Hunting for novel disease resistance genes: Observations and opportunities from the Rosaceae

Identifying effective genes for disease resistance is a bottleneck in plant improvement and requires resource-intensive phenotyping followed by molecular mapping, tagging, and (in some cases) cloning. Across plant species and pathogen types, the nucleotide binding-leucine rich repeat (NB-LRR) superfamily of genes has been repeatedly implicated in detection and response to pathogens, yielding a resistance phenotype. While NB-LRR genes can be identified from DNA sequence it is impossible to associate a specific NB-LRR gene with a cognate pathogen species or race based on sequence alone. Working in the Rosaceae, we have developed a robust, semi-automated informatics pipeline to identify NB-containing gene sequences from whole genome sequences and interpret evolutionary patterns across multiple species within the family. We have applied our comparative approach to 3 rosaceous genomes, those of apple, peach, and the woodland strawberry. Our analyses reveal 7 dominant NB gene lineages. With few exceptions, each lineage is present in each species, suggesting an ancient origin. While most NB lineages are found in each rosaceous species, species differ profoundly in terms of allelic diversity within each lineage. We are using patterns of allelic diversification across species to develop hypotheses that link DNA sequences with putative gene function. Paired with targeted sequencing of the NB gene component of genebank collections, our comparative analyses have the potential to identify plant genotypes with novel NB alleles for subsequent targeted phenotypic testing. Rose black spot (caused by Diplocarpon rosae Wolf) is a significant disease impacting landscape roses and creation of disease resistant cultivars is an important breeding goal. In the next phase of this project, we are applying our comparative genomics pipeline and targeted sequencing of the NB gene component of rose genotypes to identify markers linked to black spot resistance for marker assisted breeding.