ArticleBMC genomics2025
A haplotype-phased genome characterizes the genomic architecture and causal variants for RXf1 conferring resistance to Xanthomonas fragariae in strawberry (F. × ananassa).
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- Genetic architecture of angular leaf spot resistance in cultivated strawberry shaped by epistasis and genotype-by-environment interactions.The plant genome · 2026Article
- Chromosome-scale assemblies of flowering dogwood cultivars enable identification of candidate genes regulating anthocyanin biosynthesis in leaves and bracts.BMC plant biology · 2025Article
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3 authors.
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Abstract
backgroundCultivated octoploid strawberry (Fragaria × ananassa) is one of the most economically important fruits worldwide due to its flavor, texture, and health benefits. However, bacterial angular leaf spot (ALS) causes economic losses in fruit production and plant nurseries. All commercial strawberry varieties are susceptible to ALS. A major resistance locus, RXf1, has been reported, but the genomic structure and candidate genes underlying this resistance remain known.
resultsFine-mapping was performed using three segregating populations containing 663 individuals that were genotyped with subgenome specific seven high-resolution melting (HRM) markers to narrow the RXf1 region to a 486-kb interval on chromosome 6C. We assembled a haplotype-phased chromosome-scale genome of ALS-resistant breeding selection FL17.68-110 using highly accurate long-read sequencing and trio-binning with parental short reads. The 1.62 Gbp genome containing two haplotypes, 56 chromosomes and 193,072 annotated genes. Transcriptome analysis in response to the ALS pathogen identified a candidate gene, Resistance gene analogue 3 (RGA3), associated with the RXf1 resistance. The gene structure and sequence variations within FaRGA3 were identified between resistant and susceptible genotypes.
conclusionsOur results narrowed the RXf1 region, identified structural variations within this locus and pointed to FaRGA3 as a promising candidate gene. This information will be useful for breeders toward developing ALS-resistant strawberry varieties, and the high-quality genome will be a valuable resource for further genomics research in octoploid strawberry.
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