General and genotype-specific transcriptional responses to Fusarium ear rot in resistant and susceptible maize genotypes.

Fusarium ear rot caused by Fusarium verticillioides is a prevalent disease in maize which can severely reduce graind yields and quality, due to contamination of infected kernels with mycotoxins. Natural sources of resistance from maize genotypes are used in conventional breeding approaches, but the signals and effectors involved in resistance in this important crop species are not well understood. Early transcriptional changes associated with F. verticillioides infection were analysed in resistant CO441 and susceptible CO354 maize genotypes using RNA-Sequencing technology. Transcript levels were measured at 72 hours post-inoculation (hpi), reflecting the time point immediately preceding the onset of resistance in CO441, as determined by the absolute quantification of the fungal β-tubulin2 gene. More than 100 million sequence reads were generated for condition (inoculated/uninoculated). The sequence reads were analyzed to measure gene expression levels and determine single nucleotide polymorphisms. We observed 2,551 transcripts with statistically significant differential expression before inoculation by comparing uninoculated control samples. Overall, a more induced expression of genes was found in the CO441 genotype, distributed in all functional classes, and in particular a high percentage of differentially expressed genes was detected for the category secondary metabolism. Furthermore, a total of 2,250 and 2,442 transcripts were differentially regulated after F. verticillioides inoculation in resistant and susceptible genotypes, respectively. The genes in common were 1,028 genes and showed 5,342 SNPs variants, suggesting a certain variability in the defense responses of the two genotypes. Also at 72 hpi, secondary metabolism was the category where the most interesting differences between the two genotypes were observed to a greater extent. Pathways related to phenylalanine, tyrosine and tryptophan biosynthesis (e.g. anthranilate synthase, shikimate kinase), flavonoid biosynthesis (e.g. chalcone synthase) and lignin biosynthesis (e.g. cinnamyl-alcohol dehydrogenase) appeared to be strongly influenced by infection in the CO441 genotype with up to 11-fold induction. Response to stress and resistance categories followed. In addition, transcriptional modulation affected signal transduction, including calcium signaling, ethylene signaling, MAP kinases, receptor-like kinases, and numerous transcription factors. Even though all these genes were well represented in both genotypes, it was observed that on the whole CO441 mounts a stronger gene induction, confirming its strengthening also in the specific response to inoculation. The identification of plant candidate resistance genes that interact with fungus could be exploited in future biotechnological approaches to increase disease resistance in susceptible maize genotypes.