Transcriptome Analysis of Persea americana in Response to Phytophthora cinnamomi and Flooding / Unravelling the Oomycete-Host Defence Pathway in Persea americana Against Phytophthora cinnamomi

1. Persea americana (avocado) is an important fruit crop worldwide. However, losses in production occur as a result of damage caused by the oomycete Phytophthora cinnamomi. Phytophthora root rot (PRR) causes feeder root necrosis and leads to branch die-back and eventual tree death. Phosphite, tolerant rootstocks, and proper nursery management are currently the most effective control strategies. However, production losses are still great and development of rootstocks showing higher tolerance is being actively researched. Disease progression of PRR is further accelerated in flooded soils, with tree death occurring more rapidly. Even in the absence of PRR, flooding is detrimental to avocado and short periods of flooding can cause significant losses to industry. Despite the importance of avocado as a commercial fruit crop, genetic resources are limited. The genome has not yet been made publically available and transcriptome resources are largely limited to floral ESTs. In this study, 124 Mb of sequencing data generated using the 454 platform were used to assemble a de novo root transcriptome and identify stress-related genes. RNA for sequencing was isolated from plants inoculated with P. cinnamomi and plants exposed to a combination of P. cinnamomi and flooding stress. Several genes important in defence and response to hypoxic conditions caused by flooding were selected and expression analysis was performed. These included sucrose synthase, pyruvate decarboxylase, non-symbiotic haemoglobin, and endochitinase. In addition, the transcriptome data produced was used to design probes for an avocado gene expression microarray. These resources can be used to identify marker genes important in tolerance to both PRR and flooding.

2. One of the most serious threats to the avocado industry is Phytophthora root rot caused by Phytophthora cinnamomi (Pc). The Pc-avocado interaction has been studied in some detail but after many decades of research we still have limited success in combating the pathogen. Development of tolerant rootstocks has been identified as a priority for the avocado industry and several rootstock breeding programmes have been established. Selection for tolerance can be improved by understanding the plant-pathogen interaction. The aim of this study was to identify the phytohormone pathways upregulated in a tolerant avocado rootstock against the pathogen. Defence-related genes and phytohormone pathway associated transcripts were identified from the avocado transcriptome, with approximately 300 genes associated with the salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) pathways identified. Genes such as PAL, PR2, PR5, PR4, PR6 were found to be up-regulated during infection. PR2 was found to have a >10 fold increase in transcript abundance when compared to controls with PR4, PR5 and PR6 being up-regulated at different time points. These and other pathway-linked genes indicate a temporal modulation of defence pathways to combat the pathogen. The defence interaction is indicated to begin with SA and move into a JA-linked response which reflects the pathogen’s hemibiotrophic nature. This work will allow the changes in pathway activity to be studied under infection and allow a greater understanding of the role phytohormones play against Pc.