Transcriptome analysis of sugar beet in response to the pathogenic oomycete Aphanomyces cochlioides

Aphanomyces root rot is one of the most severe diseases in sugar beet (Beta vulgaris L.), resulting in drastic losses in sugar yield and plant degeneration. The causal agent is the soil-borne pathogen Aphanomyces cochlioides, a phytopathogenic oomycete able to infect sugar beet roots from the seedling stage until harvest. Reliable control measures and fully resistant varieties to prevent the disease on mature roots are currently not available. Furthermore, the quantitative nature of the resistance mechanisms to the root rot disease remain unclear. With the aim to identify key genes involved in plant defense responses against the root rot, we performed a transcriptome analysis of sugar beet interactions with A. cochlioides. The transcriptome responses of two partially resistant and two susceptible sugar beet breeding lines, inoculated with three A. cochlioides isolates with different geographical origins have been investigated in this study.

The results showed that the transcriptional responses to A. cochlioides infection were mainly genotype-dependent. Comparisons of transcriptome profiles of partially resistant and susceptible breeding lines revealed the presence of differentially expressed genes that play a key role in defense mechanisms during the initial stages of infection. Gene Ontology (GO) categories associated with hydrogen peroxide (H₂O₂) metabolism, detoxification and cell wall organization were significantly enriched in the differentially expressed gene set from the two partially resistant lines, while photosynthesis-related GO terms were significantly enriched in the two susceptible lines. Unique and overlapping GO categories were over-represented in specific genotype-isolate-time point interactions, indicating that different genotypes respond with common defense strategies as well as specialized responses to different isolates and time points. Transcription factors belonging to the WRKY and ERF families were up-regulated in all genotypes. Furthermore, increased expression of genes encoding for disease resistant proteins have been identified in the two partially resistant genotypes.

This research offers new insights into the transcriptomic events that regulate the sugar beet defense responses to A. cochlioides infection. The findings of this study emphasize the importance of genotype-specific interactions in response to different A. cochlioides isolates. Moreover, the results showed the up-regulation of genes that may play important roles in the defense responses to A. cochlioides which can be used to improve future breeding and to assist in the development of resistant cultivars.