Co-dominant SCAR marker, P6-25F2R5, linked to begomovirus resistance introgressions derived from S. chilense on chromosome 6 at 25 cM are described. These PCR primers amply three different size fragments corresponding to ty-3 (no introgression), Ty-3 (introgression for S. chilense LA2779) and Ty-3a (introgression from S. chilense LA1932). These introgressions for the Ty-3 locus mapped to a region that includes the FER locus (25 cM, BAC clone 56B23, AY678298). PCR reactions were completed at an annealing temperature of 53 C with forward primer, P6-25-F2, 5’ GGT AGT GGA AAT GAT GCT GCT C, and reverse primer, P6-25-R5, 5’ GCT CTG CCT ATT GTC CCA TAT ATA ACC.

Breeding for resistance is one of the most effective means of managing begomoviral diseases. In Guatemala, there are seven bipartite begomoviruses that infect tomatoes. Also, Tomato yellow leaf curl virus has recently been identified in Guatemala. A highly resistant inbred line, Gh13, with resistance to begomoviruses was selected from the hybrid, FAVI 9, which was developed by F. Vidavski and H. Czosnek, Hebrew University of Jerusalem. Gh13 had an introgression from 20-32 cM in chromosome 6 that was identical to the Ty-3 introgression from Gc9, which can be detected with the co-dominant SCAR marker, P6-25F2/R5. Sixty-four F3 families were generated from a cross of Gh13 by a susceptible inbred. These were planted in the field in Sanarate, Guatemala and the disease severity index (DSI, range 0 to 6) for each plant was taken at 42 days after transplanting. The least square means for the DSI’s for those F3 families with the Ty-3 introgression and those without the Ty-3 introgression were 2.0 and 4.5, respectively. Eighty-five% of the variation among the F3 families was explained by presence or absence of the Ty-3 introgression. Thus, this Ty-3 introgression has a major effect on begomovirus-resistance, and the molecular SCAR marker (P6-25F2/R5) can be used for predicting begomovirus-resistance in a tomato breeding program.

Resistance to begomoviruses including bipartite Tomato mottle virus (ToMoV) and monopartite Tomato yellow leaf curl virus (TYLCV) has been introgressed to cultivated tomato (Solanum lycopersicum) from S. chilense accessions LA1932, LA2779, and LA1938. Previous research demonstrated that three regions on chromosome 6 were associated with the resistance, two of which were required for a line to provide a high level of resistance. In the present study, we identified a large S. chilense introgression spanning markers from C2_At2g39690 to T0834 in LA2779-derived advanced breeding lines resistant to both TYLCV and ToMoV. A begomovirus resistance locus, Ty-3, was mapped to the marker interval between cLEG-31-P16 and T1079 on the long arm of chromosome 6. In addition to the Ty-3 locus, the large introgression also spans the Ty-1 region near the Mi gene, suggesting the possible coexistence and linkage of resistance alleles at both Ty-1 and Ty-3 loci in these lines. In contrast, LA1932-derived advanced breeding lines possess a much shorter introgression from cLEG-31-P16 to C2_At5g41480, which also carries a begomovirus resistance locus that is probably allelic at the Ty-3 locus. The PCR-based markers tightly linked to the Ty-3 locus as well as the markers near the Ty-1 region have been used in our breeding program for efficient selection of begomovirus resistance in the past three growing seasons and will be useful resources for tomato breeders around the world.