Transcriptome Analysis And Metabolite Profiling For Dissection Of Mechanisms Of Resistance To Phytophthora Root Rot (Phytophthora Rubi) In Red Raspberry (Rubus Idaeus L.)

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In red raspberry (Rubus idaeus L.) resistance to Phytophthora Root Rot (PRR), caused by P. rubi, is a critical factor in disease management. Therefore, identifying loci linked to resistance is a priority. Previous studies suggest that resistance in the cultivar 'Latham' is quantitative and induced. RNAseq was performed to investigate induced resistance in 'Latham' and susceptibility in the cultivar 'Titan'. Four sequencing libraries ('Latham' control, 'Latham' treatment, 'Titan' control, and 'Titan' treatment) were constructed from mRNA pooled across 3 time points (2 days, 5 days, and 20 days post inoculation). The libraries were sequenced independently, resulting in 15,213,629 reads from the 'Latham' control, 18,923,742 reads from the 'Latham' treatment, 18,363,149 reads from the 'Titan' control, and 18,145,135 reads from the 'Titan' treatment. Reads were aligned to the previously sequenced woodland strawberry (Fragaria vesca) genome with Bowtie/TopHat. Gene expression was quantified and differential expression was calculated with Cufflinks. This detected 15,164 genes in the 'Latham' control, 15,716 genes in the 'Latham' treatment, 14,896 genes in the 'Titan' control, and 13,991 genes in the 'Titan' treatment. The union of the four data sets included 16,956 unique genes. De novo assembly of all reads with Trinity produced over 36,000 transcripts with BLASTx hits (maximum e-value threshold of 1.0x10-3) to vascular plants and over 500 with hits to Phytophthora. Significantly differentially expressed genes between the 'Latham' control and 'Latham' treatment included genes directly involved in defense responses such as Pathogenesis Related 10 proteins (mal-d), WRKY transcription factors, and NPR1. These results suggest activation of the Salicylic Acid (SA) resistance pathway. Other defense responses commonly observed in SA mediated resistance include upregulation of key genes in the lignin biosynthetic pathway, such as caffeoylCoA O-methyltransferase and key genes in the tricarboxylic acid cycle (TCA) such as ATP citrate synthase. Metabolite profiling with GC/MS revealed few differences between treatments and controls, but significantly higher concentrations of citrate were found in the 'Latham' control compared to the 'Titan' control (p adjusted=0.0008) and in the 'Latham' treatment compared to the 'Titan' treatment (p adjusted=0.0164), suggesting that 'Latham' has increased flux through the TCA.

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Phytophthora rubi; RNAseq; gene expression


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Union Local


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Weber, Courtney A.

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Cheng, Lailiang
Smart, Christine Durbahn

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Plant Breeding

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Ph. D., Plant Breeding

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Doctor of Philosophy

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Government Document




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dissertation or thesis

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