Whitaker, V. | 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↗

bioRxiv2022

Telomere-to-Telomere and Haplotype-Phased Genome Assemblies of the Heterozygous Octoploid 'Florida Brilliance' Strawberry (Fragaria x ananassa)

The available haplotype-resolved allo-octoploid strawberry (Fragaria x ananassa Duch.) (2n = 8x = 56) genomes were assembled with the trio-binning pipeline, supplied with parental short-reads. We report here a high-quality, haplotype-phased genome assembly of a short-day cultivar, Florida Brilliance (FaFB2) without the use of parental sequences. Using Pacific Biosciences (PacBio) long reads and high-throughput chromatic capture (Hi-C) data, we completed telomere-to-telomere phased genome assemblies of both haplotypes. The N50 continuity of the two haploid assemblies were 23.7 Mb and 26.6 Mb before scaffolding and gap-filling. All 56 pseudochromosomes from the phased-1 and phased-2 assemblies contained putative telomere sequences at the 5 and/or 3 ends. A high level of collinearity between the haplotypes was confirmed by high-density genetic linkage mapping with 10,269 SNPs, and a high level of collinearity with the Royal Royce FaRR1 reference genome was observed. Genome completeness was further confirmed by consensus quality. The LTR assembly Index score for entire genome assembly was 19.72. Moreover, the BUSCO analysis detected over 99% of conserved genes in the combined phased-1 and phased-2 assembly. Both haploid assemblies were annotated using Iso-Seq data from six different Florida Brilliance tissues and RNA-Seq data representing various F. x ananassa tissues from the NCBI sequence read archive, resulting in a total of 104,099 genes. This telomere-to-telomere reference genome of Florida Brilliance will advance our knowledge of strawberry genome evolution and gene functions, and facilitate the development of new breeding tools and approaches.

genomics↗