Fine mapping and identification of candidate genes associated with powdery mildew resistance in melon (Cucumis melo L.)

Powdery mildew, a common disease of many major crop species, including melon (Cucumis melo L.), affects plant growth and fruit quality, and seriously reduces production. Using a combined morphological and molecular approach, we attribute the powdery mildew pathogen that naturally occurs in melon to Podosphaera xanthii, and specifically to physiological race 1. An investigation into the genetic basis of powdery mildew resistance in melon using the resistant accession “PI 164637” and susceptible counterpart “HDZ” reveals dominant inheritance of PM resistance at the seedling stage, supported by F2 and backcross population segregation ratios. Adult plant assessments indicate a major gene with an additive effect for powdery mildew resistance. Bulk segregant analysis coupled with high-throughput sequencing identified a significant quantitative trait locus on chromosome 6 that is associated with powdery mildew resistance. Genetic mapping narrowed down the candidate region to 63.5 kb using InDel molecular markers, harboring 12 candidate genes. The marker chr06_indel_5047127 demonstrated high accuracy in screening powdery mildew resistance in a F2 segregating population and 30 inbred lines as natural populations. Functional annotation and expression analysis of candidate genes revealed that MYB transcription factor MELO3C006700, GATA transcription factor MELO3C028829 and heparanase-like protein MELO3C006697 are promising candidate genes for powdery mildew resistance in melon. The genetic architecture underlying this resistance in melon offers valuable insights for breeding programs, and the identified markers, especially chr06_indel_5047127, may enable practical applications for marker-assisted selection in developing powdery-mildew-resistant melon varieties.