A systematic analysis of apple root resistance traits to Pythium ultimum infection and the underpinned molecular regulations of defense activation

Authors: Zhu, Yanmin; Saltzgiver, Melody

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2020
Publication Date: 5/1/2020
Publication URL: https://handle.nal.usda.gov/10113/7019800
Citation: Zhu, Y., Saltzgiver, M.J. 2020. A systematic analysis of apple root resistance traits to Pythium ultimum infection and the underpinned molecular regulations of defense activation. Horticulture Research. 7:1-11. https://doi.org/10.1038/s41438-020-0286-4.
DOI: https://doi.org/10.1038/s41438-020-0286-4

Interpretive Summary: Maximized utilization of plant resistance for sustainable and effective disease management is increasingly crucial for many crops including perennial tree fruit crops like apple. Our researches have been focused on the detailed phenotypic analysis of resistance responses in apple root, and understanding the molecular genetics underpinning the observed resistance traits using genomic approaches. Oomycete pathogen Pythium ultimum was selected as a model pathogen, which is one of the primary members in a pathogen complex causing apple replant disease. This review manuscript summarized the results in last a few years from both research fronts: 1. Phenotypic characterization of apple root resistance responses including microscopic features of root necrosis patterns between resistant and susceptible genotypes; 2. Identification of the molecular networks potentially differentiate apple root resistance and susceptibility based on a series large-scale and high-throughput genomic analyses. Implementation of a laborious and time-consuming procedure for in vitro micropropagation of apple plants made it possible for repeated infection assays on more than 60 apple rootstock genotypes. Using custom-made glass box pots and combined with continuous observation under dissection microscope, several features of root necrosis development along infected apple root were observed in a non-invasive and non-destructive manner. Based on the huge phenotyping data, a panel of apple rootstock germplasm with contrasting resistance phenotypes were identified, which are critical plant materials for analyzing the molecular mechanisms behind apple root resistance traits. On the other hand, the comprehensive datasets from a series of transcriptome and proteomic analyses generated a panoramic picture of genome-wide molecular networks regulating apple root defense activation towards P. ultimum infection for the first time. A set of apple candidate genes were identified which putatively regulate root resistance to P. ultimum infection. Using the identified panel of apple rootstock germplasm with defined resistance traits, the correlative or causal relationship between individual candidate genes and the root resistance traits are being examined. The more definitive functional identities for selected apple candidate genes are being validated by transgenic manipulation using CRISPR/Cas9 technology and subsequent analyses on the potentially altered resistance phenotypes. The current progresses set the foundation to identify the key genes which determine apple root resistance and subsequently develop and deploy molecular tools for efficient and precise incorporation of resistance traits into the next-generation of resistant apple rootstock.

Technical Abstract: Elucidating the molecular mechanisms behind apple root resistance to apple replant disease (ARD) is crucial for maximized exploitation of natural resistance in sustaining and effective disease management. Reliable and detailed resistance phenotypes are the prerequisite for dissecting the molecular regulation networks contributing to apple root resistance traits. A systematic phenotyping effort has identified a panel of apple rootstock germplasm with contrasting resistance traits to P. ultimum infection. The values of plant survival rates and biomass reduction correspond with the microscopic features of apple root necrosis progression patterns between resistant and susceptible genotypes. The presence of well-defined boundaries separating healthy and necrotic sections along the infected roots of resistant genotypes indicates an effective resistance mechanism that resulted in necrosis deterrence. In contrast, the swift progression of root necrosis and profuse hyphae growth demonstrate the inadequate defense in roots of susceptible genotypes. Implementation of a synchronized micropropagation procedure enables the continuous availability of uniform apple plants for consistent and systematic evaluation of apple root resistance traits among tested apple rootstock genotypes. Comprehensive datasets from a series of transcriptome analyses provided the first panoramic view on genome-wide transcriptional networks of apple root defense activation towards P. ultimum infection. Earlier and stronger molecular defense activation, such as those genes for pathogen perception and hormone signaling, likely represents the key points which may differentiate resistance from susceptibility in apple roots. Delayed and interrupted activation of multiple defense pathways, including those for production and transportation of antimicrobial secondary metabolites, may have led to the defective defense responses. Using the panel of apple rootstock germplasm with defined resistance traits from phenotyping effort, the roles of apple candidate genes identified by transcriptome analyses are being evaluated including using CRIPR/Cas9 mediated transgenic manipulation. The analyses of altered resistance phenotypes provide more definitive evidences on their critical roles contributing to apple root resistance. The validated roles of individual apple genes impacting root defense responses are fundamental for developing molecular tools for accurate and efficient incorporation of resistance traits into new apple rootstocks.