title: Identifying novel powdery mildew susceptibility and resistance genes in Fragaria × ananassa
Creators: name: Lynn, Samantha Claire
Publisher: name: University of Reading
Year: 2024

description: The biotrophic fungal pathogen Podosphaera aphanis causes powdery mildew (PM) disease 
on strawberry. Strawberry PM is a global problem, infecting all above ground plant organs.
The infection of PM leads to lower yields and unmarketable fruit and thus pathogen infections 
result in high economic losses. Infection of the foliage can lead to a reduction in 
photosynthesis, leading to decreased CO2 assimilation and ultimately a decrease in yield. 
When the PM fungus infects strawberry reproductive tissue, it can cause misshapen or stunted 
fruit. Control of PM disease is predominantly achieved by the application of fungicides;
however, overreliance on chemical application has led to the evolution of fungicide resistant 
strains. Generating disease resistant cultivars offers a highly favourable solution to reduce the
impact of PM on strawberries. Thus far, there are no public, validated, large effect genetic 
markers for use in improving PM disease resistance in strawberry. This project focused on 
characterising the genetic components underlying tissue specific resistance to PM disease, 
whilst ultimately identifying putative resistance genes. To achieve this goal, analysis was 
conducted across different strawberry genotypes through a genome-wide association study 
(GWAS) using phenotyping and genotyping data Multiple genetic loci associated with PM 
resistance in foliage were identified using a GWAS, with several loci displaying a high effect 
size of over 50%. Moreover, six stable Quantitative Trait Nucleotides were identified across 
both years of assessment. In a separate experiment RNA sequencing was used to identify 
differentially expressed genes in the presence of PM across three resistance types: tissue, 
cultivar and ontogenic resistance. The RNA sequencing analysis revealed a diverse 
immunogenetic resistance response associated with each different resistance type. Across
these resistance types, one gene (CAF1-11) was detected throughout, offering a promising 
candidate for PM resistance. Another highly important trait that can lead to increased
strawberry production is fruit number, a component of yield. A GWAS was also conducted to 
identify genetic loci that may be associated with fruit number. The analysis identified five genes 
that may be involved in controlling fruit number. Finally, a genomic prediction approach was 
used to determine the predictive accuracy associated with improving both strawberry PM
resistance and fruit number. This study has shown there is a large potential for using genomic 
selection to increase cultivar foliar PM resistance; however, fruit PM resistance or fruit number 
were not predicted to lead to an improvement in phenotype using a genomic prediction 
approach. Overall, this study has identified multiple novel genes potentially associated with 
PM resistance and fruit number. As such this work provides a greater understanding of the 
complex mechanisms associated with these traits whilst offering a steppingstone towards the 
development of genetic molecular markers for use in breeding elite strawberry lines.