Expression profiling by high throughput sequencing
Summary
Ascochyta blight (AB) is a devastating and aggressive disease of field peas caused by multiple pathogens and the occurrence of the combinations of these pathogens forms a disease complex of which Peyronellaea pinodes, is the most aggressive. AB symptoms include necrotic lesions on all above ground parts of the plant, which can reduce crop yield by up to 70% and result in major economic losses globally. Crop resistance to the disease is reported to be quantitative and, although several genes have been reported to be AB response genes in Spanish pea genotypes, the lines or genotypes of the Australian field pea breeding program have not been investigated. Plants have specialized defence mechanisms that enable them respond to pathogen invasion, and this involves a cascade of genes which are differentially regulated upon infection. In this study, the time-course gene expression profiles of four Australian field pea genotypes including commercial varieties, known to have varying levels of AB resistance were investigated in response to P. pinodes infection. Infected and control plants at 0, 6, 24, 48, 72 and 96HPI were sampled for RNA seq. Mapping of transcriptome sequencing data against the field pea genome resulted in about the identification of c. 6,700 differentially expressed genes. Of the 21 AB resistance genes reported in previously published studies, only seven were present on the list of DEGs generated in this study. No significant pattern was identified in gene expression for the seven genes to differentiate resistant from susceptible genotypes. However, four key genes i.e., disease response protein, malate dehydrogenase, isoflavone 2 hydrogenase and Isoflavone reductase were shown to be associated with suppression of AB disease phenotype after 96HPI. Furthermore, GO functional annotation revealed several genes associated with defence including genes associated with the Salicylic acid pathway, reactive oxygen species, programmed cell death and hypersensitive response. Although the overall result showed a lack of strong resistance in the Australian pea genotypes as well as the fact that disease suppression does not directly equal resistance, we however were able to identify potential candidates that could be pyramided from exotic material into the breeding program to assess for improved resistance.
Overall design
Comparative gene expression profiling analysis of RNA-seq data for field pea genotypes (11HP302-12HO-1, PBA WHARTON, PBA TWILIGHT, and OZP1604) at 0hpi, 6hpi, 48hpi, 72hpi and 96hpi (hours post infection)
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