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bioRxiv · 10.1101/2025.07.05.663326

Development of a Flex-Seq SNP panel for raspberry (Rubus idaeus L.) and validation through linkage map construction and identification of QTL for several traits of agronomic importance to raspberry breeding

Davik, J.·Zucchi, P.·Buti, M.·Milne, L.·Graham, J.·Sargent, D.
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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 (Parisx486), 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.

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Davik, J., Zucchi, P., Buti, M., Milne, L., Graham, J., Sargent, D.. 2025-07-09. Development of a Flex-Seq SNP panel for raspberry (Rubus idaeus L.) and validation through linkage map construction and identification of QTL for several traits of agronomic importance to raspberry breeding. https://doi.org/10.1101/2025.07.05.663326

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