De novo assembly of transcriptomes from near-isogenic maize lines for novel defence gene discovery

Abstract

Maize is an economically important crop world-wide. This is especially true in South Africa where it is a staple crop and production contributes to food security. A major threat to maize production is a fungal foliar disease, grey leaf spot, that in South Africa is caused by Cercospora zeina. Controlling this disease to prevent the current yield losses is therefore important for food security. Ideally genetically resistant crops would be used, but there are only a few known defence genes against this disease. This study addressed this gap by developing a de novo assembly pipeline to identify maize genes involved in quantitative resistance against C. zeina. The study was done on three C. zeina-challenged and three control samples from a B73 maize line that had been introgressed with a quantitative trait locus for resistance against the disease. It was hypothesised that there would be a novel gene present in the introgressed QTL region that conferred the resistance against C. zeina infection. The research presented in this dissertation is based on bioinformatics and experimental work conducted in the Molecular Plant-Pathogen Interactions (MPPI) group at the University of Pretoria, South Africa. The dissertation is presented in the form of six chapters.