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

Abstract

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) × 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) × 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) × 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.