Combining QTL mapping with transcriptomics to identify candidate genes for Fusarium resistance in maize.

Despite the economic importance of the hemibiotrophic pathogen Fusarium graminearum, it has been challenging to identify genes conferring resistance in maize because the trait is quite omplex and highly influenced by the environment. In the current study, we attempted to characterize defence responses in two maize inbred lines with different levels of resistance to the pathogen by combining information from differential gene expression analysis and quantitative trait loci mapping of resistance. Gene transcripts responding to fungal infection were captured using RNA-seq profiling of mock and fungal inoculated maize ears, and gene ontology terms associated with up-regulated gene transcripts were determined for each inbred. More genes were up regulated in the susceptible inbred relative to the resistant inbred, many of which are associated with oxidation-reduction processes potentially causing earlier programmed cell death in the susceptible inbred. Although the hypersensitive response has been effective in controlling biotrophic pathogens, hemibiotrophs can use it to their advantage to interfere with
other forms of host resistance mechanisms. We have identified differentially expressed genes located within quantitative trait loci regions of gibberella ear rot resistance previously identified using a large recombinant inbred line population; these candidate genes are involved in the biosynthesis of antimicrobial proteins and/or phytoalexins, membrane proteins (integral as well as transporters) and enzymes responsible for detoxification of xenobiotics.