Comparative transcriptome analysis reveals a preformed defense system in apple root of a resistant genotype of G.935 in the absence of pathogen

Authors: Zhu, Yanmin; Shao, Jonathan; ZHOU, ZHE - Chinese Academy Of Agricultural Sciences; Davis, Robert

Submitted to: International Journal of Plant Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/28/2017
Publication Date: 3/31/2017
Citation: Zhu, Y., Shao, J.Y., Zhou, Z., Davis, R.E. 2017. Comparative transcriptome analysis reveals a preformed defense system in apple root of a resistant genotype of G.935 in the absence of pathogen. International Journal of Plant Genomics. doi: 10.1155/2017/8950746.

Interpretive Summary: Newly available large-scale and high-throughput genomics tools, such as transcriptome analysis, are able to uncover novel mechanisms over a biological process. In our previous study, two apple rootstock cultivars were observed with contrasting resistance phenotypes, i.e. a more resistant G.935 and a very susceptible B.9, in response to infection by soilborne pathogen Pythium ultimum. As part of an effort to understand the genetic control over the observed different levels of resistance, global gene activities in pre-inoculated roots were compared side-by-side between these two cultivars in current study. We found that a large number of defense-related genes showed much higher level of expression in the root tissue of the resistant cultivar of G.935, as compared with those in the root of the susceptible B.9. Based on their predicated function, these genes encoded proteins which function at several tiers of defense responses such as pathogen detection, defense hormone signaling, antimicrobial metabolite generation and several classes of resistance proteins. The data set suggested that, even in the absence of pathogen, a more poised status or a “ready to defend” mode exists in the root tissues of the resistant cultivar G.935, but not in the root of the susceptible B.9. Therefore, the existence of a preformed defense system in the root of a resistant apple rootstock G.935, but not the susceptible B.9, was demonstrated through direct comparison of the global gene expression landscapes in apple root. This less-represented defense mechanism likely works together with the inducible sections of plant defense reactions contributing to the overall disease resistance performance in apple root.

Technical Abstract: Two apple rootstock genotypes G.935 and B.9 were recently demonstrated to exhibit distinct resistance responses following infection by P. ultimum. As part of an effort to elucidate the genetic regulation of apple root resistance to soilborne pathogens, we hypothesized that pre-inoculation transcriptome variation(s) in roots contributes to cultivar-specific disease resistance. Results from comparative transcriptome analysis in current study demonstrated the elevated transcript abundance for many genes functioning at system-wide of defense response in the root tissue of the resistant cultivar of G.935 as compared with the susceptible B.9. Based on the functional annotation, these differentially expressed genes encoded proteins function in several tiers of defense responses such as pattern recognition receptors for pathogen detection and subsequent signal transduction, defense hormone biosynthesis and signaling, transcription factors with known roles in defense activation, enzymes of secondary metabolism and various classes of resistance proteins. The data set suggested a more poised status, which is “ready to defend pathogen infection” in the root tissues of resistant cultivar G.935, compared to the susceptible B.9. The significance of such preformed defense in the absence of pathogen toward overall resistance phenotypes in apple root, and the potential fitness cost due to the over-activated defense system were discussed.