Genetic diversity and marker trait association for phytophthora resistance in chilli

Background Chilli is an important commercial crop with positive returns tendency. Phytophthora root rot causes drastic damage to chilli plant. Dearth of detecting marker trait associations is a major hinderance in practicing marker assisted selection in chilli breeding. Methods and results Herein, 110 chilli accessions were assessed for 15 agronomic traits under control and disease infected conditions for two crop seasons (2018–2019). The SSR genotyping revealed high values of major allele frequency (MAF = 0.70), genetic diversity (GD = 0.39) and Polymorphic Information Content (PIC = 0.31). Principal coordinate analysis and population structure analysis showed distribution of diverse genotypes in all groups by dividing 110 genotypes in three populations and nine sub-populations. The UPGMA based Archaeopteryx tree was in concordance with population structure analysis. Linkage disequilibrium analysis evaluated that LD decays within 3–10 bp. Marker trait association (MTA) revealed the associations of 35 SSRs with 14 morphological traits. The significant MTA for marker CAeMS073 with relative leaf damage (RLD, 0.183 R 2 ) under control and treated conditions was consistently observed in both models. The markers, CAMS173 and CAMS194 were found to be strongly associated with RLD and Disease Index (DI), respectively. The absence of MTA was detected for height of first branch. Conclusion The MTAs reported in this study can facilitate marker assisted breeding for developing chilli germplasm resistant against Phytophthora capsici .