Famula, R. | bioRxiv Science

bioRxiv2024

Genomic Architecture of the Resistance to Phytophthora Cactorum 2 (RPc2) Locus in Strawberry (Fragaria x ananassa)

Phytophthora crown rot (PhCR), caused by Phytophthora cactorum, is a soilborne disease with broad impacts to cultivated strawberries in the United States and worldwide. While a resistance locus, RPc2, has been identified in octoploid strawberries, the underlying genomic architecture and mechanism remain unclear. Here, we fine-mapped the RPc2 region to 546 kb, containing 92 genes, and constructed a chromosome-scale haplotype-phased genome of resistant breeding selection FL 16.33-8. Comparative genome analyses with high-quality octoploid reference genomes, Florida Brilliance (FaFB1) and Royal Royce (FaRR1), identified two candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1). Gene functions were validated using an Agrobacterium-mediated transient expression assay. Furthermore, by leveraging the population structure of the RPc2 locus among genetically diverse breeding populations, we unveiled the complexity of genetic architecture and recent selective sweeps associated with RPc2. Notably, the predominant resistant haplotype (RPc2-H3) is prevalent in most commercial strawberry varieties in the US. The findings from this study are facilitating the advancement of genome-assisted breeding strategies for resistance to PhCR in strawberries. SummaryO_LIPhytophthora crown rot (PhCR), caused by the soilborne pathogen Phytophthora cactorum, is a disease with broad impacts to cultivated strawberries worldwide. The Resistance to Phytophthora Cactorum 2 (RPc2) locus is widespread in important cultivars and is a target of selection in breeding programs. Despite its importance, the genomic architecture and mechanisms of RPc2 remain poorly characterized. C_LIO_LIWe performed fine-mapping and delimited the genomic region to a 546 kb segment containing 92 genes. We developed a chromosome-scale haplotype-phased genome from an elite resistant line, FL16.33-8, and made comparisons to reference genomes of Florida Brilliance (FaFB1) and Royal Royce (FaRR1) to uncover gene sequence and structural variants in resistant accessions. C_LIO_LIThrough comparative genomics and transcriptome profiling, we identified three candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1) and CNGC2. The functions of these genes were validated using a simplified Agrobacterium-mediated transformation method for transient gene expression in strawberry crowns and roots. C_LIO_LIAn examination of the population structure of the RPc2 locus among genetically diverse accessions (N=1029) revealed that the predominant H3 resistant haplotype is widespread in breeding accessions in the US, supporting the findings of a previous study on recent selective sweeps associated with RPc2. Results from this study are advancing genome-assisted breeding strategies for enhancing resistance to PhCR in strawberry. C_LI

plant biology↗

bioRxiv2019

Chromosome Evolution of Octoploid Strawberry

The allo-octoploid cultivated strawberry (Fragaria x ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. x ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information, and unifying existing chromosome nomenclatures. Through comparative genetic mapping, we show that the genomes of geographically diverse wild octoploids are effectively diploidized and completely collinear. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported both its origin and domestication through repeated cycles of interspecific hybridization.

genomics↗