Sequencing ESTs of the avocado transcriptome to study the tolerant response to Phytophthora cinnamomi

Abstract

Avocado (Persea americana Mill.) is an important crop whose cultivation is severely threatened by Phytophthora cinnamomi Rands. The South African avocado industry makes an important contribution to the world’s avocado supply, and is one of the world’s largest exporters. If the current Phytophthora root rot problem is not addressed soon, the losses encountered by the avocado industry may become so extensive that it results in job losses. The scant information that is available for P. cinnamomi interaction studies indicate that there is no gene-for-gene interaction yet described between the pathogen and host. Avocado genomics are not well understood either and there is not much sequence data available for this basal angiosperm. The data available comprises of sequence that was generated in marker studies on fruit and flowering organs. It is now possible to generate large amounts of sequence data using highthroughput sequencing platforms and identify defence-related genes. The identification of defence-related genes in a tolerant rootstock will allow us to characterize the avocado-P. cinnamomi interaction on a molecular level. The aim of this MSc was to identify defence-related genes in a tolerant rootstock and characterize their expression in order to understand the avocado-P. cinnamomi interaction. Chapter 1 provides a comprehensive overview of the advances in molecular work conducted on avocado thus far. A background of avocado rootstock development is provided with details of molecular markers developed for use in avocado. Additionally, an introduction is also given to high-throughput sequencing and its application to non-model crops such as avocado. Chapter 2 describes the mRNA isolation and EST pyrosequencing of avocado roots. Gene annotation of metabolic, cell wall associated and stress response genes are provided along with the characterisation of defence-related genes. Chapter 3 reports of the expression profiling of defence-related genes obtained from avocado root ESTs. The expression of nine defence-related genes are studied over six time points in P. cinnamomi infected R0.09 tolerant avocado roots. Chapter 4 provides a general discussion of the result obtained in this study along with future applications of the sequencing data produced.