Development and evaluation of a cucumber TILLING population

BMC Research Notes

Table 3 Nucleotide substitutions recovered in query genes by TILLING screen

Gene	Amplicon	Amplicon size, bp	% GC content	% Exons	Mutated family	SNP	Diagnostic CAPS	Location/substitution	M3 Progeny analyzed: WT/WT : Heteroz.: mut/mut
Phytoene desaturase-3 (PDS-3), Csa002881	pdsB	622	36.5	55	53	C5310T		Intron 8	2 : 4 : 2
	pdsB				188	nd		Intron 8	nd
	pdsD	1198	34.5	23	254	C3997T	-	Intron 6	2 : 3 : 0
	pdsD				70	nd		Intron 6	nd
ACC synthase (F), Csa012150	acsA	1111	39	70	none	-	-	-	-
ACC synthase (F), Csa012150	acsB	1025	41	96	48	C594T	Dra I	Intron 2	4 : 9 : 5
Ramosus-3 (RMS-3), Csa010158	Rms3A	513	47	72	none	-	-	-	-
Ramosus-3 (RMS-3), Csa010158	Rms3B	639	43	70	540	G1376A	-	Gln191Gln	3 : 4 : 0
Ramosus-4 (RMS-4), Csa003326	Rms4A	1222	51	86	53	C767T	-	Thr256Ile	3 : 10 : 3
	Rms4B	929	46	100	928	C1258T	Sac I / Xba I	Leu420Leu	7 : 7 : 0
	Rms4C	798	45	84	none	-	-	-	-
Cucumber MADS1 (Cum1), Csa000681	Cum1B	575	35	41	none	-	-	-	-
Cucumber MADS1 (Cum1), Csa000681	Cum1D	702	34	30	none	-	-	-	-
Self-pruning (sp), Csa010707	SpB	704	29.8	39	none	-	-	-	-
Total		10,766	39.7	63	8

Genes are indicated by name and by accession numbers (cucumber genome project, http://cucumber.genomics.org.cn). Amplicon size (calculated between internal primer pairs) is shown, as well as the GC composition and the ratio of coding sequence (exons) to total amplicon length. Mutated position is determined according to the genomic sequence, from the start codon (ATG), and its location, either in an intron or in the protein coding-sequence, is indicated. Nd – non determined. CAPS marker in ACC synthase gene: the wild type amplicon is digested by Dra I, mutant amplicon is uncut. CAPS marker in RMS4: wild type amplicon is digested by Sac I (and also Xba I), no restriction in the mutant. A small number of M₂ progeny was genotyped to demonstrate inheritance of the nucleotide substitution. The total sequence screened (10,766 bp) was calculated by summing up all the internal amplicons, and detracting the overlapping regions found between the Acs (F) and Rms-4 amplicons (see Figure 4).

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