Searching for candidate genes contributing to Fusarium graminearum resistance in a recombinant inbred population.

Preventing Fusarium graminearum infection (gibberella ear rot, GER) and the associated mycotoxin contamination of grain continues to be a top priority for Canadian corn producers. It has been challenging to identify genes conferring Fusarium resistance in cereals because the trait is quite complex and highly influenced by the environment. A recombinant inbred population of 410 lines was constructed from the GER tolerant CO441 inbred developed at AAFC and the GER susceptible reference inbred B73. This population has been phenotyped over several field seasons for GER silk and kernel resistance, smut resistance, kernel drydown rate, and other agronomic traits. Genotyping-By-Sequencing was applied to map ten quantitative trait loci (QTL) each for GERsilk and GERkernel resistance, including four which co-localized in the same chromosomal regions. We surveyed the transcriptomes of the parental lines during early Fusarium graminearum infection to characterize their defence response. Gene transcripts responding to fungal infection were captured using RNA-seq profiling of mock and fungal inoculated CO441 and B73 maize ears. 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, hemibiotroph pathogens such as F. graminearum can use it to their advantage to interfere with other forms of host resistance mechanisms. We identified differentially expressed genes located within our QTL regions of GER resistance and have further documented their expression profiles by droplet digital PCR.