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Systematic phenotyping, comparative transcriptomics and functional validation of genes implicated in apple root resistance traits

Yanmin Zhu: USDA ARS

<div>Apple replant disease is a major obstacle to establishing an economically viable apple orchard at replant sites. The primary control method is pre-plant soil chemical fumigation, which is expensive and comes with environmental and regulatory concerns. Maximized exploitation of innate resistance requires elucidation of resistance mechanisms in apple roots. Apple root resistance traits were evaluated for more than 60 accessions from ‘Ottawa 3’ x ‘Robusta 5’ progeny in response to infection by <em>Pythium ultimum</em>, <em>Rhizoctonia solani</em> and <em>Pratylenchus penetrans</em>. Plant survival rates to <em>P. ultimum</em> infection ranged from 5% to 95% between more susceptible and resistant accessions. The higher survival rates were correlated with deterred necrosis progression along the infected roots. Resistance to <em>P. ultimum </em>among genotypes seems to correspond with that of <em>R. solani</em>, but no relationship with resistance to <em>P. penetrans </em>was observed. Two RNA-seq based transcriptome analyses allowed identification of candidate genes potentially regulating the differential defense activation patterns. These candidate genes include those functioning at pathogen sensing, defense hormone signaling, and synthesis and transport of secondary metabolites. Selected candidate genes are being validated for their association with resistance traits. Definitive roles of these genes in conferring resistance will be examined through <em>in planta</em> expression manipulation by over-expression and/or knock-out by CRISPR.</div>