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Table 3 Nucleotide substitutions recovered in query genes by TILLING screen

From: Development and evaluation of a cucumber TILLING population

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
    188 nd   Intron 8 nd
pdsD 1198 34.5 23 254 C3997T - Intron 6 2 : 3 : 0
    70 nd   Intron 6 nd
ACC synthase (F), Csa012150 acsA 1111 39 70 none - - - -
acsB 1025 41 96 48 C594T Dra I Intron 2 4 : 9 : 5
Ramosus-3 (RMS-3), Csa010158 Rms3A 513 47 72 none - - - -
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 - - - -
Cum1D 702 34 30 none - - - -
Self-pruning (sp), Csa010707 SpB 704 29.8 39 none - - - -
Total   10,766 39.7 63 8     
  1. 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).