Uncovering the mechanism of pumpkin brown etch transcriptomic and microscopy analysis of affected fruit

Abstract

Brown etch is a major issue for Australian pumpkin growers, particularly producers of butternut varieties. It regularly results in significant losses on farm through product quality downgrades or rejections at markets. Losses of 50% are common, and in some cases whole crops may be abandoned as uneconomic to harvest due to the large percentage of affected fruit. Initial symptoms are orange-brown spots, which appear on fully grown, immature fruit. These progressively enlarge, sometimes covering almost the entire fruit. The brown area lesions stop expanding once the fruit matures. Two main techniques were used to investigate the underlying cause and effects of the lesions: microscopy and global RNA sequencing. These were used to examine the morphological basis and to determine if genes or pathways are altered during the onset and progression of the disorder that may shed light on the causal mechanisms. Mature Butternut Pumpkin fruit samples (Butternut squash) for the assays were collected from a farm in Tully, Queensland. Scanning electron micrographs showed marked differences in cell wall structure between the tissues in unaffected, affected and material taken from the leading edge of the lesions. This indicates ectopic deposition of secondary cell walls in the affected tissues and is indicative of an active cellular process rather than a sudden loss of cell function and ensuing cell and tissue death. Analysis of the RNA-seq data has given clues as to the mechanism underlying the onset and progression of cell wall changes in affected tissues. In particular, a number of differentially expressed genes related to the phenylpropanoid pathway were identified. This pathway is known to be involved in plant defence and stress responses.