Etiology and diversity of Alternaria leaf blotch and fruit spot of apples in Australia

Apples are one of the most commonly produced fruits, grown in all temperate regions of the world. They are the second most produced fruit in Australia, and are grown in all states. Over the last decade, diseases caused by Alternaria, Alternaria leaf blotch and Alternaria fruit spot, caused annual losses to the Australian apple industry. Control of Alternaria fruit and leaf disease has been erratic. No reliable disease management strategies exist for Alternaria due to a lack of adequate information on the disease cycle and the identity of the causal agent(s) in Australia. The aim of the research described in this thesis was to identify and determine pathogenic diversity of the species of Alternaria associated with Alternaria leaf blotch and Alternaria fruit spot and their epidemiology. The findings of this research underpin the development of improved disease management strategies. Specifically, this research sought to determine (i) the identity of the species of Alternaria associated with leaf blotch and fruit spot, (ii) the pathogenic variation among the species of Alternaria to apple leaves and fruit, (iii) the competitive fitness of different species of Alternaria, (iv) the timing of infection and disease development in apple orchards and (v) the sources and seasonal dynamics of Alternaria inoculum. To identify the species of Alternaria involved in the pathosystems, DNA sequencing of the endopolygalacturonase gene region and the Alternaria allergen a1 gene of genomic DNA and morphological examination of colony characteristics and sporulation patterns of 51 isolates obtained from leaves and fruit from all Australian growing regions was performed. The results showed that multiple phylogenetic Alternaria species-groups are associated with leaf blotch and fruit spot on apple including A. arborescens, A. tenuissima/ A. mali, A. alternata/ A. tenuissima and A. longipes. The most prevalent species-group was A. arborescens, which occurred in all Australian regions. The three other species-groups were mostly related to the diseases in orchards from Queensland and New South Wales (Chapter 2). Detached leaf and in planta fruit inoculations were performed to determine the pathogenic variation of the four Alternaria species-groups. This showed that all four species-groups were pathogenic to leaves, but in most cases only isolates of A. tenuissima/ A. mali and A. alternata/ A. tenuissima were pathogenic to fruit. The pathogenicity of the isolates was not specific to the tissue it was obtained from, which indicated cross-pathogenicity to apple leaves and fruit (Chapter 3). The competitive fitness of the four species-groups of Alternaria was examined by comparison of saprophytic fitness traits, mycelial growth rate, fecundity and competitive spore production. The results showed that A. arborescens had a competitive fitness advantage based on significant higher fecundity than the other three species-groups. This may explain its higher prevalence in orchards of all Australian states compared to the other three species-groups (Chapter 4). The timing of infection and temporal and spatial disease development for leaf blotch and fruit spot of apple under natural field conditions was determined in field trials. These results showed leaves were infected about 20 days after bloom (DAB) and infection of fruit occurred about 100 DAB. The lower canopy of trees showed higher levels of disease incidence than the upper canopy, and shoot leaves showed higher levels of leaf blotch disease incidence than spur leaves. Climatic factors were tested for their influence on disease incidence. Temperature, relative humidity and rainfall significantly influenced both leaf blotch and fruit spot incidence (Chapter 5). Field trials determined the potential sources of Alternaria inoculum in the orchard, leaf residue on the orchard floor, canopy leaves, twigs and buds and their relative contribution throughout the growing season. Overwintering of spores occurred mainly on leaf residue, while twigs and buds in the canopy played a minimal role. The most significant period of spore production on leaf residue occurred between dormancy and bloom, and then during the fruit growth stage on canopy leaves and twigs. A strong association between temperature, rainfall and relative humidity was observed to influence spore production dynamics (Chapter 6). The findings from this study improved knowledge of the etiology of Alternaria leaf blotch and fruit spot. The disease cycle is described and disease management strategies now have a solid epidemiological basis. Specific areas that require further research of the Alternaria pathogens and Alternaria leaf blotch and fruit spot on apple beyond the scope of this study are discussed (Chapter 7).