Soybean response to rust and Sclerotinia stem rot under different biotic and abiotic conditions

English:  The annual increase in soybean production to meet the increasing demands is limited by environmental constraints, fungal diseases and insect pests. Sclerotinia stem rot (caused by Sclerotinia sclerotiorum) is increasing in importance both locally and globally and the wide host range challenges disease management strategies. Soybean rust (caused by Phakopsora pachyrhizi) is a serious yield limiting foliar disease that has increased in importance due to rapid spread over large geographic areas. Reliable and repeatable screening methods have limited the quest for stable resistance to these diseases. Genetic variability in S. sclerotiorum isolates need elucidation since this could assist in the identification of stable resistance. Similalry, understanding the physiological processes associated with host response to to the respective pathogens could be useful in identifying new mechanisms of resistance or the timely implementing of appropriate control strategies. The absence of disease resistant cultivars, in particular to soybean rust, has necessitated extensive use of fungicides as a control method to ensure acceptable yields.  A study was conducted to compare the reaction of experimental soybean lines to soybean rust in the greenhouse and evaluate epidemiological factors that need to be considered in field evaluations of germplasm. Greenhouse trials indicated significant differences in rust severity between lines while field data illustrated the importance of differences in relative life time at disease onset, apparent infection rate, AUDPC and relative life time at which 100% disease severity was reached. The importance of multiple evaluation criteria was emphasized. Constraints to achieving acceptable levels of disease resistance are the absence of a correlation between greenhouse and field results and repeatability of data over seasons and localities. Although lines differed in disease severity only Selection 43 showed a combination of late disease onset and slow apparent infection rate and hence a significant level of rust resistance. However, an extended study, which includes a variety of South African P. pachyrhizi races, is needed to determine the stability of the identified resistance.  Yield losses associated with soybean rust in varieties from three maturity groups as well as the effects of row spacing and fungicide application on disease development were evaluated. Disease onset was closely related to host growth stage and fungicides had little effect on delaying the disease. The apparent infection rate was higher in 45 cm, compared with 90 cm, row widths in the absence of fungicide applications while greater reductions in apparent infection rate due to fungicide applications were recorded in the wider rows. These responses were also reflected in AUDPC and yield. Differences in these variables between sprayed and unsprayed plots were more pronounced in the long maturity cultivar compared with the shorter maturity cultivars but the extent of these differences is dependent of spray efficiency. Differences in cultivar responses to the disease and row spacing do not provide adequate control and fungicide applications remain primary disease control strategy against soybean rust.  Physiological changes associated with soybean growth stage in field trials indicated that soybean rust onset and development are determined by the activity of key pathogenesis-related enzymes. Environmental effects had a relatively small effect on disease severity once infection is initiated. Host responses to rust infection were directly related to the decline in chitinase and β-1,3-glucanase which coincided with flowering and pod formation and the subsequent rapid increase in rust severity. Plots that received fertilizer treatments indicated that chitinase, β -1,3- glucanase, peroxidase and phenol content were related to the form of nitrogen received. Higher chitinase activity, in particular, was also associated with lower disease severity.  Evaluation of cultivars for resistance to Sclerotinia stem rot in the greenhouse and field failed to identify sources of resistance although lower risk cultivars were observed in field trials. Most cultivars were susceptible to Sclerotinia stem rot even when conditions were sub-optimal for disease development. A poor correlation between greenhouse and field data was observed. Field trials indicated that cultivars react differently to changing environmental conditions and disease potentials and high genotype x environment interactions were recorded. Data indicate that local cultivars still lack the desired level of resistance to Sclerotinia stem rot or stability to changing disease potentials.  In vitro studies indicated that S. sclerotiorum is favoured by cool to moderate temperatures (20°C and 25°C) while extreme cold or hot temperatures impair growth. Molecular characterisation of isolates using AFLP analysis revealed a relatively uniform distribution with evidence of genetic diversity within and amongst isolates across the five provinces evaluated. A low, recombination frequency suggests that the population is in a developing stage which is emphasized by isolates found on the end of the minimal spanning network. No correlation between host plant or locality and genetic similarity was observed but AFLP proved to be a valuable tool to characterize S. sclerotiorum isolates.