	1.00	0.41	0.63
Disu098	F: GCTAGGAGAGGGTGTTGGAC	4	98–126	0.78	0.20	0.76	0.14	0.44
Disu098	R: TGGTAGCCTTGCCTCTTTCC	4	98–126	0.78	0.20	0.76	0.14	0.44
Disu100*	F: TGTGGACTTGTCATATATGGGC	2	120–122	0.36	0.40	− 0.14	0.51	0.72
Disu100*	R: TTCATCCATGCTGTCACAAATG	2	120–122	0.36	0.40	− 0.14	0.51	0.72
Disu201^‡	F: TGGAGAGAATTTCAGACATGGG	2	156–158	0.53	0.00	1.00	0.39	0.61
Disu201^‡	R: CTAGCCCAAGATCCATTGGC	2	156–158	0.53	0.00	1.00	0.39	0.61
Disu261	F: AAACCATACGCGGGAGAAGG	2	150–166	0.60	0.33	0.50	0.38	0.59
Disu261	R: GAAGGGAAGATCATGCAGGAG	2	150–166	0.60	0.33	0.50	0.38	0.59
Disu393	F: AGTGAGCAAGGGAATGTGTG	2	155–157	0.36	0.40	− 0.14	0.51	0.72
Disu393	R: GGGTGCTGTCTCTTGATTGG	2	155–157	0.36	0.40	− 0.14	0.51	0.72
Disu448*	F: CAGGTTTCGTTACTGCAGGAC	2	154–156	0.20	0.20	–	0.69	0.83
Disu448*	R: TCTGGTGACCTGAGATGCAC	2	154–156	0.20	0.20	–	0.69	0.83
Disu476*	F: AAACAGGGAAACAAGGTGCG	3	162–174	0.60	0.80	− 0.39	0.29	0.55
Disu476*	R: GACTGCGCCCTTTCTGTTAG	3	162–174	0.60	0.80	− 0.39	0.29	0.55
Disu487*^‡	F: TATCATGTCACAAGCACGCG	2	148–160	0.20	0.20	–	0.69	0.83
Disu487*^‡	R: GTCTTCTTCACGACAGCACC	2	148–160	0.20	0.20	–	0.69	0.83
Disu783*	F: CCTTGCCTTGCCTTCAATCC	3	126–134	0.51	0.60	− 0.20	0.34	0.61
Disu783*	R: CCATCCTTTCTCCTACACAGAC	3	126–134	0.51	0.60	− 0.20	0.34	0.61
Disu847	F: AAAGTCGCCTCTCACACACC	2	138–140	0.20	0.20	–	0.69	0.83
Disu847	R: TCAGAGCCTCCTTGTAAGCG	2	138–140	0.20	0.20	–	0.69	0.83
	Recommended^#
Disu050	F: CTCCCACATTCAGCAAACTTTC	3	160–166	0.51	0.20	0.64	0.34	0.61
Disu050	R: CCAGGCAGTGATGACTCTAC	3	160–166	0.51	0.20	0.64	0.34	0.61
Disu071^‡ +	F: TTGAGATGCATTGCCGTGG	3	168–172	0.73	0.33	0.60	0.23	0.50
Disu071^‡ +	R: CCATGGTTTCTGCATCGTGG	3	168–172	0.73	0.33	0.60	0.23	0.50
Disu076 +	F: TTCCAGCCGCTCTTATGACC	2	125–129	0.53	0.00	1.00	0.41	0.63
Disu076 +	R: TCATGTGCTTATTGGCCATCTG	2	125–129	0.53	0.00	1.00	0.41	0.63
Disu127	F: CCACCACCACCATGCATAG	2	162–164	0.36	0.00	1.00	0.51	0.72
Disu127	R: CATTTGCTCCCATGCTGAAG	2	162–164	0.36	0.00	1.00	0.51	0.72
Disu138	F: GGGACACATGACTCCTCTTATC	2	167–169	0.53	0.00	1.00	0.41	0.63
Disu138	R: CCACTCCACCTTATACTACCAC	2	167–169	0.53	0.00	1.00	0.41	0.63
Disu149	F: GAGCGTGCATGGTAGTTTCC	4	160–168	0.73	1.00	− 0.43	0.18	0.47
Disu149	R: GGTTCTCATAGCAGACGGAG	4	160–168	0.73	1.00	− 0.43	0.18	0.47
Disu151^‡ +	F: CATTGTGCTCGCTACGCAG	2	135–137	0.36	0.00	1.00	0.51	0.72
Disu151^‡ +	R: CTAGGTGTCAAGAGCCAGGG	2	135–137	0.36	0.00	1.00	0.51	0.72
Disu480	F: CCTGCCTTCTAGTCCTGTGG	2	112–116	0.47	0.20	0.60	0.42	0.65
Disu480	R: AGCAAGCAGGATCAGGAAGG	2	112–116	0.47	0.20	0.60	0.42	0.65
Disu501	F: TGGCCACATCTTCAGCATTAAG	2	155–157	0.47	0.60	− 0.33	0.42	0.65
Disu501	R: GCACCTAACACAGTTACAGGC	2	155–157	0.47	0.60	− 0.33	0.42	0.65
Disu542^‡ +	F: AAACTACAGGCACGTACAGC	2	128–130	0.20	0.20	–	0.69	0.83
Disu542^‡ +	R: TTGAGAGATGAGGTGCGGTC	2	128–130	0.20	0.20	–	0.69	0.83
Disu545	F: TGTTGTCCAAGCTGTGTCTG	2	148–150	0.20	0.20	–	0.69	0.83
Disu545	R: TGGCAGCTGGTACCTAACAG	2	148–150	0.20	0.20	–	0.69	0.83
Disu556 +	F: GCCAATTAAATCTACCTGCCAC	2	168–174	0.25	0.25	–	0.63	0.80
Disu556 +	R: GCCAAGACTCAAACCCAGG	2	168–174	0.25	0.25	–	0.63	0.80
Disu582	F: TCTGTGGTGGTAGCTGTGAC	2	144–152	0.36	0.00	1.00	0.51	0.72
Disu582	R: TGGCACAGAGACACCCATG	2	144–152	0.36	0.00	1.00	0.51	0.72
Disu593^‡ +	F: CCACGTCCCAGGTCAAGAG	3	164–166	0.56	0.20	0.67	0.38	0.59
Disu593^‡ +	R: AGCTGTTCCTGGTGGCTC	3	164–166	0.56	0.20	0.67	0.38	0.59
Disu733	F: TGGCACAGAGACACCCATG	2	151–159	0.36	0.00	1.00	0.51	0.72
Disu733	R: TCTGTGGTGGTAGCTGTGAC	2	151–159	0.36	0.00	1.00	0.51	0.72
Disu748^‡	F: CCTTGATTGGTGGGTTCCC	3	106–116	0.64	0.80	− 0.28	0.26	0.53
Disu748^‡	R: AGAGAGAGCGCACGTGTG	3	106–116	0.64	0.80	− 0.28	0.26	0.53
	Not recommended
Disu269^‡ + a	F: CAAGACCACACCTGCTTGTC	3	115–152	0.60	0.33	0.50	0.30	0.58
Disu269^‡ + a	R: ACTCACTCATCACCCAGCC	3	115–152	0.60	0.33	0.50	0.30	0.58
Disu863^‡ + b	F: GAAGCTGTATGTCCGGATGC	2	162–166	0.36	0.40	− 0.14	0.51	0.72
Disu863^‡ + b	R: GCTAAACAGACCTTCCTCAGAG	2	162–166	0.36	0.40	− 0.14	0.51	0.72

A is the number of alleles per locus, H_E and H_O are expected and observed heterozygosity, respectively. P_ID is the probability of identity and P_ID(sib) is the probability of identity between siblings. F_IS reflects deviation from Hardy–Weinberg proportions. Results are based on samples of six individuals initially tested. Among the highly recommended markers, an asterisk (*) indicates those that produced exceptionally good results. A dagger (^‡) indicates that primers amplify tapir amplicons (though with very different sizes than for rhino); species identity may be established with mtDNA. A plus sign ( +) indicates primers that may amplify human DNA (see Table S4 for differences in size range). The primers listed as "recommended" (#) may be subject to further improvement with additional optimization. Reasons primers were not recommended: a-failed to amplify; b-lack polymorphism in Indonesian samples. The size range includes an M13 forward sequence (TGTAAAACGACGGCCAGT) added to the 5′ end of each forward primer (but not shown as part of the forward primer sequences above). The P_ID and P_ID(sib) are calculated by the method of Waits et al. 2001 (reference 20)

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