Table 2 CAPS makers of Chamaecyparis obtusa and their BLASTX search results

From: Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implications for management and conservation

Locus	Forward primer	Reverse primer	°C	Fragment size (bp)	Restriction enzyme	Putative function	No of clone in blast hit to non-redundant cDNA database of
							C. obtusa	C. japonica	Pinus taeda	Arabidopsis	Oryza sativa
CC0272	GGCGTTCGACTCAGTTGATT	TTGGGCCAGCCTTTCC	57	500	DdeI	T10824 auxin-induced protein (clone MII-3) -mung bean	5	7	22	5	15
CC0292	AGGCGGCGTTCAAGC	TGCCAAGCAATCTGAGAGAG	57	700	MspI	VQ motif-containing protein [Arabidopsis thaliana]	0	1	2	4	1
CC0344	TTATAGTAATGGCGGATTCA	TCTCCGCCATTACAAGA	57	450	RsaI	no blast hit	0	2	0	0	0
CC0352	GAAATTTCAAGCGGTGTT	CGAATATGGCAGATAGTCAAT	57	>1500	TaqI	HS7M_PHAVU heat shock 70 kd protein, mitochondrial precursor	6	7	19	18	32
CC0530	GGCATGCTGTAGTGAATGTC	TAGACCTCAGGTTCCCAAGTA	57	>1500	Bst0I	putative ascorbate oxidase [Oryza sativa (japonica cultivar-group)]	1	3	7	34	20
CC0550 ^a	TCAAGCCAACTTCTGTGTCGT	ATGCCATCTTCCCATTCGT	55	600	MspI	CHI1_TULBA Chitinase 1 precursor (Tulip bulb chitinase-1) (TBC-1)	0	1	3	0	11
CC0592 ^a	ATTTGAGTTAGTTTGCGATGG	AGAAGATCCTCCTGCGTAAT	57	>1500	HinfI	unknown [Arabidopsis thaliana]	6	3	1	1	7
CC0731 ^a	TGCGCGCTTTCGGAGTTT	GTCCACGCAGACGACCAGTTC	57	600	Bst0I	RL2_LYCES 60S ribosomal protein l2 (l8) (ribosomal protein tl2)	1	4	10	5	6
CC0737 ^a	TCTCTAATGTGGCAGCTCTTT	TGGAACTTATGCTACATCCCT	57	600	DraI	RLA0_SOYBN 60S acidic ribosomal protein P0	1	5	5	3	5
CC0822 ^a	TGTCTGCCCATTGAGAAGT	TCAGATGCCATGTTGATAAGA	57	600	HinfI	PRLI-interacting factor K [Arabidopsis thaliana]	1	1	1	1	1
CC0831	GCTCGTGCATCAAGGA	TGGGTTAAAAATAACTGGACA	54	>1500	SspI	unknown protein [Oryza sativa (japonica cultivar-group)]	0	2	3	3	3
CC0832	AAAGATCAAGCGTATCAATGC	CAGAAGATCCTCCTGCGTAAT	57	>1500	HinfI	unknown [Arabidopsis thaliana]	5	8	2	2	7
CC0838	TGCGGGGGATTACTCA	TCCCTATTCGACTGCATAAAG	57	500	HaeIII	Thaumatin-like protein [Pseudotsuga menziesii]	3	13	38	24	19
CC0858	GGTGGAAGAAGAGCCGCTTGT	AAACTGGCGCCCATTGAGTC	62	900	SinI	erg-1 [Solanum tuberosum]	5	8	20	8	10
CC0860	AACAGCGCGCAAGTCTACA	CTAAGCCCTTTCACCACGAAT	57	1000	HhaI	Histone H3.2 [Arabidopsis thaliana]	4	6	21	15	9
CC0951	GCGAAAGGCATTTGATGATAA	CAGACCAGCCGTCACAGTT	60	1300	RsaI	JW0071 asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) -soybean	1	1	4	3	1
CC0958	CTCAATGGCCGCTATTTCACT	GAAGCCAAACGAGAAGCAATG	57	500	StyI	no blast hit	0	1	7	0	0
CC0983	GTTCGATCTGGGATCAACA	AACATGACTCCTTACCACCAC	62	700	ALP^b	unknown [Glycine max]	1	2	2	3	1
CC0991	ATGCCAGGCTGATTTCTACAA	GACACAAGCCAAACATTCACA	57	>1500	RsaI	unknown [Xerophyta humilis]	1	1	2	1	1
CC1172	GCGCGCTTTCGTAGTTTGGAC	GGAGCATCACGACGCACTGTA	60	600	HinfI	RL2_LYCES 60S ribosomal protein l2 (l8) (ribosomal protein tl2)	1	4	10	5	6
CC1187	CAGATCCTGCACCATGTGGAA	CAAACTGCCATGGCCAGACT	62	450	RsaI	no blast hit	0	1	0	0	0
CC1287	TCAACTACTACTGGGCATCTG	ACCACTTGGCTCCTTCTT	57	500	SspI	EF1A_MANES elongation factor 1-alpha (ef-1-alpha)	5	5	31	10	31
CC1319	ATAGTAATGGCGGATTCAAAT	CGCCATTACAAGAACATAAGC	60	450	DdeI	no blast hit	0	2	0	0	0
CC1371	TCCGCAAGCATTTGAAGTAGG	GCCACACTCCCACAACCACT	60	700	TaqI	MSP1 protein, putative/intramitochondrial sorting protein, putative [Arabidopsis thaliana]	2	1	7	23	39
CC1415 ^a	AATTAACCTTATCCGCTCGTT	ACAATAAGAGTGGCGATGC	57	>1500	AluI	light stress-responsive one-helix protein (OHP2) [Arabidopsis thaliana]	0	1	1	1	0
CC1432	TGGTGATGTACACGCCTGGTT	CGTTGAAATTCTCGGGAGCAT	62	1200	MspI	major intrinsic protein-like [Oryza sativa (japonica cultivar-group)]	0	1	1	5	3
CC1463	TGGATGATGCGTCGTTGC	TCGAGAGAAATGACCCGTTTG	57	800	HaeIII	OST3/OST6 family protein [Arabidopsis thaliana]	0	1	1	2	3
CC1606	TAACCAGCTTTGCCCTCAG	ATACAATTCGCGGCTACCATA	62	1000	AluI	tuber-specific and sucrose-responsive element binding factor [Solanum tuberosum]	2	6	45	128	58
CC1625	CTCCAGACAGCGGTTCTTATG	TGCCATGGACTTCCTCTTCT	62	1100	RsaI	ASR protein [Ginkgo biloba]	0	4	31	0	9
CC1697	GCCAGGCTGATTTCTACAA	AGACACAAGCCAAACATTCAC	62	>1500	RsaI	unknown [Xerophyta humilis]	1	1	2	1	1
CC1798	GGCGGCGGAGATTACTGTA	TAGAAGACGCGCATTTGAGAA	57	800	AluI	putative class I chitinase [Cryptomeria japonica]	3	8	28	14	26
CC1799	AAACGCAGTCGAGAGGATGAG	CACCGGCAGATTCCAGTCTA	57	600	HhaI	no blast hit	0	2	9	0	0
CC1944	GAAGGATTATGTGGCACTT	GGGCGTAATTACCTACTATTG	62	>1500	RsaI	no blast hit	0	1	1	0	0
CC2196	CGGCGTATTCACCTTACAGAC	GCCAGAATAAACTTGCCATTG	62	600	AluI	similar to hypothetical protein [Rattus norvegicus]	2	4	13	59	66
CC2237	AGAAATGGCCAACTGCTGAG	TTGCCCTGAAGTGTAACCAAA	57	700	TaqI	gt-2-related [Arabidopsis thaliana]	0	2	1	1	0
CC2435 ^a	GCAGGCAGTTCAGAGTTTT	TCCCGAAGAGAGTTTTATGG	57	800	MspI	Zgc:73363 protein [Danio rerio]	3	5	11	9	19
CC2448	ATCCTAAGTCCCCAGAAAGT	GAATTGGAATGGCATAAAGA	57	>1500	TaqI	cytochrome P450 [Pyrus communis]	6	16	64	124	71
CC2478	CGGGCAAGCATTTCTGTTCT	AGTTTGAGGAGGCATTATTT	57	900	BanII	enoyl-CoA hydratase/isomerase family protein [Arabidopsis thaliana]	0	1	1	1	1
CC2588	CTGCCGCTGCCGTTTATTCC	TTATCCACGACGTACACACC	57	700	MspI	no blast hit	0	1	0	0	0
CC2750	GGCAGCACACAGACAACACA	GATACTTCTCAGGCCCAACT	62	>1500	TaqI	potassium channel tetramerisation domain-containing protein [Arabidopsis thaliana]	0	1	0	2	1
CC2831 ^a	GGCGATGGCAGCAAACGAAG	CACGCACCACTCCACCCTAC	62	500	EcoRI+ BamHI	GCN5-related N-acetyltransferase (GNAT) family protein [Arabidopsis thaliana]	0	1	2	2	2
CC2860	CTAAAGGGAAACAAATCAGG	TACTCGTCTTCTAACCGTCA	57	800	DdeI	strictosidine synthase family protein [Arabidopsis thaliana]	2	1	8	14	10
CC2920	CCGCCACATTCACGCCCTCT	CGCAGTTCCAGTAGTTTCTC	62	900	MspI	Similar to hypothetical protein - potato (S31196) [Oryza sativa (japonica cultivar-group)]	2	5	27	43	76
CC2921	TTTTGGCGGTGGGAGGAATG	CAAGAATCGGTGAAGAACAG	62	>1500	TaqI	DNA-damage-repair/toleration protein (DRT102) [Arabidopsis thaliana]	1	1	1	1	0
CC3162	ATGGAGTCGCCACAAAAGAC	GTCTCGCATCAAATCTCCGT	60	700	HhaI	cell death associated protein [Nicotiana tabacum]	5	5	20	7	45
CC3455	TAACAAGGGAAAACACAGCA	CCGCATCCCATTGAACAGCA	60	1000	RsaI	no blast hit	1	3	8	2	14
CC3583 ^a	CCCACATCATCTTGTAGGGC	GCAGGGCTCCAAGTTTACAG	60	>1500	TaqI	no blast hit	0	1	0	0	0
CC3872	AGCGGAAGTACCCTTTGGAT	GGTTCCCAGTGATTTCCTGA	60	>1500	NdeII	EIN3-like protein [Lycopersicon esculentum]	2	1	0	6	10
CD0312	CCCGACGGACCAACAGAACT	CCCCTGTGCCGTTCCAATAC	60	700	RsaI	allene oxide synthase [Nicotiana attenuata]	1	3	3	2	7
CD0776 ^a	CTTGCTCACCGCATAAACTG	GTTGATCTGCGTGGGTTTAG	58	700	TaqI	no blast hit	0	3	0	0	0
CD1179	TGGGTTTGGGCATAAGTCTG	TTGCCCCTGTTGTTTTATCC	58	1000	MspI	erg-1 [Solanum tuberosum]	5	9	20	8	10

^aDominant marker.
^bAmplicon length polymorphism.

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Table 2 CAPS makers of Chamaecyparis obtusa and their BLASTX search results

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