Inheritance analysis of anthracnose resistance and marker-assisted selection in introgression populations of chili (Capsicum annuum L.)

•The resistance in the Capsicum annuum introgression lines derived from C. chinense (PBC932: PR1) and C. baccatum (PBC80: PR2) were controlled by major recessive genes independently.•The SCAR-Indel and SSR-HpmsE032 markers were used for validation in populations derived from PR1 and PR2, respectively.•The resistance banding pattern amplified by SCAR-Indel and SSR-HpmsE032 markers was 100bp and 231bp fragments, respectively.•The selection efficacy of the simultaneous use of two markers (SCAR-Indel and SSR-HpmsE032 markers) increased to 77% in a three-way population, thus, a large number of seedlings could be discarded in the process of combining resistance derived from two sources.