Transcriptome profiling of two maize inbreds with distinct responses to Gibberella ear rot disease to identify candidate resistance genes


Kebede, A.Z., Johnston, A., Schneiderman, D., Bosnich, W., Harris, L.J. (2018). Transcriptome profiling of two maize inbreds with distinct responses to Gibberella ear rot disease to identify candidate resistance genes. BMC Genomics, [online] 19(1),

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Gibberella ear rot is a major disease of corn in Canada caused by a fungus that can also infect many other cereal crops like wheat, barley and oats. The fungus makes cereal grain mouldy and contaminates the grain with toxic compounds so that it is unfit to eat by humans and animals. The AAFC corn breeding program has developed corn lines which are more resistant to Gibberella ear rot but the underlying mechanism is not understood. We had previously found that this resistance could be mapped to specific regions on five of the 10 corn chromosomes. In this study, we compared how a corn line that was very susceptible to gibberella ear rot and a corn line that had good disease resistance responded to fungal infection. We found that when corn kernels were infected, the expression of 1223 genes increased in both susceptible and resistant lines. Many of the genes that were turned on in the susceptible line after infection were already turned on in the resistant line before infection. We then selected a subset of 81 genes which mapped within the chromosome regions associated with ear rot resistance which we have designated as candidate resistance genes. If we can understand how these genes work, we could potentially understand the most effective ways that the corn plant can resist fungal diseases, to help develop more resistant corn plants in the future.


Background: Gibberella ear rot (GER) is one of the most economically important fungal diseases of maize in the temperate zone due to moldy grain contaminated with health threatening mycotoxins. To develop resistant genotypes and control the disease, understanding the host-pathogen interaction is essential. Results: RNA-Seq-derived transcriptome profiles of fungal- and mock-inoculated developing kernel tissues of two maize inbred lines were used to identify differentially expressed transcripts and propose candidate genes mapping within GER resistance quantitative trait loci (QTL). A total of 1255 transcripts were significantly (P≤0.05) up regulated due to fungal infection in both susceptible and resistant inbreds. A greater number of transcripts were up regulated in the former (1174) than the latter (497) and increased as the infection progressed from 1 to 2 days after inoculation. Focusing on differentially expressed genes located within QTL regions for GER resistance, we identified 81 genes involved in membrane transport, hormone regulation, cell wall modification, cell detoxification, and biosynthesis of pathogenesis related proteins and phytoalexins as candidate genes contributing to resistance. Applying droplet digital PCR, we validated the expression profiles of a subset of these candidate genes from QTL regions contributed by the resistant inbred on chromosomes 1, 2 and 9. Conclusion: By screening global gene expression profiles for differentially expressed genes mapping within resistance QTL regions, we have identified candidate genes for gibberella ear rot resistance on several maize chromosomes which could potentially lead to a better understanding of Fusarium resistance mechanisms.

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