Dataset: Identification of candidate genes associated with tolerance to Apple Replant Disease (ARD) by genome-wide transcriptome analysis

Apple replant disease (ARD) is an economic risk in apple production worldwide. Several studies on the response of apple plants to ARD have been documented, but less is known about the genetic mechanisms behind this symptomatology. The aim of our work was to find differentially expressed genes in response to ARD in Malus by RNA sequencing. For this, we compared transcriptome data of the rootstock ‘M9’ (susceptible) and the wild apple genotype M. ×robusta 5 (Mr5, tolerant) after cultivation in ARD soil and disinfected ARD soil, respectively. RNAseq of the 12 root samples resulted in 549.6 million raw reads, with an average of 46 million 100-bp single ended reads per sample. After quality control, 494.1 million reads were mapped to the apple reference genome (Malus ×domestica cv. 'Golden Delicious' v1.1) and assigned to 72,569 Gene IDs (Dataset 1). Comparing ARD soil versus disinfected ARD soil, 1,206 DEGs were identified based on a log2 fold change, (LFC) ≥ 1 for up– and ≤ –1 for downregulation (p< 0.05) (Dataset 2).