QTL analysis of crown gall disease resistance in apple: first plant R gene candidates effective against Rhizobium rhizogenes (Ti)

In apple ( Malus spp.), crown gall disease, caused by the bacterial pathogens Rhizobium radiobacter (Ti) and R. rhizogenes (Ti), can be severe. To control the disease, breeding of apple rootstocks that exhibit crown gall resistance is a promising approach. In this study, we used a full-sib F 1 population derived from a ‘JM7’ (susceptible) × Sanashi 63 (resistant) cross to identify quantitative trait loci (QTLs) that control resistance to tumour-inducing Rhizobium isolates found in apple production areas in Japan. Three stable QTLs, associated with a wide range of crown gall resistances, were identified in three linkage groups (LGs). QTLs for resistance to isolates Peach CG8331, Nagano 1 and Nagano 2 co-localised at the middle of LG 2 in Sanashi 63, where the crown gall resistance gene Cg (renamed as Rrr1 in this study) was previously identified. Similarly, in ‘JM7’, QTLs were identified on LG 11 for resistance to isolates ARAT-001, ARAT-002 and Kazuno 2, and on LG 15 for resistance to isolate ARAT-001. Fine-mapping of Rrr1 and nucleotide sequencing of a contig obtained from two bacterial artificial chromosome (BAC) clones delimited the Rrr1 gene to a region spanning 217 kb. In silico gene prediction from the region identified four genes encoding the Toll-interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class plant resistance genes.