Molecular mapping and development of SSR markers associated with Chilli leaf curl virus resistance in chilli (Capsicum annuum L.)

Chilli leaf curl virus (ChLCV), caused by whiteflies transmitted begomoviruses, poses a significant threat to chilli cultivation and production all over the world. Exploring host plant resistance and identification of associated molecular markers will accelerate resistance breeding. QTL-seq analysis was employed in the IHR4615(R) x IHR2451(S) F2 population to identify QTLs associated with ChLCV-Raichur isolate resistance. A significant QTL was mapped on chromosome 6 associated with ChLCV-Raichur isolate resistance. Defense-related genes were predicted within the identified locus. Further refining of the identified locus with simple sequence repeats (SSR) markers led to the identification of two SSR markers IHR-LCV-SSR-76 and IHR-LCV-SSR-165 associated with the ChLCV-Raichur isolate resistance with 89.50 and 72.50 % prediction efficacy, respectively in IHR4615(R) x IHR2451(S) F2 population. These markers are located at 7 cM and 17.65 cM genetic distances from the resistant gene. These markers were further validated in another resistant source-based F2 population of IHR4392(S) x IHR4597(R). The developed and validated molecular markers can be explored in marker-assisted breeding programs aiming at developing resistant cultivars/ F1 hybrids of chilli.