Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

▪ Abstract We hypothesize that the evolutionary potential of a pathogen population is reflected in its population genetic structure. Pathogen populations with a high evolutionary potential are more likely to overcome genetic resistance than pathogen populations with a low evolutionary potential. We propose a flexible framework to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure. According to this framework, pathogens that pose the greatest risk of breaking down resistance genes have a mixed reproduction system, a high potential for genotype flow, large effective population sizes, and high mutation rates. The lowest risk pathogens are those with strict asexual reproduction, low potential for gene flow, small effective population sizes, and low mutation rates. We present examples of high-risk and low-risk pathogens. We propose general guidelines for a rational approach to breed durable resistance according to the evolutionary potential of the pathogen.

Pathogen population genetics, evolutionary potential, and durable resistance

Biocontrol fungi (BCF) are agents that control plant diseases. These include the well-known Trichoderma spp. and the recently described Sebacinales spp. They have the ability to control numerous foliar, root, and fruit pathogens and even invertebrates such as nematodes. However, this is only a subset of their abilities. We now know that they also have the ability to ameliorate a wide range of abiotic stresses, and some of them can also alleviate physiological stresses such as seed aging. They can also enhance nutrient uptake in plants and can substantially increase nitrogen use efficiency in crops. These abilities may be more important to agriculture than disease control. Some strains also have abilities to improve photosynthetic efficiency and probably respiratory activities of plants. All of these capabilities are a consequence of their abilities to reprogram plant gene expression, probably through activation of a limited number of general plant pathways.

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Induced Systemic Resistance and Plant Responses to Fungal Biocontrol Agents

This review summarizes recent research in Australia on: (i) climate and geophysical trends over the last few decades; (ii) projections for climate change in the 21st century; (iii) predicted impacts from modelling studies on particular ecosystems and native species; and (iv) ecological effects that have apparently occurred as a response to recent warming. Consistent with global trends, Australia has warmed ~ 0.8 � C over the last century with minimum temperatures warming faster than maxima. There have been significant regional trends in rainfall with the northern, eastern and southern parts of the continent receiving greater rainfall and the western region receiving less. Higher rainfall has been associated with an increase in the number of rain days and heavy rainfall events. Sea surface temperatures on the Great Barrier Reef have increased and are associated with an increase in the frequency and severity of coral bleaching and mortality. Sea level rises in Australia have been regionally variable, and considerably less than the global average. Snow cover and duration have declined significantly at some sites in the Snowy Mountains. CSIRO projections for future climatic changes indicate increases in annual average temperatures of 0.4-2.0 � C by 2030 (relative to 1990) and 1.0-6.0 � C by 2070. Considerable uncertainty remains as to future changes in rainfall, El Nino Southern Oscillation events and tropical cyclone activity. Overall increases in potential evaporation over much of the continent are predicted as well as continued reductions in the extent and duration of snow cover. Future changes in temperature and rainfall are predicted to have significant impacts on most vegetation types that have been modelled to date, although the interactive effect of continuing increases in atmospheric CO 2 has not been incorporated into most modelling studies. Elevated CO 2 will most likely mitigate some of the impacts of climate change by reducing water stress. Future impacts on particular ecosystems include increased forest growth, alterations in competitive regimes between C3 and C4 grasses, increasing encroachment of woody shrubs into arid and semiarid rangelands, continued incursion of mangrove communities into freshwater wetlands, increasing frequency of coral bleaching, and establishment of woody species at increasingly higher elevations in the alpine zone. Modelling of potential impacts on specific Australian taxa using bioclimatic analysis programs such as BIOCLIM consistently predicts contraction and/or fragmentation of species' current ranges. The bioclimates of some species of plants and vertebrates are predicted to disappear entirely with as little as 0.5-1.0 � C of warming. Australia lacks the long-term datasets and tradition of phenological monitoring that have allowed the detection of climate-change-related trends in the Northern Hemisphere. Long-term changes in Australian vegetation can be mostly attributed to alterations in fire regimes, clearing and grazing, but some trends, such as encroachment of rainforest into eucalypt woodlands, and establishment of trees in subalpine meadows probably have a climatic component. Shifts in species distributions toward the south (bats, birds), upward in elevation (alpine mammals) or along changing rainfall contours (birds, semiarid reptiles), have recently been documented and offer circumstantial evidence that temperature and rainfall trends are already affecting geographic ranges. Future research directions suggested include giving more emphasis to the study of climatic impacts and understanding the factors that control species distributions, incorporating the effects of elevated CO 2 into climatic modelling for vegetation and selecting suitable species as indicators of climate-induced change.

Climate change and Australia: Trends, projections and impacts

It is accepted that most fungal avirulence genes encode virulence factors that are called effectors. Most fungal effectors are secreted, cysteine-rich proteins, and a role in virulence has been shown for a few of them, including Avr2 and Avr4 of Cladosporium fulvum, which inhibit plant cysteine proteases and protect chitin in fungal cell walls against plant chitinases, respectively. In resistant plants, effectors are directly or indirectly recognized by cognate resistance proteins that reside either inside the plant cell or on plasma membranes. Several secreted effectors function inside the host cell, but the uptake mechanism is not yet known. Variation observed among fungal effectors shows two types of selection that appear to relate to whether they interact directly or indirectly with their cognate resistance proteins. Direct interactions seem to favor point mutations in effector genes, leading to amino acid substitutions, whereas indirect interactions seem to favor jettison of effector genes.

Fungal Effector Proteins

Riverina - a vigorous subterranean clover for medium to high rainfall waterlogged soils

Denmark - a persistent late flowering subterranean clover for high rainfall grazing

The conidia and resting hyphae of the northern anthracnose pathogen of Trifolium species, Kabatiella caulivora, were effectively carried by, and maintained long-term viability on, a range of materials, including metals, fabrics, woods and plastics. Conidia and hyphae became thick-walled and melanized with time. There were significant (P < 0.001) differences in conidia/resting hyphae survival between carrier materials and between temperature regimes. At 23 °C/8 °C day/night, conidia and resting hyphae remained viable on steel, corrugated iron, galvanized steel, all tested fabrics, wood and random mixed materials for up to 8 months. At 36 °C/14 °C day/night, conidia and resting hyphae remained viable for up to 8 months, but only on cotton, denim, fleece, silk, leather, paper, plastic and all wood materials. At 45 °C/15 °C day/night, conidia and resting hyphae remained viable up to 8 months only on fleece wool, Eucalyptus marginata (jarrah wood) and paper. There were significant differences between carrier materials in their abilities to retain conidia and resting hyphae after washing (P < 0.001). Metabolic activity was confirmed for conidia and resting hyphae recovered after 8 months and K. caulivora colonies successfully re-established on potato dextrose agar. Findings confirmed the critical importance of materials as long-term carriers of viable K. caulivora conidia and resting hyphae, highlighting the potential for spread of a highly virulent K. caulivora race within and outside Australia via farming equipment, clothing and other associated materials. Results also have wider biosecurity implications for the transportation of fungal-infested carrier materials previously considered as low risk.

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Long-term viability of the northern anthracnose pathogen, Kabatiella caulivora, facilitates its transportation and spread

Sclerotinia sclerotiorum is a necrotrophic fungus causing devastating stem rot and associated yield losses of canola/rapeseed (Brassica napus) worldwide, including in Australia. Developing host resistance against Sclerotinia stem rot is critical if this disease in canola/rapeseed is to be successfully managed, as cultural or chemical control options provide only partial or sporadic control. Three B. napus breeding populations, C2, C5 and C6, including the parents, F1, F2, BC1P1 and BC2P2, were utilised in a field study with an objective of exploring the inheritance pattern of disease resistance (based on stem lesion length, SLL), the genetic relationships of disease with stem diameter (SD) or days to flowering (DTF), and to compare these new adult plant stem resistances against S. sclerotiorum with those of seedling (cotyledon and leaf) resistances in earlier studies. Heritability (broad-sense) of SLL, was 0.57 and 0.73 for populations C2 at 3 and 5 weeks post-inoculation, and was 0.21 for C5 at 5 weeks post-inoculation. Additive genetic variance was evident within all three populations for DTF but not for SD. Narrow sense heritability for DTF was 0.48 (C2), 0.42 (C5) and 0.32 (C6). SD, DTF and SLL were all inherited independently with no significant genetic covariance between traits in bivariate analysis. Genetic variance for SLL in populations C2 and C5 was entirely non-additive, and there was significant non-additive genetic covariance of SLL at 3 and 5 weeks post-inoculation. Generation means analysis in population C2 supported the conclusion that complex epistatic interactions controlled SLL. Several C2 and C5 progeny showed high adult plant stem resistance which may be critical in developing enhanced stem resistance in canola/rapeseed. While population C6 showed no genetic variation for SLL resistance in this study, it showed significant non-additive genetic variance at the cotyledon and leaf stages in earlier studies. We conclude that host resistance varies across different plant growth stages and breeding must be targeted for resistance at each growth stage. In populations C2, C5 and C6, resistance to S. sclerotiorum in stem, leaf and cotyledon is always controlled by non-additive effects such as complex epistasis or dominance. Overall, our findings in relation to the quantitative inheritance of Sclerotinia stem rot resistance, together with the new, high-level resistances identified, will enable breeders to select/develop genotypes with enhanced resistances to S. sclerotiorum.

Quantitative Inheritance of Sclerotinia Stem Rot Resistance in Brassica napus and Relationship to Cotyledon and Leaf Resistances.

Studies were undertaken to characterise the interactions of eight Sclerotinia sclerotiorum isolates/pathotypes on leaves of intact plants of 17 Arabidopsis thaliana ecotypes. For lesion diameter and lesion incidence, there were significant (P ≤ 0.001) effects of pathogen isolates, A. thaliana ecotypes, and a significant interaction between isolates and ecotypes in all three experiments. Resistance to S. sclerotiorum infection across the ecotypes ranged from highly susceptible through to resistant and the bioassay was sensitive enough to allow assessment of small differences in partial relative resistances across the ecotypes. While some A. thaliana ecotypes, such as Sha, Bay-0, Ws-1 and Ws-2, were found to be highly susceptible to all S. sclerotiorum isolates tested, others, such as Er-0, Jea and Cvi-0, showed a consistent level of resistance, and of these latter, Er-0 showed the highest and most consistent expression of resistance. In contrast, Col-0, Nd-0 and Oy-0 responses ranged from relative resistant to highly susceptible, depending upon the isolate being tested. Some isolates, such as MBRS1, elicited a wide range of resistance responses across the ecotypes, making these isolates most useful for screening the full range of A. thaliana ecotypes for their responses to S. sclerotiorum. In contrast, other isolates such as ‘Cabbage’ only generated lesions over a very narrow size range of host resistance response and hence could limit the ability of such isolates to differentiate resistances across diverse A. thaliana populations. Increasing the number of ecotypes tested increased the capacity to differentiate both the levels of relative resistance amongst test ecotypes and the varying levels of aggressiveness between different isolates. This is the first known study to demonstrate how Arabidopsis resistance responses can be expressed or compromised by variation in aggressiveness amongst different S. sclerotiorum isolates and/or pathotypes.

Martin J. Barbetti

Papers

Riverina - a vigorous subterranean clover for medium to high rainfall waterlogged soils

Denmark - a persistent late flowering subterranean clover for high rainfall grazing

Long-term viability of the northern anthracnose pathogen, Kabatiella caulivora, facilitates its transportation and spread

Quantitative Inheritance of Sclerotinia Stem Rot Resistance in Brassica napus and Relationship to Cotyledon and Leaf Resistances.

Host response of Arabidopsis thaliana ecotypes is determined by Sclerotinia sclerotiorum isolate type