Dr. Adre Minnaar-Ontong & Dr. Chrisna Steyn
University of the Free State, Department of Plant Sciences, Plant Breeding Division
Edited: Lisa Rothmann, South African Sclerotinia Research Network
References available from the author – BothaC@ufs.ac.za
Written for the Oilseed Focus Magazine September 2019
A population is a group of individuals that share a common gene pool and originate from a limited geographic area. Fungal strains are classified as a set of isolates that are not able to be identified as different or distinct from each other and can be differentiated from other isolates (Figure 1). As these individuals, adapt to their local conditions, their gene pool changes. The goal of population genetic studies is to describe the changes, determine their causes, and understand their consequences for the individuals, population and community they are part of. The genetic structure reflects the evolutionary history and potential of the population. Multiple environmental changes can affect the genetic structure of fungal populations. These include, but are not limited to, host availability (e.g. resistant varieties), geographic site and climate, timing of agricultural practices such as planting, frequency and concentration of fungicide and fertiliser applications, irrigation, and crop rotation and timing of infection and disease initiation. As a result, the genetic structure of a population is not always reflected in the geographical distribution of the individuals involved. Understanding the genetic structure of a fungal pathogen’s population assists in the evaluation and improvement of disease management strategies. A primary use of this tool is in plant breeding, the incorporation/manipulation of host crop genetics to withstand pathogen infection. The final goal is the development of resistant or tolerant cultivars that will combat disease development and spread but still produce acceptable yields.
Sclerotinia sclerotiorum is classified as one of the world’s most omnipresent and successful plant pathogens. It is a homothallic ascomycete that causes numerous devastating diseases on seedlings, mature plants and harvested products. This pathogen has a wide variety of agronomically important host crops, including cash crops (i.e. oilseeds) and horticultural crops (i.e. fruits and vegetables). The broad host range enables the species to persist and spread easily making control of this pathogen difficult. Symptoms vary according to the host plant and environment. In general, the beginning of disease is visible as soft, water-soaked lesions and wilting of infected stems and branches. When host plant dies, the tissue takes on a white bleached appearance, with white mycelium externally or internally, in turn forming hardened melanised sclerotia, the survival structure. These structures further confound the management of the disease. Disease has the ability to initiate in two manners originating from sclerotia, (i) with fungal mass of mycelium, alternatively (ii) after the release of ascospores from apothecia, mushroom-like structures produced by the pathogen. Widespread infection occurs if favourable environmental conditions with temperatures between 16°C and 25°C and a concurrent high relative humidity or leaf wetness. The fungus is able to infect and colonize healthy tissue and produce new sclerotia within 10 to 14 days.These structures have the ability to survive up to 12 years making disease control and crop rotation systems problematic. In recent years, an increase in Sclerotinia stem rot on soybeans and Sclerotinia head rot on sunflowers had been recorded across the world and in South Africa. A possibility to explain this may be due to the increase in area planted with soybeans, as the commodity price is more competitive than that of maize, the extreme drought experienced, across South Africa, over the past 5 years that forced farmers to review their regular crop choices and turn to alternative sources of income. The ability of sunflowers to produce relatively constant yields under unfavorable weather conditions, having more drought tolerance and classified as a low input crop, mean they have become an attractive choice for farmers to implement in a crop rotation systems. These factors have contributed to the expansion of sunflower production to areas where it was not predominant in the past. The increase and spread of host plants advanced the increase in disease incidence, especially in late-planted sunflowers. In past seasons, severe infections were observed when late rains occurred providing days or even weeks of cool wet weather, favourable for ascospore infection. Sunflowers were also at flowering stage during these periods which is a particularly critical stage for infection. Furthermore, the spreading of the disease could also be due to a lack of resistant cultivars, effective chemical fungicides and biological control, as well as the many unknown factors associated with agronomic practices. Losses due to S. sclerotiorum result directly from loss in yield and indirectly from reduced crop quality and loss in grade. In Sclerotinia affected plants, seed quality characteristics such as a reduction in seed size, seed germination as well as a reduction in oil content are affected.
Population studies have been conducted to give insight into the genetic structure of S. sclerotiorum populations across the world. To date, only a preliminary study on 77 S. sclerotiorum isolates has been conducted for South Africa, at the University of the Free States (UFS) Plant Science Department. Extensive research on more than 950 isolates across eight of the nine South African provinces are underway at the UFS to resolve the genetic structure of this population. Isolates are collected from fields all over South Africa and pure cultures are made. From these isolates, DNA is extraction is done and compared with each other and other isolates using various laboratory techniques and equipment. The results are analysed using specialized statistical software. Sclerotinia sclerotiorum is a homothallic fungus, meaning it has male and female reproductive structures on the same thallus and thus a significant amount of self-fertilization takes place. The homothallic nature of this pathogen suggests a limited amount of gene flow and therefore low levels of genetic diversity; however, the preliminary study indicated significant levels of genetic diversity. This may be due environmental pressure on the pathogen forcing change to survive in areas not previously occupied by die pathogen, resulting in a more diverse gene pool.
The population are mostly clonal that shows that the population had been around for a considerable period (in South Africa S. sclerotiorum was first identified in 1979). Additionally, the genetic diversity suggests variation in pathogen aggressiveness (i.e. variable ability to cause disease on susceptible hosts) might occur within the population. The results are incorporated into a pre-breeding program in the greenhouse where further evaluations are done. Promising lines are planted in the field for evaluation under natural conditions and selection for further studies can then be made.
In the preliminary study, no association can be found between the aggressiveness of the pathogen to location or host. This indicates that the Sclerotinia sclerotiorum population in South African are uniform and forms part of a worldwide population. This could be an advantage for breeders as sources of resistance are available in other countries and these genes could be incorporated into local cultivars and assist in the development of cultivars that have sustainable resistance over all regions. Constant monitoring of the genetic structure provides critical information on potentially new pathogen genotypes that may evolve and are better adapted to certain areas or are more pathogenic than currently known. Although, these techniques are considered costly, monitoring the genetic structure and the application/addition/incorporation of resistant or tolerant genes to our local cultivars could provide a sustainable management option to an integrated pest control program.