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A soil- and site-dependent complex of diverse microbial populations causes apple replant disease (ARD), which leads to economic losses for tree nurseries and apple producers due to reduced plant growth and diminished fruit yields. Soil fumigation has been widely used to mitigate ARD, but the application of these chemicals is restricted in the European Union. Hence, other counteractions have to be developed. Genomics-based breeding may be used to select ARD-tolerant genotypes; however, molecular responses of ARD are not well understood. Recent studies revealed that biotic stress-associated genes involved in typical defense reactions are activated but do not result in an adequate response to ARD. The objective of this study was to analyze selected responsive genes in a time-course experiment to test for expression kinetics. Cultivating the ARD-susceptible apple rootstock ‘M26’ on ARD-affected soil resulted in significantly reduced growth as early as 7 days after planting. Genes involved in phytoalexin biosynthesis were upregulated in ARD samples as early as 3 days after planting and reached up to 26-fold changes at Day 10, which resulted in high amounts of 3-hydroxy-5-methoxybiphenyl, aucuparin, noraucuparin, 2-hydroxy-4-methoxydibenzofuran, 2′-hydroxyaucuparin and noreriobofuran. For the first time, these phytoalexins were detected, identified and quantified in apple roots. The lack of a sufficient defense response may be due to impaired sequestration and/or exudation of the potentially cytotoxic phytoalexins and perturbed formation of reactive oxygen species, leading to root damage in ARD soils. The findings provide a basis for comparative studies of the defense processes in more ARD-tolerant rootstocks.

Impaired defense reactions in apple replant disease-affected roots of Malus domestica ‘M26’