Abstract/Summary

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.