A CAPS marker, FER-G8, for detection of Ty3 and Ty3a alleles associated with S. chilense introgressions for begomovirus resistance in tomato breeding lines

Several different accessions of S. chilense have been used as sources of begomovirus resistance genes. Zamir et al. (1994) used LA1969 as a source of Ty-1 gene in chromosome 6 (ca. 8 cM). LA1969 was also the source of resistance against Tomato yellow leaf curl virus (TYLCV) for new lines developed in Cuba (Piňón et al., 2005). Scott and his team (Agrama and Scott, 2006; Scott, 2001; Scott et al., 1995) have used several accessions of S. chilense as sources of resistance to TYLCV and Tomato mottle virus (ToMoV). Lines from Scott’s program at the University of Florida were evaluated in Guatemala (Mejía et al., 2005); and the line Gc9 with resistance from LA2779 and line Gc171 from LA2779/LA1932 were highly resistant to bipartite begomoviruses. The begomovirus resistance Ty-1 and Ty-3 loci on chromosome 6 for advanced breeding lines derived from LA2779 were mapped between C2_At2g39690 (5.3 cM) to T0834 (32 cM) (Ji et al., 2007). The partially dominant Ty-3 gene was mapped region between cLEG-31-P16 (20 cM) and T1079 (27 cM) (Ji and Scott, 2006). The line Gc9 has an introgression from on chromosome 6 from the REX-1 locus (6 cM) to T0834 (32 cM), which would include the loci for Ty-1 and Ty-3 (Maxwell, unpublished data). SCAR or CAPS markers have been developed to detect the Ty-1 and Ty-3 loci (see this web site). Unfortunately, the co-dominant SCAR marker, FLUW25, only detected the Ty-3 introgression from LA2779 and not the introgression from LA1932, line Gc171. Thus, it was expected that this Gc171 might have a different introgression. The FLUW25 primers amplify DNA in the region of the FER BAC clone (56B23, AY678298) at 25 cM on chromosome 6. Primers were designed for several of the genes associated with this BAC clone. For the gene 8 and gene 10, three different sequences were obtained for Heinz 1706 (S. lycopersicum), Gc9 (S. chilense LA2779), and Gc171 (S. chilense LA1932) (Martin and Maxwell, unpublished data). This report describes the development of a CAPS marker to detect the alleles associated with S. lycopersicum (ty-1), S. chilense LA2779 (Ty-3), and S. chilense LA1932 (Ty-3a) at gene 8 of the FER BAC clone (AY678298).