A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta

Berendzen, Kenneth; Searle, Iain; Ravenscroft, Dean; Koncz, Csaba; Batschauer, Alfred; Coupland, George; Somssich, Imre E; Ülker, Bekir

doi:10.1186/1746-4811-1-4

Plant Methods

Table 1 List of chromosomal positions of BSA markers detecting polymorphism between A. thaliana ecotypes Col-0 and Ler.

From: A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta

Chr	Marker	Forward primer (5'-3')	Reverse primer (5'-3')	Col-0 (bp)	Ler(bp)
I	nga63	GCCTAAACCAAGGCACAGAAG	TCATCAGTATTCGACCCAAG	87	99
I	F3F19	CCACAAAACAATTTGGTTCACTC	TCCCGTTGGGGATATTAAAG	100, 143	243
I	F20D23	TTATGCCAACTCATGTGGAAAG	TGTCAAAGCGTCTGGTTCTG	233	254
I	F12K8	ACCAACACCACAACAAACGAC	CTTTTTCTGTTCTTCCGCTATTC	171	192
I	F3I6	AGATGGAAGAGGAGGAGATGG	TGCATGTATATGATGAGCGAGAG	251	311
I	SO392	GTTGTTGATCGCAGCTTGATAAG	TTTGGAGTTAGACACGGATCTG	142	156
I	F7P12	TCGAGGATATGTTTCGTGTTTG	ACAGTTTTGATGCATTGTGTGAG	315	100, 215
I	F1I21	TCGTAAATTGTGACTGGGAGA	CCCTGTAGATCTGTTGTTTTAG	308	113, 195
I	ciw1	ACATTTTCTCAATCCTTACTC	GAGAGCTTCTTTATTTGTGAT	159	135
I	nga280	CCTGATCTCACGGACAATAGTG	GGCTCCATAAAAAGTGCACC	106	86
I	F23H11	GATATGGGAGTAAGTATGAAATCGG	TTCGTCCGGGTAAAAGTCAAG	300	250
I	NF514a	GTTGAGTCTTGGCATCACAGTTC	CTGCCTGAAATTGTCGAAAC	221	240
I	F20P5	GATACGTTCAAAATTAGGGACTTC	TGTATTTTGCTAATTGAGGTTATGG	218	186
I	AthATPase	CCTGGGAACGGTTCGATTCGAG	GTTCACAGAGAGACTCATAAACCA	86	70
II	T20F6	CGTTCGAAACTGAATTAGCTG	ACCATCTTTGTTGAGCCCTTC	297	347
II	F18P14	ATTCCCGCAATTTATTTTGTTC	GTTTGATGGCAGATTTGTTTTC	123	144
II	ciw3	GGAAACTCAATGAAATCCACTT	GTGAACTTGTTGTGAGCTTTGA	230	200
II	F26B6	CTCTATCTGCCCACGAACAAG	GCCATTGCAAAAGAACATCAG	233	274
II	F16P2	CAGCAATCAAATAACGTGGTG	CTCTCTTCTTTCTTCGCCATTAG	237	167
II	F4P9	TGGTCCATACCCATTTCATAAC	ATGAATTTTCATTCTACTGTTTTG	299	262
II	T2H17	ATTGCATACCACGCAGTTCAC	CCATTTTGCCCTTTCCTTCTAC	250	274
II	AthBIO2b	TGACCTCCTCTTCCATGGAG	TTAACAGAAACCCAAAGCTTTC	141	209
III	nga172	AGCTGCTTCCTTATAGCGTCC	CCATCCGAATGCCATTGTTC	162	136
III	nga162	CATGCAATTTGCATCTGAGG	CTCTGTCACTCTTTTCCTCTGG	107	89
III	MSA6	TTGGAGGTGCTCTTAGGTTC	GGGCTTTTCACATACGCTTTC	175	225
III	ciw11a	GTTTTTTCTAATCCCCGAGTTGAG	GAAGAAATTCCTAAAGCATTC	192	242
III	N7N14	CAATACACTTTATCCAGATGCTG	GGGATTTGTTGATTGAAAAAGGAC	150	143
III	T6H20	CGGCTGAAACTTGGAAGGGAC	AGGAAGAACGTGTGATTGTG	273	293
III	ciw4	GTTCATTAAACTTGCGTGTGT	TACGGTCAGATTGAGTGATTC	189	215
III	K27K19	TGCTTTTGAAGAGATGGTTATTAGG	CCCCATTTCACTTATCATTGG	216	198
III	nga6a	AGCGAATCCGAAAATAATGGAG	TGGATTTCTTCCTCTCTTCAC	159	137
IV	ciw5	GGTTAAAAATTAGGGTTACGA	AGATTTACGTGGAAGCAAT	164	144
IV	F14G16	ACAAACCGATCAGCATTCAAG	GCCTTTGTCACGGATTCAAC	250	198
IV	T3H13	TTTGGTGGGTCAAGAGTCAAG	GCAAAAGTCATTACGGACAATAC	275	229
IV	T26M18	CAATTAGCGGAGGCCACTTC	GGGCAAAAGCTTCCAGTAC	330	271
IV	FCALL	CCACCGTCAACATCCCTAAC	GCTCTTATACTTCTCAGCTCTTGTC	170	180
IV	F28A21	GCATCATCATTCATCACCAAC	TGTGAAGTGTTTGTCTTTGTG	198	169
IV	F16G20	TGTCAACCAATCGCCTTAGTC	TTAATGTCCATTATTGGAACGC	113	79
IV	F26K10	AGAGAGCACGATGCCTGATAG	AATGCTTCAGCGATTGAGAAC	180	205
IV	F6E21	TTCTTTGTTCAAGTTCCATGTCTC	CGGTGATTGTCTCAAGTGTTTG	199	225
IV	F23E13	TGACCGTTGAAAGTGTTGTTG	GCCCGAGAAGCCTGATAG	264	246
V	MHF15	CTCCTCCTTTAATTTTCTCTCTGTG	AGTTCCAGCTTTGGACTTCTTC	295	268
V	nga151a	ATCTCATACTGACCCATATGTTCC	ATTGTACAGTCTAAAAGCGAGAG	198	170
V	ciw8a	TACTAGTGAAACCTTTCTCAG	TTTTATGTTTTCTTCAATCAGTTAG	100	135
V	nga139	AGGGTTTCGTTTCACTATCCAG	TGAGAGCTACCAGATCCGATG	174	132
V	T1N24	CCGATGGCATAACAAGTAGAG	GGGAAAGGTACACATATACAAAAGG	383	356
V	nga76	GGAGAAAATGTCACTCTCCAC	AGGCATGGGAGACATTTACG	231	250
V	ciw9	CAGACGTATCAAATGACAAATG	GACTACTGCTCAAACTATTCGG	165	145
V	MPL12	GTCCCCAAAACCAATCATAAG	TCCGAGTGAGAAGAGAGTTTG	319	293
V	K9P8	TTATGGGTTTCTCAGAGTTTCTCAC	TTGTATGCGTTTGCTTTTTCC	284	251
V	MNC17	GTACCGGATCTGTGTTGTGAAG	GTGCTCAAGGAAATGGGATAG	168	187
V	MQB2	CTTTGATAGTAACCTTTTTCAAACCA	TGCCATTTATTTGGTCAACAC	252	231

DNA oligonucleotide primer pairs are listed according to their positions from the top to the bottom of each chromosome. The size (bp) of PCR amplification products from Col-0 and Ler are depicted in the last two columns to the right. F, forward primer and R, reverse primer.

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ISSN: 1746-4811

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