Phenology of infection on apple fruit by sooty blotch and flyspeck species in Iowa apple orchards and phylogenetic analysis to assess the evolutionary origins of sooty blotch and flyspeck on apple

Ismail, Siti Izera
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The sooty blotch and flyspeck (SBFS) complex is comprised of more than 80 species of fungi which colonize the surface of apple fruit. The dark blotches caused by SBFS species result in economically significant damage to apple in humid production regions worldwide. Despite rapid progress in clarifying the taxonomy and ecology of SBFS fungi, there is no information available about species-specific patterns in the timing of fruit infection. A motivation for obtaining this knowledge is that it may set the stage for development of more efficient SBFS management practices, since the species that are prevalent in apparent orchards vary among geographic regions. The first objective of this study was therefore to determine whether there are species-specific patterns in the timing of SBFS infection on apple fruit. To answer this question, an experiment was conducted in six commercial apple orchards in central Iowa in 2009 and 2010. Beginning 10-21 days after petal fall, apples were covered individually by fruit bags. A subsample of apples (cv. Golden Delicious) was exposed for each of seven consecutive 2-week-long exposure periods, and then rebagged from the end of the exposure period until harvest. All individual colonies that were visible at harvest were identified using a PCR-RFLP protocol. A total of 15 species were identified. The results provided the first evidence that some SBFS species differ significantly from others in the timing of fruit infection, and found that seven SBFS species displayed the same general temporal pattern: in each species, fruit infections that resulted in formation of visible colonies at harvest peaked during the first half of the fruit development period and generally decreased thereafter.

The second objective of my PhD research concerned a previously unexplored topic: the evolutionary origin of SBFS fungi. Although about 90% of SBFS species are in the order Capnodiales, evolutionary origins of major SBFS lineages in this order remain unknown. Previous phylogenetic analysis suggested that most SBFS fungi share a close evolutionary history with plant-parasitic species. The objective of this study was to assess the evolutionary origins of major SBFS lineages on apple by using ancestral state reconstruction of the 28S nuclear large subunit (LSU) region of rDNA and the second largest subunits RNA polymerase II (RPB2) region. The datasets were broadly sampled and included well-described non-SBFS as well as SBFS species in the Capnodiales. The resulting phylogeny, using a Bayesian approach, showed strong support for an evolutionary relationship between SBFS fungi and plant-parasitic fungi for some families in the Capnodiales. We performed ancestral state reconstruction with BayesMultiState,

which provided strong evidence that the ancestor of Capnodiales was a plant parasitic lifestyle. Knowledge gained from this study may help to better understand the ecology and evolution of fungi that inhabit plant surfaces.

evolutionary origins, infection, phenology, phylogenetic analysis, sooty blotch and flyspeck