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Phytophthora is a genus of destructive plant pathogens. Certain species are damaging to native ecosystems, forestry, and the horticultural sector, and there is evidence of their dissemination in plant imports. Horticultural nurseries are central nodes of the plant trade and previous studies have found a high diversity of Phytophthora associated with plant nursery stock. It was subsequently hypothesized that green waste disposal sites in nurseries could harbour diverse Phytophthora communities and act as a pathogen reservoir and conduit, facilitating further Phytophthora infection of nursery stock and its spread into the wider environment. This project identified Phytophthora species associated with green waste at three Scottish nurseries by sampling material from waste piles, water run-off from piles, and roots from discarded plants. Species were identified using a baiting method and sequencing of environmental DNA. Plant nursery green waste was shown to harbour diverse and varied Phytophthora species assemblages, with differences among nurseries reflecting biosecurity management practices. Eighteen Phytophthora species were detected in the samples, including the highly destructive pathogens P. ramorum and P. austrocedri. Results suggest that the improved management of waste, for example through effective on-site composting, is essential to reduce the risk of Phytophthora pathogens spreading from nurseries into the wider environment.

‘Crumbly’ fruit is a developmental disorder in raspberry that results in malformed and unsaleable fruits. For the first time, we define two distinct crumbly phenotypes as part of this work. A consistent crumbly fruit phenotype affecting the majority of fruits every season, which we refer to as crumbly fruit disorder (CFD) and a second phenotype where symptoms vary across seasons as malformed fruit disorder (MFD). Here, segregation of crumbly fruit of the MFD phenotype was examined in a full-sib family and three QTL (Quantitative Trait Loci) were identified on a high density GbS (Genotype by Sequencing) linkage map. This included a new QTL and more accurate location of two previously identified QTLs. A microarray experiment using normal and crumbly fruit at three different developmental stages identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within the three QTL. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of crumbly fruit. These candidate genes provided insights regarding the molecular mechanisms involved in the genetic control of crumbly fruit in red raspberry. This study will contribute to new breeding strategies and diagnostics through the selection of molecular markers associated with the crumbly trait.