A multiplex marker set for microsatellite typing and sexing of sooty terns Onychoprion fuscatus

Garrett, Lucy J. H.; Dawson, Deborah A.; Horsburgh, Gavin J.; Reynolds, S. James

doi:10.1186/s13104-017-3084-9

BMC Research Notes

Table 1 Multiplex sets for sooty tern (Onychoprion fuscatus) microsatellite genotyping including three sex-typing markers

From: A multiplex marker set for microsatellite typing and sexing of sooty terns Onychoprion fuscatus

Locus	Clone name, NCBI accession number/references	Repeat motif	Primer sequence (5′–3′)		Multiplex/fluoro-label (F)	n	A	Observed (expected) allele size range (bp)	H_O	H_E	P _HWE	Est null allele freq.
Ofu1	Trn17616	CA₍₁₇₎	F	TGTTTAAGCAGTAAAGACAAAGCCTAC	7/NED	22	12	202–227	0.96	0.89	0.76	− 0.05
	LT903723		R	GGTGCGTTTAGAGTGCTTCTTTAG				(211)
Ofu2	Trn23851	AC₍₁₅₎	F	GGCTGTAGCGAGCAGTTAGG	2/HEX	22	8	189–359	0.78	0.80	0.74	0.02
	LT903724		R	GAAGCTTGGGTGCAGGTG				(209)
Ofu3	Trn25452	CA₍₁₆₎	F	GGCTGTAGCGAGCAGTTAGG	5/6-FAM	23	10	144–166	0.78	0.80	0.43	0.01
	LT903725		R	GAAGCTTGGGTGCAGGTG				(170)
Ofu4	Trn4256	AC₍₁₈₎	F	CCTGTTGCCAAGAAATAAATCTTAC	5/HEX	22	13	141–175	1.00	0.89	0.29	− 0.07
	LT903726		R	TGAAGAAGCGTGGCTGTG				(150)
Ofu5	Trn171	TG₍₂₁₎	F	TCCCTACTTGACTTTGGAAACATC	4/6-FAM	20	12	86–131	0.95	0.91	0.81	− 0.04
	LT903727		R	TGTACAACACTGTTCCATCATGC				(103)
Ofu6	Trn352	CA₍₁₆₎	F	GCGTTCGGCATCAAGTTAG	7/HEX	22	9	265–281	0.86	0.83	0.90	0.05
	LT903728		R	ATCCCTGCAAAGCACACAG				(282)
Ofu7	Trn436	TG₍₁₉₎	F	TTGCTACAAACCTTGGTTATTGAC	4/NED	22	10	154–184	0.77	0.85	0.23	0.04
	LT903729		R	GCAACCTTAGCATTACCTAGCTG				(165)
Ofu8	Trn640	GA₍₁₅₎	F	GGGTTACTGCTGGTCAGAGC	1/6-FAM	23	14	272–328	0.91	0.85	0.63	− 0.06
	LT903730		R	GCTCTAGGCCAATTTCATCATC				(289)
Ofu9	Trn643	TG₍₂₀₎	F	CTAAGCTGAAATTCCTGAACTGG	6/6-FAM	23	14	174–206	0.96	0.92	0.40	− 0.03
	LT903731		R	CAACTACAGACATCCCACAAGC				(185)
Ofu10	Trn16824	CTT₍₂₆₎	F	GGAAGGAGCATTCAGTCTGC	2/NED	20	17	132–210	1.00	0.95	0.91	− 0.04
	LT903732		R	GATGCTCAGATGCTTGCTAGG				(167)
Ofu11	Trn13992	TATC₍₁₅₎	F	AAAGTCTGTCACACATCCAACG	1/6-FAM	22	8	155–203	0.77	0.72	0.53	− 0.05
	LT903733		R	CACGGTGCCAGTTAATAATGC				(203)
Ofu12	Trn129	CT₍₁₄₎	F	TTAAGCAGAAAGCCAGAGTGG	3/6-FAM	22	9	300–330	0.73	0.80	0.14	0.04
	LT903734		R	CTTAGTGTGCTTGGTAAAGACTGAAC				(314)
Ofu13	Ofu839	TCCA₍₁₄₎	F	GAGGCCACCCTTACACCTC	6/HEX	22	8	142–171	0.86	0.83	0.46	− 0.04
	LT903735		R	AAATGAGCTTGGCTTTACGC				(169)
Ofu14	Ofu897	CA₍₁₄₎	F	GATCTTTCCCAGTAGCACCTATG	4/HEX	19	7	350–365	0.79	0.82	0.63	− 0.00
	LT903736		R	CCACCTGGCTGGATAACAG				(349)
Ofu15	Trn191	CA₍₁₄₎	F	AAAGAGTCTCCACCTGAAGCAG	2/6-FAM	22	10	333–354	0.86	0.86	0.97	− 0.02
	LT903737		R	AGCAATATCCCTGGCAGTACC				(340)
Ofu16	Trn484	CA₍₁₃₎	F	TTTCCTCCTGAGACTTGCGTA	6/6-FAM	22	7	314–327	0.55	0.68	0.20	0.09
	LT903738		R	AAACCAAACTGGCATCAAATAAGT				(324)
Ofu17	Trn715	AC₍₁₂₎	F	CACCTTATCAAGGGCAATGG	5/NED	23	10	185–207	0.74	0.87	0.11	0.08
	LT903739		R	TTGGATGGATAAAGCAAGCTG				(194)
Ofu18	Trn269	TC₍₁₂₎	F	ATCCCTGTCACTCCCATGAC	1/HEX	22	5	298–306	0.64	0.76	0.25	0.08
	LT903740		R	TGCACATGGAAAGTTGCTTC				(303)
Ofu19	Trn15	AC₍₁₂₎	F	TTAGCCCTTTACCCAAATGC	6/6-FAM	23	8	94–116	0.74	0.72	0.95	− 0.03
	LT903741		R	ATTACGTCAGCCTCCTCCAG				(115)
Ofu20	Trn551	TTGG₍₁₁₎	F	CCCAGTGACTCGCTTGCT	3/HEX	22	9	216–262	0.86	0.86	0.35	− 0.00
	LT903742		R	CTGCAACAGCCTTTCAGTCA				(221)
Ofu21	Trn121	GT₍₁₁₎	F	GGCTTAGAAATACTGCCTTTGC	5/6-FAM	22	20	269–321	1.00	0.95	0.36	0.04
	LT903743		R	CTGCTGGTCTGTAAACCATTTATC				(278)
Ofu22	Trn652	AC₍₁₁₎	F	TTTGCAACAGAAACCTTATCCTG	6/NED	23	6	152–164	0.70	0.70	0.35	− 0.00
	LT903744		R	TATATTGCCTCTGGCCGTTG				(162)
Ofu23	Trn407	CCAT₍₁₀₎	F	CCTGCATATCCCAATATCATCC	1/HEX	20	10	142–183	0.80	0.86	0.53	0.02
	LT903745		R	GGGAGGTTCAGGTTGTAATGC				(171)
Ofu24	Trn442	ATCT₍₉₎	F	ATGCATGGAAGCTGCTAACC	3/6-FAM	22	8	148–177	0.91	0.84	0.44	− 0.05
	LT903746		R	ATCTGAGGTGGTCATCATTCTTAAC				(169)
Ofu25	Trn126	TTTGT₍₈₎	F	TAGACCAGGCTGCTCAAAGC	5/HEX	22	10	221–226	0.73	0.73	0.42	0.00
	LT903747		R	TCCACCTCACCGTACTGGAT				(239)
Ofu26	Trn825	AAAC₍₈₎	F	CCTGGGAATAAACAGGAAAGC	4/6-FAM	22	4	189–198	0.64	0.59	0.59	− 0.05
	LT903748		R	ATCAGCCAAGGTTTGACCAC				(190)
Z002A	[11]	–	–	–	2/6-FAM	13 M	1	249 (Z)	0	–	–	–
			–	–		10F	2	249 (Z) and 252 (W)	1.00	–	–	–
Z002D	[11]	–	–	–	1/6-FAM	13 M	1	127 (Z)	0	–	–	–
			–	–		10F	2	122 (W) and 127 (Z)	1.00	–	–	–
Z43B	[12]	–	–	–	7/6-FAM	13 M	1	270 (Z)	0	–	–	–
			–	–		10F	2	266 (W) and 270 (Z)	1.00	–	–	–

NCBI National Center for Biotechnology Information; Primer sequence F forward, R reverse, https://www.ncbi.nlm.nih.gov/bioproject/PRJEB21955, n is the number of individuals tested and M is the number of males and F is the number of females identified using the sex-typing markers (Z002A, Z002B [11] and Z43B [12]), A is the number of alleles observed, H_O is the observed heterozygosity, H_E is the expected heterozygosity, P_HWE is the probability of deviation from Hardy–Weinberg equilibrium, Est null allele Freq. is the estimated null allele frequency. The same PCR profile was used for all multiplexes as follows: 95 °C for 15 min, followed by 44 cycles of 94 °C for 30 s, 56 °C for 90 s, 72 °C for 90 s and a final step of 72 °C for 30 min

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ISSN: 1756-0500

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