2025/07/09 by Jahn Davik, Paolo Zucchi, Matteo Buti +3 · 1 voice
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Environmental Science · #Berry genetics and cultivation research #Plant Pathogens and Fungal Diseases #Turfgrass Adaptation and Management
paper · pdf · doi:10.1101/2025.07.05.663326
openalex publication_date 2025/07/09 · openalex created_date 2025/07/10 · openalex updated_date 2026/07/22
Abstract High-throughput and reproducible genotyping platforms are critical for advancing genetic research and breeding in horticultural crops. Here, the development and validation of a custom single nucleotide polymorphism (SNP) panel using the Flex-Seq genotyping platform for red raspberry ( Rubus idaeus L.) is described. SNPs were derived from existing linkage maps and RNA-seq data, resulting in a panel of 5,639 high-confidence, bi-allelic markers distributed across the seven chromosomes of the R. idaeus ‘Malling Jewel’ reference genome. The panel was used to genotype 457 red raspberry accessions including 161 individuals from a bi-parental mapping population (Paris×486), enabling the construction of high-density linkage maps and the identification of quantitative trait loci (QTL) for fruit size, leaf colour, plant vigour, and thorn density. Genome-wide association studies (GWAS) identified a major QTL for thornlessness on chromosome 4, co-locating with a candidate HOX3 gene, and multiple QTLs associated with anthocyanin biosynthesis genes for leaf colour. The SNP panel demonstrated utility for linkage mapping and trait association analyses, offering a powerful resource for marker-assisted selection and genetic improvement in red raspberry.