Apple replant disease (ARD) is a soil-borne disease that arises from replanting apple trees on land previously used for apple cultivation. There is interest in biomarkers that can reliably assess the severity of ARD by quantifying how strongly apple plants react to the disease in soils of different agro-environments. Thus far, transcriptomic studies of ARD-affected plants have examined only a few soils at a time, revealing that expression patterns vary among different soils. Here, we analyzed the expression of 90 candidate genes in the roots of apple plants (rootstock genotype ‘M.26’) grown in ARD-affected soils from 151 sites across Germany to test whether a consistent pattern of gene expression under ARD-conditions exists. Additionally, the expression of the candidate genes was analyzed in the leaves of apple plants grown in 18 different ARD-affected soils. Most of the genes (72) showed significantly upregulated expression in roots under ARD conditions, while only 11 showed significantly upregulated expression in leaves, suggesting that these genes play a significant role in the ARD reaction in roots but only a limited or no role in leaves. The candidate genes were evaluated for their potential as ARD biomarkers, defined by their consistently increased expression under ARD conditions across different soils and correlation with ARD severity. The accordingly selected ARD biomarker genes in roots include genes involved in phytoalexin biosynthesis, lignin metabolism, ethylene metabolism, cyanogenesis, detoxification, programmed-cell-death, and plant defense. These biomarkers have the potential to assess the severity of ARD and open up new possibilities for disease diagnosis.

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