Powdery mildew is an important disease of crop plants. In strawberry, the disease is caused by the obligate biotrophic fungus Podosphoera ophonis (syn: Sphoeratheco mocu/oris f. sp. Fragorioe) and causes significant economic loss in the cultivated strawberry. This study used the diploid species Fragorio vesco as a model to study plant pathogen interactions. Initial studies involved in the identification of mildew resistance locus 0 (MLO) genes in the diploid species, F. vesco f. vesco and identified 17 FvMLO genes. Real-time quantitative PCR (qRT-PCR) results showed differential expression of 12 FvMLO genes in four strawberry varieties, F. vesco f. vesco (Fv), F. vesco ssp. vesco accession Hawaii 4 (HW), F. vesco f. semperf/orens line "Yellow Wonder 5AF7" (YW) and Eluica (octoploid strawberry). The FvML03 gene which is orthologous to the Arabidopsis AtML02, AtML06 and AtML012 and tomato S/ML01 genes required for powdery mildew susceptibility was highly expressed (164 fold) in YW compared to other FvMLO genes across varieties. The results showed that FvMLO genes can be used as potential candidates to engineer powdery mildew resistance in strawberry based on MLO suppression. To investigate the molecular mechanism underlying strawberry-powdery mildew interaction, RNA-seq was employed to generate a large transcriptome dataset in HW and YW at 1 d and 8 d after powdery mildew infection. We identified about 999 million (92%) reads mapped to the F. vesco genome. Transcripts were identified from a total of 23,470 and 23,464 genes in HW and YW, respectively at all three stages (control, 1DAI and 8DAI). Differential gene expression analysis identified 1,567, 1,846 and 1,145 upregulated genes between control and 1DAI, control and 8DAI, and 1DAI and ! lDAI, respectively in HW. Similarly, 1,336, 1,619 and 968 genes were upregulated in YW. Also 646, 1,098 and 624 down regulated genes were identified in HW, while 571, 754 and 627 genes were downregulated in YW between all three stages, respectively. The study also investigated differentially expressed genes (log2 fold changes <:5) between control and 1DAI in both HW and YW. A large number of genes related to secondary metabolism, signal transduction, transcriptional regulation and disease resistance were expressed predominantly either in HW or YW. These included flavonoid 3' -monooxygenase, peroxidase 15, glucan endo-1, 3-beta-glucosidase 2, receptor-like kinases, transcription factors, germin-like proteins, F-box proteins, NB-ARC and NBS-LRR proteins. This first application of RNA-seq to any pathogen interaction in strawberry provides wealth of genomic information for future studies in understanding molecular and cellular processes of the strawberry defence response to powdery mildew. It was also shown that metabolic lSN hydroponic isotope labelling of entire plants (HILEP) can be achieved in strawberry for quantitative proteomics analysis.