Abstract Phytophthora crown rot, caused by Phytophthora cactorum , is a soilborne disease with broad impacts on cultivated strawberry ( Fragaria × ananassa ). A resistance locus, RPc2 , was previously identified in octoploid strawberries, but the underlying genomic architecture and causal genes remained uncharacterized. In this study, we fine‐mapped RPc2 from a 1.12 Mb interval to a 546 kb region containing 92 genes by genotyping an association panel of 339 accessions with high‐resolution subgenome‐specific markers. To discover candidate genes, a chromosome‐scale haplotype‐phased genome of the resistant breeding line FL16.33‐8 was assembled and validated with a high‐density genetic map and comparative analyses with high‐quality phased octoploid reference genomes, Florida Brilliance and Royal Royce. Transcriptome profiling following pathogen inoculation combined with comparative genomics identified wall‐associated kinase 1 ( WAK1 ) and cyclic nucleotide‐gated channel ( CNGC1 CNGC2 ) as strong candidates within the RPc2 region. Using an efficient Agrobacterium ‐mediated transient expression assay, we confirmed their role in resistance to P . cactorum in strawberry. RNA interference knockdown of these genes increased disease severity, while overexpression of WAK1 or CNGC1 reduced crown rot symptoms in susceptible backgrounds. Furthermore, population analyses of 1029 global accessions revealed that the predominant‐resistant haplotype ( RPc2 ‐ H3 ) is common in modern cultivars and shows evidence of positive selection in breeding programs. Taken together, our study refines the genomic region of RPc2 , identifies and functionally validates WAK1 and CNGC1/2 for the resistance to Phytophthora crown rot, and demonstrates that RPc2‐H3 has been selected globally. These findings from this study would facilitate the advancement of genome‐assisted breeding strategies for resistance to Phytophthora crown rot in strawberry.
Han et al. (Fri,) studied this question.