Screening and validation of Ty-1, Ty-3 and Ty-3a specific markers in Solanum chilense accessions for resistance to tomato leaf curl virus

Tomato leaf curl virus (ToLCV) is the most destructive disease of tomato causing fruit yield losses of up to 90–100%. The tomato cultivars are highly susceptible to ToLCV. There are six resistance genes; Ty-1 , Ty-2 , Ty-3 , Ty-4 , ty-5 and Ty-6 which are being practically utilized in resistance breeding. Ty-3 and Ty-4 showed highly stable resistance to ToLCV but searching for new genes is a key interest in long-term breeding programmes. In the present experiment, eight Solanum chilense accessions along with three cultivars or advance breeding lines were screened under field conditions prevailing high disease pressure to find new sources of resistance. All accessions of S. chilense were resistant to ToLCV. Ty-1 , Ty-1 / Ty-3 linked five each of sequence-based markers (WU_M17, WUR_M25, WU_M27, WU_M29 and WU_M31) and five SCAR markers (P6-25-F2/P6-25-R5, FLUW-25 F, UF_TY3-P19, Ualty3a and Ualty3b) were validated with all accessions for identification of novel alleles. Ualty3b marker amplified Ty-1 and Ty-3 amplicons only in LA2879, LA1930, LA1969, LA2748 and LA2773 and no amplicons were observed in LA1938, LA2759 and LA1958. This suggests that Ty-1 / Ty-3 genes that possibly exist in these accessions need to be explored in the breeding program. Marker P6-25-F2 amplified Ty-3 specific 630 bp amplicons in LA2879, LA1930, LA1969 and LA2773. The marker P6-25-F2 also amplified 450 bp amplicons of allele-specific Ty-3a in LA1938, LA2879, LA1969 and LA2748. Both Ty-3 and Ty-3a alleles were amplified in LA2879 and LA1969. The marker and field screening results showed that accessions LA1938, LA2879, LA1969 and LA2748 carry novel alleles resistant to ToLCV and are the potential sources for introgression of ToLCV resistant genes into commercial tomato cultivars.