Elucidating the genetic mechanisms underlying tolerance to apple replant disease (ARD)

Apple replant disease (ARD) is a soil-borne disease, which is increasingly problematic for tree nurseries and orchards worldwide. Although, ARD is known for centuries, the ultimate causes remain unknown. The phenomenon occurs after repeated replanting of the same plant species on the same soil, leading to the soil losing its capacity to support the growth of the species. As a result, the replanted plants are characterized by a poor vegetative development, and reduced yield in terms of quantity and quality. The use of ARD-tolerant rootstocks is a sustainable approach to control this phenomenon, however, only a few Malus ARD-tolerant genotypes have been described. Moreover, less is known about the genetic mechanisms underlying these tolerances. Identifying ARD-tolerant genotypes and understanding the molecular basis for tolerance are prerequisites for future rootstock breeding. Six Malus accessions of the genebank at JKI in Dresden were previously identified as ARD-tolerant in a greenhouse bio-test. Since the previous classification was based on only one soil origin, these accessions were tested in a greenhouse bio-test using three different soil types in this study - thus confirming their ARD-tolerant status. To identify potential candidate genes related to ARD-tolerance, a comparative transcriptome study was performed. For this, the gene expression between the susceptible rootstock M.9 and the tolerant wild apple accession M. × robusta 5 were compared by RNA sequencing after cultivation on ARD-soil and disinfected (γ) ARD-soil. As a result, 81 candidate genes with a significant response in expression were selected for further validation.