Breeding corn for resistance to Fusarium ear rot: an integrated approach of transcriptomics, metabolomics and genomics.

Fusarium verticillioides is a fungal maize pathogen that causes ear rot and contaminates the grains with fumonisin mycotoxins. Genomic regions and candidate genes for kernel resistance to F. verticillioides infection were detected through the comparison of resistant and susceptible maize inbred lines, by adopting three different approaches: transcriptomic (RNASeq), metabolomics analyses and Quantitative Trait Locus (QTL) mapping. Comparison of expression levels between inoculated vs. uninoculated and resistant vs. susceptible transcriptomes revealed a total number of 6,951 differentially expressed genes. Differences in constitutive gene expression were observed in the uninoculated samples. The resistant genotype showed a higher level of expression of genes distributed over all functional classes, in particular those related to secondary metabolism category. After F. verticillioides inoculation, a similar response was observed in both genotypes, although the magnitude of induction was much greater in the resistant genotype, including numerous transcripts encoding components of signal transduction cascades and enzymes required for the synthesis of secondary metabolites. The same kernel samples were subjected to a metabolomics analysis by liquid chromatography in combination with high resolution mass spectrometry. The use of stable isotopic labelling combined to MetExtract algorithm allowed the automatic detection and prediction of carbon atoms of only compounds of biological origin. The most intense ion species was selected for each feature group and 534 feature groups, corresponding to likewise metabolites, were issued. Several databases were screened for the metabolite search of the highest m/z within each feature group restricted by the count of the carbon atoms. A total of 222 metabolites resulted significantly affected by F. verticillioides inoculation. Annotation revealed that a large amount was involved in the synthesis of oxylipins, phenylpropanoids, flavonoids, benzoxizanoids, hydroxycinnamic acid amides and aromatic amino acids. A segregating F2:3 population of 188 progenies was developed crossing resistant and susceptible genotypes. Fusarium ear rot (FER) severity and FB1 fumonisin contamination content were evaluated over two years and two sowing dates (early and late) on ears artificially inoculated with F. verticillioides by the use of either side-needle or toothpick inoculation techniques. Significant positive correlations (P<0.01) were detected between FER and FB1 contamination, ranging from 0.72 to 0.81. A genetic map was generated for the cross, based on 72 microsatellite markers and 341 single nucleotide polymorphisms derived from Genotyping-by-Sequencing. QTL analyses revealed six QTLs for FER, eight QTLs for FB1 contamination and three of them were in common between the two traits, located on linkage group 2, 7 and 9. Finally, 25 candidate genes for resistance to F. verticillioides were identified combining transcriptomic data with QTL mapping, providing a set of genes that could be further studied to evaluate their usefulness in marker assisted selection.