Role of the Rdr1 gene family in the black spot resistance in roses

Abstract

Black spot disease, caused by the hemibiotrophic ascomycete Diplocarpon rosae, is the most severe disease in field-grown roses. The Rdr1 locus, comprising nine highly similar TNL-genes, was previously characterised in roses and it is known to confer resistance to black spot. To identify the active Rdr1 gene, we analysed stable transgenic roses harbouring single members of the Rdr1 locus in a disease assay. muRdr1A was identified as the functional Rdr1 and it provides resistance to 13 different single-spore isolates of Diplocarpon rosae belonging to six different races; so far, Rdr1 is only overcome by two races. The identification and phylogenetic analysis of Rdr1-family members from the two recently available genomes of the diploid old Chinese Rosa chinensis cultivar ‘Old Blush’, together with nine different rose species, resulted in a genomic organisation of the Rdr1-family in two major clusters at the distal end of chromosome 1 with different ancient origins. Genes belonging to cluster 2, like the functional muRdr1A, were subjected to a faster evolution compared to genes from cluster 1 due to known processes, such as higher rates of recombination, gene conversion, and birth and death processes. In addition, phylogenetic analysis with additional Rdr1 homologues identified in other Rosaceae, i.e. Fragaria, Malus, Prunus and Rubus, resulted in the hypothesis that the Rdr1-family moved to its current position after the split of Rubeae from other groups within Rosoideae. Transcriptomic analysis during the compatible interaction of roses and D. rosae indicated an initial PTI reaction which is either insufficient, avoided or suppressed by D. rosae. As for the incompatible interaction of roses and D. rosae caused by Rdr1, two genes (peroxidase superfamily protein and Kunitz family trypsin and protease inhibitor protein) showed significant higher expressions in the incompatible interaction compared to the compatible interaction, independently of the genetic background. In conclusion, Rdr1 can be used as the starting point for the breeding of rose varieties with a durable broad spectrum resistance against D. rosae. Furthermore, the genomic organisation and the sequence information of the Rdr1-family provided in this study is a valuable source to analyse the role of Rdr1 homologs in disease resistance in other species.