Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus

Table 1 CAPS markers converted from RFLP markers and microsyntenic ESTs^*

Arabidopsis gene^†	C/P/H^‡	Molecular markers mapped in the dgt region^§	Type	Expect value^¶	Primer sequences^#	Restriction enzyme
AT4g38580	-	CT190^¥	RFLP	-	5'-TTCTCGTCGCTAAAGGCAGT-3' 5'-TCACACAAAACAATGGGTGTTCTT-3'	HinfI
AT4g38620	2 / 2 / 40
AT4g38630	1 / 1 / 1
AT4g38660	1 / 2 / 16
AT4g38670	1 / 2 / 15
AT4g38680	1 / 1 / 1	TC98260 (GRP)	EST	1.7e^-40	5'-GTGCCTCACAATCAAAGGGTTTTA-3' 5'-CTCCATAACCACGATTTCCTCCTC-3'	RsaI
AT4g38690	4 / 4 / 5	TC92082 (PPLC)	EST	1.4e^-84	5'-TGGTTGAGCTGATTTTCTTGGTTT-3' 5'-CCTGGTTCTGATTATCGCTCAGAT-3'	HinfI
AT4g38700	1 / 2 / 5	AW624844 (DRRP)	EST	1.2e^-28	5'-AAACGTCATGGGCTAAGAGAGTTG-3' 5'-TCTAGATGCAATGGCTTGTTTTCC-3'	ApoI
AT4g38730	-	TG389	RFLP	-	5'-TCACTAGCTCAAGGGAGTCATCTG-3' 5'-ACCACTTTGACCATCATCGCAAGC-3'	HinfI
AT4g38740	1 / 3 / 10	TC89380 (PPI)	EST	5.2e^-76	5'-CAAATCCAAAGGTTTTCTTTGACC-3' 5'-CTGGTAGAAGCAACACAACAACCA-3'	HaeIII
AT4g38790	1 / 2 / 4
AT4g38810	1 / 2 / 2	TC85079 (EFP)	EST	4.0e^-129	5'-CGAAACTGGCTTCCCTTCTA-3' 5'-AGTCAGGTGATGGACGGTTC-3'	BanI
AT4g38830	10 / 12 /146
AT4g38840	1 / 1 / 6
AT4g38850	-	TG269	RFLP	-	5'-CAAATTCTTCCTCAGCTTGACT-3' 5'-TGATCTCACATCTTGCTTGCG-3'	DdeI
AT4g38880	1 / 1 / 1	TC87150 (APRT)	EST	3.8e^-90	5'-CAGAAAAATGACTTGGAGGGAGAG-3' 5'-CCAAGATTGTGAGGCTGTTAAAGG-3'	RsaI
AT4g38900	1 / 1 / 3	TC47447 (bZIP)	EST	1.3e^-98	5'-AACTTGGAAGCGTCTGCACT-3' 5'-GGACGACCTGTTTTCTGCAT-3'	RsaI
AT4g34830	1 / 1 / 1	BG643476	EST	5.3e^-86	5'-GGTTGATGGACTGCATAAAAATCC-3' 5'-TGCAAATTCCCAATTTACCATTTT-3'	HhaI
AT4g35050	2 / 3 / 4

^*The conversion rate of the amplicons, generated from ESTs in the target region, to CAPS was 75% (30/40) and 20% of CAPS markers (6/30) were successfully mapped in the dgt region. ^†Genes in MSR1 with exceptions of AT4g34830 and AT4g35050 in MSR2. ^‡C/P/H, the number of CAPS markers developed/the number of PCR products investigated/the number of TBLASTN matches of interest (< e^-20). ^§Abbreviations in parentheses: GRP, glycine-rich protein; PPLC, phosphatidylinositol-specific phospholipase C precursor; DRRP, disease-resistance response protein; PPI, cyclophilin-type peptidyl-prolyl isomerase; EFP, EF-hand containing protein-like protein; APRT, amidophosphoribosyl transferase; bZIP; basic leucine zipper transcription factor. ^¶Each value represents the E-value of a TBLASTN search using the Arabidopsis microsyntenic gene against the Tomato Gene Index using the Blosum 62 scoring matrix and default parameters. The E-value of a BLASTN search using tomato RFLP markers is not described in this table (see text). ^#Oligonucleotide sequences are only indicated for each MEST marker. ^¥ Amplified by modified PCR conditions: 3 min 30 sec for elongation and 2.5 mM MgCl₂.

ISSN: 1474-760X