Multi-omics integration reveals candidate genes and molecular mechanisms associated with resistance to sugarcane smut

Abstract

Sugarcane smut, caused by the fungus Sporisorium scitamineum (Syd.), is one of the main diseases affecting sugarcane and is capable of causing severe yield losses in susceptible varieties. Given the limitations of classical breeding, mainly due to the genetic complexity of sugarcane cultivars, molecular and omics approaches have gained increasing prominence for studying the genetic basis of traits such as disease resistance. In this context, we investigated sugarcane resistance to smut through the integration of association mapping methods and transcriptomics. A panel of 155 genotypes was genotyped with 33,335 SNP markers and inoculated with S. scitamineum generating three phenotypic variables. These data were jointly analyzed through genome-wide association analyses to identify marker-trait associations. In addition, transcriptomic analyses were performed using publicly available datasets from four studies evaluating sugarcane responses to smut. The integration of these multi-omics data enabled the identification of candidate genes involved in structural reinforcement, immune signaling, redox homeostasis, genome maintenance, and cellular adaptation. These findings provide valuable molecular resources for functional validation and breeding strategies aimed at developing sugarcane cultivars with enhanced smut resistance.