RESEARCH PROJECTS  //  Research Report 2018/2019

New Research Projects

Promotion of soybean and groundnuts in a crop rotation system

Ms AS de Beer
ARC Grain Crops Institute, Potchefstroom

No progress was made with the said project. Alternatives will be investigated by the Research Priority Committee.

Breeding for resistance against Sclerotinia sclerotiorum in soybean and sunflower

Ms L Rothmann and Prof N McLaren
University of the Free State

The fungal pathogen Sclerotinia sclerotiorum has an intriguing epidemiology as it has the potential to cause plant diseases in more than 400 host species (Bolton, Thomma & Nelson, 2006). In South Africa, primary risk crops are soybean and sunflower, with an increasing risk in canola (Ramusi & Flett, 2015). Initial symptoms include a watery soft rot or bleached effect of tissues, followed by a white cottony mycelial growth (a typical sign of the pathogen) and eventually the necrosis and shredding of plant organs (Purdy, 1979; Bolton et al., 2006). Losses due to S. sclerotiorum result directly from loss in yield and indirectly from reduced grain quality. In affected plants, seed quality characteristics such as reduced seed size, seed germination as well as a reduction in oil content are affected. Seed germination significantly decreases as S. sclerotiorum incidence increases (Hoffman et al., 1998). In sunflower fields, yield loss depends on the number of plants infected as well as the type of infection that occurs and the growth stage at which infection took place (Nelson & Lamey, 2011).

Significant yield losses, and thus economic impacts, caused by S. sclerotiorum diseases across hosts may be reached when disease incidence is between 20% and 100%, as was recorded across Europe and North America (Twengström et al., 1998; Bolton et al., 2006; Koch et al., 2007; Harikrishnan & Del Rio, 2008; Peltier et al., 2016;). Sclerotinia stem rot of soybean is caused by the fungus S. sclerotiorum (Lib.) de Bary and was first confirmed in South Africa in 1979 (Thompson & van der Westhuizen, 1979) on soybean from the Lichtenburg area, although it occurred locally long before then. The effects of Sclerotinia stem rot of canola gained more attention in South Africa during 2014 due to its greater prevalence (GrainSA, 2016). Ms. Rohmann's research (current PhD; unpublished) in conjunction with Crop Estimates Committee (CEC) data over a 10-year period and more than 40 production localities indicated that locality accounted for 27% and 33% of variation in disease incidence and seasonal variation for only 7% and 5%, for sunflower head rot and soybean stem rot, respectively. Regions with the highest mean incidences (12.5%-34.5%) recorded over the 10 years, were in KwaZulu-Natal, North West, Mpumalanga and Gauteng. The South African National Standard recognises six main climatic regions (Conradie, 2012), and the above localities stretch across three of these, resulting in multiple weather scenarios for the development of S. sclerotiorum diseases.

Sclerotinia species have a unique advantage as plant pathogens due to their ability to generate melanised hyphal masses, termed sclerotia, which serve as both a diagnostic sign and survival structures (Purdy, 1979; Saharan & Mehta, 2008). Internationally, significant variation among S. sclerotiorum strains exists and varying sclerotial development and germination responses among strains have been recorded. However, locally variation is limited and this is being further quantified by the Plant Breeding division at the UFS (Steyn, 2015; Foley, Dogramaci & Underwood, 2016). Sclerotia can survive in the soil for 3 to 10 years and survival is dependent on numerous factors including sclerotial size and shape, soil type and chemistry, soil microbial populations likely to degrade sclerotia, previous crops planted and weather conditions (Awabi & Grogan, 1979; Dillard & Grogan, 1985; Twengström et al., 1998). Thus, S. sclerotiorum has the ability to ensure that once a soil is held captive by its' sclerotial presence it can withstand many years of siege. The advantage of sclerotia is further brought into play with regard to the production of primary inoculum and the initial onslaught of disease initiation. Sclerotinia sclerotiorum sclerotia may undergo myceliogenic or carpogenic germination as two methods of disease initiation (Saharan & Mehta, 2008).

Myceliogenic germination, the production of hyphae and mycelium directly from sclerotia, is the battering ram for direct sub-terrain infection that drives most soilborne host infections (Purdy, 1979; Bolton et al., 2006). Airborne assaults are as a result of carpogenic germination, the initiation of stipes followed by apothecia formation, which are responsible for the forcible discharge of ascospores (Saharan & Mehta, 2008). Ascospore inoculum is not only found in the field in which the host crop is produced or infected but may originate from neighbouring fields more than 100m away, which provides S. sclerotiorum with a spatial ambush attack (Steadman, 1983; Twengström et al., 1998).

Sclerotia in the upper 2 to 3cm of the soil profile, are considered epidemiologically competent, as the formation of stipes longer than 3cm on apothecia is rare under natural conditions, and stipes that form on sclerotia that are deeper than 3cm cannot reach the sunlight needed for apothecial development (Clarkson et al., 2004). Thus, the micro-climate found in this level of the soil is strongly associated with the successful gemination of sclerotia. Soil temperatures below 5°C or above 35°C are known to inhibit carpogenic germination. The soil moisture in the upper 3cm varies greatly due to surface weather conditions, notably air temperature, relative humidity and wind as well as the growth stage of the crop. The latter is related to crop canopy density, with a denser canopy increasing relative humidity and, therefore, soil moisture in the upper 3cm (Abawi & Grogan, 1979). Cook et al. (1975) found that sclerotia at greater than 3cm burial depths remained under exogenous dormancy, largely due to reduced soil moisture fluctuations which served as an anti-sclerotium germination stimulus. Literature reports contradictory effects of tillage practices on the germination of sclerotia (Saharan & Mehta, 2008). No-till practices were associated with fewer apothecia, and thus a reduced soybean stem rot incidence, however, no-till and minimum tillage created a more conducive microclimate by preserving the soil moisture and lowering the soil temperature (Mila et al., 2003).

Environmental stimuli which initiate S. sclerotiorum infections and host responses include air and soil temperature and moisture at meso- and micro-climate levels. Meso-climate weather variables required to initiate infection, either ascospore or myceliogenic, include the combination of 48-72 hours of continuous atmospheric temperatures from 20°C to 29°C, moisture from rain, dew, fog or relative humidity exceeding 85% and soil moisture of more than 30% (Abawi & Grogan, 1979; Koch et al., 2007; Peltier et al., 2016).

The economic importance of many of the crops affected by Sclerotinia spp. emphasises the importance of effective disease management strategies. Management of these diseases through rotation with non-host crops is limited by the extensive host range and duration of survival of sclerotia in soil. Agronomic management decisions – such as cultivar selection, proper irrigation management, planting dates and plant density – can also contribute to lowering disease severity (Boland & Hall, 1988; Twengstrom et al., 1998; Clarkson et al., 2004). The use of tillage practices in fields previously infested with S. sclerotiorum to manage diseases caused by S. sclerotiorum remains a point of contention. Coniothyrium minitans is used as a biological control agent for fields previously infested with S. sclerotiorum and is commercially available in South Africa (Craven et al., 2016).

Cultivar selection is the preferred method of Sclerotinia disease management in South Africa, as it is economically viable. The development of resistant cultivars to Sclerotinia diseases would be ideal as it would provide producers with a longer-term solution to reduce disease risk. However, it comes with challenges as resistance in the traditional sense does not exist, thus the cultivars carry a high risk for potential disease development under favourable environmental conditions. Identification of resistance is hampered by the absence of easy and reliable screening methods as well as limited genetic variability available for resistance to S. sclerotiorum (Grafton, 1998). Information collected on the genetic structure of isolates could assist in the breeding of cultivars with durable resistance (Zhao & Meng, 2003). An understanding of the genetic structure of the pathogen population is especially important when devising disease management and resistance screening strategies (Sexton & Howlett, 2004). Significant variation in sclerotial development and germination responses among S. sclerotiorium strains has been recorded internationally (Saharan & Mehta, 2008). However, low recombination frequencies have been recorded in South Africa and strong similarities between isolates within and across provinces has been reported, suggesting that the population is young and developing (Steyn, 2015). Despite the impact of the disease on crops and the numerous breeding and selection efforts, progress has been limited and acceptable levels of resistance to S. sclerotiorum have not been forthcoming, especially in South Africa. Plant architecture, maturity and flowering date are host characterises which have been highly associated with disease escape in controlled environments. However, the stability of soybean cultivar responses to stem rot epidemics varies across management strategies, localities and thus severity differs significantly across production regions (McLaren & Craven, 2008). Furthermore, the selection of genotypes which can tolerate high disease potentials are limited due to the responses in the glasshouse and laboratory not correlating with those recorded in the field. Therefore, in the quest for resistance to Sclerotinia diseases, all aspects of disease screening need to be considered.

Timely fungicide applications, at critical host growth stages, can provide an effective management measure for Sclerotinia diseases. Currently, there are a limited number of preventative registered active ingredients in South Africa for fungicide use, namely only on pea and sunflower; and include benomyl and procymidone (CropLife, 2015). However, the cost of fungicides and their application efficacy in addition to the potential need for multiple applications are constraints to the wider use of chemical control (Harikrishnan & Del Rio, 2008; Ramusi & Flett, 2015; GrainSA, 2016). Due to the occasional failure of fungicide applications to control the target disease as well as factors such as cost and environmental hazards, the development of cultivars with disease resistance is still the desired method for disease management as it is more economical and the environmental impact is reduced (Pham et al., 2010). Grafton (1998) indicated that the nature of inheritance of resistance and the relative importance of physiological resistance, plant architecture and disease escape mechanisms under field conditions show potential for exploitation.

The importance of prevention of the disease is pivotal and can be seen from the above literature. Therefore, key focus areas which require further investigation were identified. Namely, the need to identify (currently underway) and validate critical weather variables that drive epidemic development. The identification and confirmation of the infection pathway and its critical role in chemical placement and inoculation procedures for the evaluation of cultivars which are currently planted. The identification of potential genetic resources for the development of tolerant or resistant lines, this is feasible as source of resistance are available internationally. We believe that combining knowledge from these research areas will provide local producers with pratical answers to a complec pathosystem.