Genetic variability of Macrophomina phaseolina associated with charcoal rot of sesame in expanding agricultural areas of Central-West Brazil

Sesame ( Sesamum indicum L.) is a rapidly expanding oilseed crop in Brazil. This study aimed to identify the causal agent of charcoal rot in sesame-producing areas of Goiás and Mato Grosso and to characterize the pathogen isolates morphologically, molecularly, and genetically. Symptomatic stems were collected in three municipalities, and sixty-one fungal isolates were identified as Macrophomina phaseolina based on cultural and microscopic traits, PCR with species-specific primers, and partial ITS sequencing. Pathogenicity tests reproduced field symptoms and confirmed the pathogen through re-isolation, fulfilling Koch’s postulates. Genetic diversity analysis using seven ISSR markers revealed a high proportion of polymorphic loci (97.2%) and considerable variability among isolates, with clustering patterns mainly associated with geographic origin. In greenhouse assays, cultivar BRS Anahí showed lower disease severity (51.16% disease index), while Trebol exhibited the highest severity (68.06% disease index), and K3 showed intermediate values (58.56% disease index), with significant differences among cultivars ( p = 0.0363). This study reports the first confirmed occurrence of charcoal rot caused by M. phaseolina in Central-West Brazil and reveals genetic diversity among isolates, as well as differences in disease severity among sesame cultivars.