Genetic and Transcriptomic Analysis of Age Related Resistance to Phytophthora capsici in Developing Cucumber Fruit

Developing cucumber (Cucumis sativus L.) fruit cv. Vlaspik exhibit age related resistance (ARR) to infection by the oomycete pathogen Phytophthora capsici. Very young fruit undergoing cell division and rapid fruit expansion are highly susceptible. However, after approaching full size at approximately 12-16 days post pollination (dpp), they become resistant, exhibiting minimal or no visible pathogen growth and symptom development limited to the site of inoculation. The transition away from the period of exponential growth is accompanied a by transcriptional shift to increased expression of defense related genes. While observed in numerous host pathogen systems, the genetic basis of ARR is poorly understood.  Here we show that expression of ARR, which is associated with the fruit surface, varies among cucumber cultivars, and is differentially expressed among isolates of P. capsici. Inheritance of ARR in progeny of ‘Vlaspik’ appears to be associated with a major dominant factor. RNA-seq transcriptome analysis was performed to identify differences in gene expression between peel samples from ARR+ (Vlaspik) and ARR- (GY14) genotypes during susceptible and resistant stages of development. Three biological replicates, each comprised of a pool of two fruits, were sampled for each treatment. Sequencing was by Illumina HiSeq2500 with 50nt SE reads. Each sample averaged 25M reads, of which an average of 89% mapped uniquely to the cucumber genome. Principal component analysis of differentially expressed genes (DEGs) revealed a primary age effect and secondary genotype effect. A pipeline was established for detecting DEGs that are specifically differentially regulated at resistant stages of ARR+ fruit, but not in ARR- or young fruit stages.