Broad spectrum of resistance to tuber-invading diseases of potato

Potato is the third most important food crop in the world with production exceeding 320 million tonnes per year. Major soilborne diseases of concern to the Australian potato industry include common scab, powdery scab, black scurf and the post-harvest disease tuber soft rot. These diseases have negative impacts on the French fry potato processing sector where the cultivar 'Russet Burbank' is the most important commercial cultivar used. Common scab is caused by infection of developing tubers with Streptomyces spp. Previous research has developed common scab resistant somaclonal variants of Russet Burbank using a somatic cell-selection breeding technique, with the pathogens toxin (thaxtomin A) used as a positive selective agent. The current study involved determining the breadth and possible mechanism of resistance of these novel variants of Russet Burbank to other important tuber diseases such as powdery scab caused by Spongospora subterranea f.sp. subterranea (a protozoan), black scurf caused by Rhizoctonia solani (a fungus), tuber soft rot caused by Pectobacterium atrosepticum and P. carotovorum (both bacteria species). This study also involved measurement of Spongospora subterranea f.sp. subterranea root infection and developing model systems to track infection and provide an early indication of putative controls which may improve management options for powdery scab. A series of glasshouse experiments, field trials and in vitro assays were conducted to challenge five common scab resistant variants of c.v.Russet Burbank against Spongospora subterranea f.sp. subterranea, R. solani, P. atrosepticum and P. caratovorum. Pathogen inoculation techniques, sequential harvest and modified disease assessment methods were followed to evaluate the concurrent resistance level to these pathogens compared to the parent cultivar. Trial results identified three variants expressing tuber resistance to these pathogens, the clone A380 showed 66%, 51% and 65 % less powdery scab, tuber soft rot and black scurf, respectively than the parent c.v. Russet Burbank. This enhanced resistance did not extend to root and stolon infection, demonstrated by no significant differences between clones and parent for root infection and galling caused by Spongospora subterranea f.sp.subterranea, or root infection and stolon pruning caused by R. solani. These trials showed that the somaclonal variants resistant to common scab have a broad spectrum of resistance to a very diverse range of tuber-invading pathogens. Further work extended to investigate this novel tuber resistance by measuring morphological traits of interest and changes in relative gene expression in a series of glass house, field trial and in vitro experiments. A novel pot-mesh system enabled the accurate identification of tuber age such that sequential histology assessments, measuring cellular suberin content and the number of phellem cell layers and thickness, could be tracked through critical tuber development phases, with pathogen and variant effects compared for variant and parent clones. Furthermore, expression of genes associated with suberin synthesis and with salicylic acid, jasmonic acid and ethylene defence signalling pathways were quantified periodically using real-time PCR following pathogen and thaxtomin challenge. Results of all trials showed that the number of phellem cell layers, phellem cell layer thickness and the cell content of suberin was greater in the common scab resistant clone A380 than the parent Russet Burbank. Supporting the histology assessment, the expression of genes associated with suberin synthesis (CYP86A33, StKCS6 and POP_A) was greater in A380 than in the parent cultivar Russet Burbank. In contrast, the expression of genes associated with the innate host defence pathogenesis pathways (salicylic acid, jasmonic acid and ethylene) whilst induced by treatment with the pathogen's toxin-thaxtomin D, were not different between resistant clone A380 and the parent. This project also examined genetic alterations within the disease-resistant somaclonal variants of Russet Burbank. Recently integrated 8303 single nucleotide polymorphism (SNP) markers (Illumina 8K SNP chip) from the potato genome sequencing consortium were employed to examine the polymorphic changes in 30 somaclonal variants and 11 commercial clones of Russet Burbank. The results revealed that several common scab resistant clones (e.g. TC9T4, A386, TC9M1 and A168a) had quantifiable differences from their parent cultivar in chromosome 1, 2, 3, 4, 5, 8 and 11. In contrast, no detectable differences to the parent cultivar within the SNPs examined were found in clone A380. Further analysis including whole genome re sequencing is needed to understand the genetic and epigenetic changes within this clone that result in its disease resistance traits. Finally, this project has contributed to our understanding of Spongospora subterranea f.sp. subterranea root infection. Previous studies have not determined whether there exist variation in susceptibility of potato roots to infection with host maturity. This study assessed the effect of delayed inoculation on root infection rate (zoosporangial infection and quantity of Spongospora subterranea f.sp. subterranea DNA within roots) and root gall formation in time-course experiments. Analysis showed that 30 days after inoculation zoosporangial formation occurred and 60 days after inoculation root galls formed regardless of root age at the time of infection. Pathogen detection tools were then used to assess the effect of fungicide application on root infection parameters. Results showed that fungicides such as Fluazinam (seed and furrow treatment ) and Mancozeb (seed treatment) slowed the epidemic rate and reduced the overall extent of disease but did not delay the onset of infection. This study demonstrated that the pathogen monitoring system can successfully model pathogen development and could be applied in further epidemiological studies.