Identification of molecular marker linked to resistance gene loci against Indian isolate of Phytophthora capsici L. causing root rot in chilli (Capsicum annuum L.)

Phytophthora root rot caused by Phytophthora capsici L. is a serious threat for chilli production in India. The identification and incorporation of gene loci linked to resistance can help in breeding resistant varieties or F1 hybrids through marker-assisted selection (MAS). The present study was conducted to identify molecular markers associated with the resistance gene loci that confer P. capsici root rot (PcRR) resistance against the virulent Indian isolate. The public domain molecular markers, namely CAMS 405, Hpms 1–62, Hpmshs MADS, SSR 9, and CAMS 839, linked to the PcRR resistance loci were validated in IHR3575; resistant derivative of Criollo de Morelos 334 (CM334) and IHR3476; highly susceptible genotype and their derived populations. New SSR markers, HpmsE034 and HpmsE062 linked to PcRR resistance against the Indian isolate were identified through a bulked segregant analysis (BSA) using F2 and F2:3 populations. HpmsE034 and HpmsE062 differentiated contrasting parents and corresponding DNA bulks and F2 individuals with the highest co-segregation of phenotypic data. The sequence analysis of HpmsE034 loci revealed 93.36% homology with the known SRC2 resistance loci in pepper. The combined use of previously reported markers with a newly identified marker HpmsE034 showed cumulative 100% phenotypic variation expected (PVE), and it can be useful in the precise MAS of a polygenically controlled Phytophthora root rot resistance gene in chilli against the Indian isolate.