Homologs of the FB_MR5 fire blight resistance gene of Malus ×robusta 5 are present in other Malus wild species accessions

Breeding for fire blight resistance is a major goal of nearly all apple breeding programs worldwide. Resources for resistance can be found in Malus wild species accession such as Malus ×robusta 5 (Mr5) which carries the FB_MR5 CC-NBS-LRR fire blight resistance gene. To study the occurrence of FB_MR5 in other genetic resources of Malus, a total of 394 wild species accessions of three international germplasm collections were screened using the markers CH03e03 and FEM18 that flank the FB_MR5 locus of Mr5. Five accessions exhibited the allele sizes linked to FB_MR5 for both markers. All five accessions belong to the species M. ×robusta (Carrière) Rehder. In addition, several accessions of other closely related Malus wild species amplified the 224 bp fragment linked to FEM18 and a slightly larger fragment for CH03e03. The presence and expression of FB_MR5 and homologs in M. ×robusta and four more accessions were further tested using gene-specific primers. Fragments of identical size could be detected in six different genotypes of M. ×robusta. Sequence analysis revealed the presence of alleles of FB_MR5 in the accessions ‘Korea’ and ‘Leucocarpa’. Homologs of FB_MR5 were found in different accessions of Malus prunifolia and Malus baccata, two Malus species closely related to M. ×robusta. Their functionality is suggested by results obtained by artificial shoot inoculation with the pathogen. Based on the results using the simple sequence repeat (SSR) markers CH03e03 and FEM18, the gene-specific primers and the analysis of the ‘Golden Delicious’ whole genome sequence, we assume that FB_MR5 is a unique gene which most likely evolved from M. baccata as the common ancestor of M. ×robusta and M. prunifolia.