Abstract The study was designed to validate the previously reported 34 SSR markers using 78 chilli genotypes to detect significant trait specific markers as well as superior genotypes resistant to Phytophthora capsici root rot (PcRR). In this context, the identification of germplasm with higher yield per plant (YPP) leads to hype in stress tolerance index (STI) in genotypes, Chakwal3 (11.98), Greenfire (10.14), Advanta5017 (9.94) and Chakwal4 (7.8). The identified genotypes were also found as resistant and moderately resistant due to existence of below 50% of disease incidence. Moreover, biplot showed the interrelation of STI with YPP through the formation of acute angle by their respective vectors. In the current study, the markers Hpms1172 and CAMS177 was found significant for STI. However, the marker CAMS066 was found associated with relative cell injury, CA06g27450 with disease incidence and CAMS173 with relative leaf damage. The bright bands on gel pictures of significant markers showed the association of these markers with resistant genotypes i.e. Chakwal3, Advanta-5017 and Chakwal4 as well as with a single moderately resistant genotype i.e. Greenfire. The markerstudes confirmed the phenotypic data by showing association of markers i.e. Hpms1172 and CAMS177, r with stress tolerance index. The principal coordinate analysis aligned with the results obtained from marker-assisted selection. Thus, currently practiced marker assisted selection detected high yielding genotypes in PcRR disease stress condition that will be helpful in progressing breeding programs in chilli.

Validation of SSR markers for identification of high-yielding and Phytophthora Capsici root rot resistant chilli genotypes