RNA-Sequencing as a tool for the analysis of the pathosystem maize-Fusarium verticillioides.

Fusarium verticillioides is the causal agent of Fusarium ear rot in maize and contaminates the grain with fumonisins, a family of mycotoxins that affects feed and food. Concern is increasing about the fumonisins because of emerginig evidences of their involvement in several human and animal diseases. To clarify the molecular processes undergoing in maize upon infection, the RNA-Seq technology has been applied to characterize the expression profile of resistant and susceptible kernels of maize 72 hours after F. verticillioides infection. More than 100 million sequence reads were generated for condition (infected/uninfected). The sequence reads were analyzed to measure gene expression levels, to detect alternative splicing events and single nucleotide polymorphisms. We observed 2,006 and 2,629 differentially expressed genes 72 hours after infection for the resistant and susceptible maize genotypes, respectively, of which 927 were in common and showed 5,342 SNPs variants. About 320,000 and 175,000 reads mapped on Fusarium genome in the susceptible and resistant genotypes, respectively, and 129 fungal genes were differentially regulated in both lines. This exhaustive overview of gene expression dynamics demonstrates the utility of RNA-Seq for identifying single nucleotide polymorphisms and describing how plant transcriptomes change during pathogen infection. The identification of differentially expressed plant genes that interact with fungus will produce useful tools for the identification of candidate genes, the development of molecular markers and their use for selection of resistant maize genotypes by means of marker assisted selection.