Academic literature on the topic 'Horticultural crop protection (incl. pests, diseases and weeds)'

Abstract Protection of greenhouse-grown horticultural crops, including ornamentals and vegetables, from damage caused by insect pests involves implementing strategies such as insecticidal and/or biological control. However, cultural control may also mitigate plant damage caused by insect pests, as well as plant diseases including fungi and bacteria. An important cultural control is sanitation. Herein, we review the use and potential impact of sanitation practices as a part of an integrated pest management program for greenhouse production. These include removing weeds from inside and around the greenhouse perimeter, disposing of plant and growing medium debris from inside the greenhouse, and managing algae within the greenhouse. Weeds serve as alternate hosts for insects, such as aphids (Aphididae), whiteflies (Aleyrodidae), and thrips (Thripidae), that can spread plant viruses among greenhouse-grown horticultural crops. Sanitation practices that may reduce problems with weeds include installing geotextile fabric barriers underneath benches and on walkways, hand removal, mowing around greenhouse perimeters, and/or applying herbicides. Plant and growing medium debris serve as sources of insect pests, such as whiteflies, thrips, and fungus gnats (Sciaridae). Therefore, removal of plant and growing medium debris from within greenhouses and/or placement into refuse containers with tight-sealing lids before disposal may reduce problems with insect pests. Algae provides a habitat for fungus gnats and shore flies (Ephydridae) to breed. Overwatering and overfertilizing plants contributes to algae growth. Applying disinfectants or algaecides may mitigate problems with algae accumulating in greenhouses. In addition to reducing insect pest problems, sanitation practices may help reduce inputs from insecticide applications.

Microbial bio-control agents play an important role in integrated pest management in modern agriculture for managing pests without affecting environment and humans. Recently, microbial bio-control agents are gaining more attention as they are easy to use, safe and an alternative eco-friendly approach of hazardous pesticide chemicals. Biological control agents are ecologically sustainable and effective crop protection approach in agriculture and horticultural crops including organic systems. Predator, parasitism or other natural mechanism can be use to reduce the pest such as insects, mites, weeds and plant diseases.

The Tasmanian lacewing (Micromus tasmaniae Walker) is one of the most common aphid predators occurring in lucerne crops in New Zealand. A comparison of sampling techniques, and the output from a simulation model, suggest that the abundance of this lacewing may have been significantly underestimated in the past. Although the occurrence of aphid predators was erratic M. tasmaniae occurred more often and in far greater numbers (up to 100 m⁻²) than any other predator species. A simulation model for lacewing development in the field indicated that the large adult populations which occurred could be accounted for on the basis of reproductive recruitment. Independent evidence that immigration was not involved in the occurrence of these large populations was gathered using directional flight traps around the field perimeter. The major factors influencing lacewing population dynamics were the availability of aphid prey and, in the autumn, parasitism. Otherwise, survival of all life-histoty stages was high with no evidence of egg or larval cannibalism. Several instances of high lacewing mortality were identified by the model and the lack of any obvious cause for these highlights inadequacies in the understanding of lacewing bionomics. The model, which used a linear relationship (day-degrees) between development and temperature, was incapable of accurately predicting lacewing emergence under field temperatures which fluctuated outside the linear region of the development rate curve. Temperature thresholds and thermal requirements estimated under fluctuating temperatures similar to those in the field produced almost identical model output to those estimated under constant temperatures in the laboratory. Prey species was capable of influencing the rate of lacewing development. M. tasmaniae has the attributes necessary to produce large populations in the short time available between lucerne harvests. The asymptote of the functional response curve is low but the efficiency at converting aphids to eggs is high. Therefore, the lacewing is able to attain maximun reproductive output at low prey densities. A low temperature threshold for development (4-5° C), rapid development and short preoviposition period results in a short generation time (49 days at 15° C). Long adult life, high fecundity and the absence of any form of estivation or diapause, results in complete overlap of generations and multiple generations per year. M. tasmaniae's role as an aphid predator is restricted by its low appetite for prey and by the lucerne management regime currently practiced in New Zealand. Because it consumes relatively few aphids per day the lacewing's ability to destroy large aphid populations is limited. However, this may be offset by its ability to attack aphids early in the aphid population growth phase, and by the large numbers of lacewings which may occur. Under the present lucerne management schemes the large lacewing populations which do occur are forced out of the fields, or die, following harvest. A number of management options for increasing the lacewings impact as an aphid predator are briefly discussed.

Management of insect pests is one of the most important aspects of crop agronomy in the agricultural industry. This has become increasingly sophisticated as new approaches based on a greater understanding of individual pests and their biology are developed and used in Integrated Pest Management (IPM) programs to target pest populations at critical development periods to reduce potential injury to the crop. Our understanding of Thysanoptera biology and ecology in vegetables is restricted to a few key pest species, and very little attention has been given to other thrips species that dwell within these systems. This has produced a large gap in our understanding of the population dynamics of pest and non-pest species in vegetable agro-ecosystems. This deficit restricts the capacity to develop IPM strategies for the important pest thrips species. To contribute to our understanding of the Thysanoptera and the relationship of this insect order with the vegetable agro-ecosystem, this study determined the thrips species assemblage in French bean (Phaseolus vulgaris, var. ‘Labrador’), lettuce (Lactucta sativa, var. ‘Rador’), tomato (Solanum lycopersicum, indeterminate trial variety courtesy of Syngenta©) and zucchini (Cucurbita pepo, var. ‘Amanda’) agro-ecosystems, and further investigated: the temporal distribution of thrips populations on a crop phenological scale; the variability of the spatial distribution of thrips clusters; the effect of weather on thrips relative abundance; and the reproductive host association between thrips and the four crops. Investigations undertaken in this three-year study (27th December 2011 to 3rd June 2012; 24th December 2012 to 4th June 2013; 27th December 2013 to 17th June 2014) determined that four thrips species assemblages exist in each of the four agro-ecosystems. These comprised of key thrips species including Frankliniella occidentalis (Pergande) and Megalurothrips usitatus (Bagnall) in French bean, Desmothrips tenuicornis (Bagnall), F. occidentalis and F. schultzei (Trybom) in lettuce, F. occidentalis, F. schultzei and Pseudanaphothrips achaetus (Bagnall) in tomato and F. occidentalis, F. schultzei and Tenothrips frici (Uzel) in zucchini. French bean and zucchini supported the greatest diversity and abundance of thrips, whilst tomato supported the least within the assemblage. This study represents the first published description of thrips species assemblages in these important vegetable crops.

Early identification and control of insect pests and diseases is a key aspect of profitable crop production, especially for high input, high value horticultural crops. Remote sensing approaches using sensor technologies to detect insect pests and diseases have been previously demonstrated in a range of field crops and were researched in this project as a tool for plant health monitoring in chilli crops. A methodology for image capture using a multispectral camera mounted on an Unmanned Aerial Vehicle (UAV) and image processing based on distribution of individual pixel values in collected images was developed. This methodology was demonstrated to be as effective as manual crop scouting in early detection of insect pest and disease affected plants within a crop but could be automated to significantly reduce the cost of crop health monitoring. Initial method development trials demonstrated that detectable changes in NDVI, but not temperature changes measured using a thermal camera, occurred on leaves affected by bacterial spot disease before obvious visible symptoms were apparent. Bacterial spot (Xanthomonas euvesicatoria (Xeu)) is a ubiquitous disease infecting field-grown chilli crops, particularly during warm and humid conditions, and symptoms of infection were not apparent until about 7 days after inoculation of leaves with the pathogen. The age of inoculated leaves did not significantly affect the rate of change of NDVI. Non-inoculated leaves tended to have a lower NDVI value on plants with a greater number of inoculated leaves than on plants with none or few inoculated leaves. iii Aphids Myzus persicae (Sulzer) cause significant damage to chilli crops both directly via feeding on the host plant and indirectly as vectors for virus transmission. Reflectance data, obtained by multispectral, hyperspectral and thermal sensors, showed that the reflectance of aphid infested leaves in near infrared wavelengths decreased with time as the aphid population infesting a leaf increased. Remote sensing data acquired from low-altitude UAV flights deliver high spectral and spatial resolutions, with sufficient pixels representing individual leaf reflectance to allow detection of changes occurring when disease infection or insect pest infestation first occurs in part of a plant. This capacity for detection at early infection/infestation stage is crucial for effective management in high value horticultural crops. Conventional remote sensing approaches may detect changes occurring at a whole plant or region within a crop but lack the resolution capacity to readily detect changes at the sub-plant level. A five-band multispectral camera (MicaSense, RedEdge) and a low-altitude (15m) airborne platform provided adequate data, recording changes in reflectance imagery. The effectiveness of multispectral imagery decreased as flight altitude increased. The project has demonstrated that early identification of insect pest and pathogen-induced plant stress in chilli crops can be achieved using a methodology that can be automated to deliver a low-cost strategy for horticultural producers

Pseudomonas syringae pv. tomato causing bacterial speck disease in tomatoes is a significant threat to commercial field tomato production in most growing regions of Australia and globally. Infection of crops with this pathogen can cause significant reductions in fruit quality and yields. There are limited pesticide control options available for bacterial diseases in tomato, with copper-based bactericides currently one of the few registered products globally. The state of Queensland (QLD) in Australia produces approximately 69% of Australia’s fresh market outdoor tomatoes estimated at a value of AUD$122 billion. P. syringae pv. tomato consistently threatens tomato production in QLD and other Eastern Australian states and many producers report copper products fail to adequately control disease progression. To date no studies have tested for copper tolerance in P. syringae pv. tomato in QLD Australia, despite reports of tolerance in many other countries. This study found that 100% of the P. syringae pv. tomato isolates collected were tolerant to copper and this tolerance was linked to the presence of cop genes in their genetic profiles. This is the first systematic study of copper tolerance prevalence in Eastern Australia, particularly QLD, and the first study analysing the genetic basis of copper tolerance in Australian P. syringae pv. tomato. Published copper tolerance and copper efficacy studies on bacterial disease control report a wide range of response data, generated under varying field and laboratory conditions, making it difficult to draw strong conclusions from individual studies. Therefore, a systematic literature review was completed, investigating the prevalence of copper tolerance, the relative efficacy of copper for the control of disease and the identification of key emerging alternative products to copper for disease control. Results highlighted that copper tolerance is a global issue, which is affecting the usefulness of copper-based products for the control of bacterial diseases. A large range of alternative products for disease control were identified and the efficacy of eight key products were evaluated. However, there was a limited volume of published efficacy data available of for these alternative products, particularly for the control of disease caused by P. syringae pv. tomato. The systematic literature review also identified inconsistencies with in vitro copper tolerance screening methodology for P. syringae pv. tomato in current literature, particularly in relation to the appropriate media to use, copper tolerance thresholds and inadequate reporting of media pH and/or pH adjustment steps. The effect of media and pH on copper tolerance results was therefore investigated, including the use of a pH buffering agent. Copper tolerance thresholds with different media were found to vary significantly and outside of a specific pH range, copper tolerance data was unreliable. A recommended methodology for copper tolerance screening was developed and published. This refined methodology was used to screen P. syringae pv. tomato isolates from a number of geographically distinct regions of QLD, New South Wales (NSW) and Victoria (VIC). To date, no published studies are available on copper tolerance stability in P. syringae pv. tomato. Understanding the stability or biological fitness of copper tolerance in P. syringae pv. tomato can provide valuable insights into how copper-based disease control programs could be modified to mediate or even reduce the prevalence copper tolerance. Therefore, the stability of copper tolerance in study isolates was investigated through in vivo experiments. Findings suggested that copper tolerance may not be stable in all isolates when copper selection pressure is removed in vivo. Despite a general consensus that plasmid cop genes are essential for copper tolerance in P. syringae pv. tomato, the gene and protein characterisation work undertaken to form these conclusions is solely based on isolates collected in America. Additionally, Australian P. syringae pv. tomato are yet to be genetically characterised. Polymerase Chain Reaction (PCR) assays and genomic analysis were used to explore the genetic basis of copper tolerance in Australian isolates, with a particular focus on the cop genes. Genetic analysis identified putative Cop-protein coding regions on a Cop operon and a CopA/B complex in Australian isolates. The analysis also suggested that the Cop operons may be located on either plasmid or chromosomal DNA, depending on the isolate studied. This study is the first detailed investigation of the genetic basis of tolerance in this species outside of America. This study presents a range of novel findings which are of significance to both the scientific community and the agricultural industry. The presence of widespread copper tolerance has serious implications for commercial tomato producers. Bacterial disease management programs need to be revised to mediate resistance development and provide a more environmentally sustainable approach to crop production.

In Australia, phytoplasmas have consistently been associated with the papaya (Carica papaya L.) diseases known as papaya dieback (PpDB), yellow crinkle (PpYC) and mosaic (PpM). PpDB is the most economically important of these diseases, followed by PpYC. The investigations presented in this thesis have therefore focused primarily on PpDB. Analysis of the DNA sequences of the 168 rRNA gene and the 168-23S rRNA intergenic spacer region (SR) of the PpDB, PpYC and PpM phytoplasmas showed that the PpYC and PpM phytoplasma DNA sequences were identical to each other, but were distinctly different to that of the PpDB phytoplasma. A phylogenetic tree based on 16S rRNA sequences revealed that PpDB is most closely related to the Australian grapevine yellows (AGY) phytoplasma and the Phormium yellow leaf (PYL) phytoplasma from New Zealand, forming a distinct group within subclade xii. PpYC and PpM phytoplasmas are most closely related to the tomato big bud (TBB) phytoplasma from Australia, within subclade iii. It was proposed that the PpDB phytoplasma be included in the taxon "Candidatus Phytoplasma australiense", and that the ppye and PpM phytoplasmas be assigned to a new taxon, "Candidatus P. australiense". Histological studies and mapping of phytoplasma distribution using PCR revealed that it is likely that phytoplasma cells are present in very low titre and that, while the plant appears to limit proliferation of the PpDB phytoplasma, this defence response is associated with a rapid decline of the papaya plant. Immature leaf material was sampled weekly for eight months from 60 plants in a commercial papaya plantation, to estimate the minimum time between inoculation and symptom expression of PpDB, PpYC and PpM. The PpDB phytoplasma was detected by PCR one week prior to, or the same week as, external symptoms were first observed, while phytoplasma DNA was detected between three and eleven weeks prior to expression of PpM symptoms. Examination of lateral shoot regrowth on papaya plants that had recovered from PpDB or were cut back (ratooned) when they initially exhibited PpDB, PpYC or PpM symptoms, revealed that the PpDB phytoplasma did not persist in plants after the initial expression of symptoms. In contrast, the PpYC and PpM phytoplasmas usually persisted in the lower parts of the plant, and then infected the new lateral shoots as they developed. Dodder (Cuscuta australis R. Brown) was used as a phloem bridge between papaya plants affected by PpDB, PpYC and PpM, and periwinkle (Catharanthus roseus G. Don) plants. "Candidatus P. australasiense", but not the PpDB phytoplasma, was transmitted to periwinkle. The inability to transmit the PpDB phytoplasma corresponds with the view that in papaya, this phytoplasma is likely to be present at low titre, is a highly virulent pathogen, and disrupts phloem function before external disease symptoms are observed. Based on the results of this study it is recommended that ratooning of PpDB-affected plants and removal of PpYC- and PpM-affected plants are the best strategies currently available for the management of these diseases. Suggestions for future research and disease control strategies are discussed.

This research has examined the effects of soil compaction, and common agricultural management strategies used to overcome soil compaction, on soil bacterial and fungal activity and diversity. Soil microbial communities, bacteria and fungi in particular, play essential roles in the maintenance of soil health, where high soil microbial diversity might strongly contribute to the natural disease suppression. The activity and diversity of soil microbial communities is, however, strongly dependent on other soil characteristics, especially soil physical parameters. Soil compaction indicated by increased bulk density is the most soil physical parameter that directly modifies soil environment where crops and diseases exist in, but it might also indirectly cause more disease by affecting the composition of soil microbial communities in the soil. Many strategies have been used to attempt to overcome compaction in temperate environments, but they have been poorly studied/less successful in tropical and subtropical environments. This thesis, therefore, looks at the impact of compaction, and methods used to reduce compaction, on the soil microbial profile, and its capacity to resist introduced diseases.

Spiders are naturally occurring predators of insects in agroecosystems. The use of broad spectrum pesticides in agriculture is likely to disrupted spider communities and have a negative impact on their role as biocontrollers. The overall abundance, the species richness, diversity and guild structure of spiders in tropical mango orchards in central Queensland were investigated in this study. Experiments were performed to assess the potential of spiders as natural predators to pest insects in mango orchards. The effects of pesticides on the spider communities were assessed to establish the extent to which the communities were disrupted and the extent of recovery from this type of disturbance. The short term (acute) and long term (chronic) effects were investigated. The spiders in unsprayed mango orchards were relatively high in abundance, species richness and species diversity. Spiders were present in significant numbers at all sampling times,both day and at night, and during all seasons. The results suggest that spiders do not capture large numbers of prey. However spider exhibit a diversity of capturing techniques so that they capture a variety of insects. The most common guild was the orb-weavers. The spider abundance and diversity four days after spraying with methidathion suggested that recovery of spider after disruption such as the use of pesticides' occurs quickly. Presumably this recovery occurs due to spiders moving into the orchard from surrounding bush land. The long term use of pesticide does appear to disrupt the community and as evidenced by decreases in the abundance, species richness and diversity of spiders. While it is unlikely that pesticide usage will be eliminated in most commercial mango orchards, this study demonstrates that spiders are potentially important biocontrollers and that they are adversely affected by pesticide use. In the longer term, it will be desirable to develop IPM strategies to minimise pesticide use and maximise the role of spiders as biocontrollers. Such strategies will depend on studies such as this one and extensions of it.

Insect species complexes challenge entomologists in a variety of ways ranging from quarantine protection to pest management. Billbugs (Coleoptera: Curculionidae: Sphenophorus spp. Schönherr) represent one such species complex that has been problematic from a pest management perspective. These grass-feeding weevils reduce the aesthetic and functional qualities of turfgrass. Sixty-four species of billbugs are native to North America, and at least ten are associated with damage to turfgrass. Billbug species are sympatric in distribution and their species composition and seasonal biology varies regionally. Since their management relies heavily on proper choice of insecticide active ingredients and timing of insecticide applications that target specific life stages, understanding billbug seasonal biology underpins the development of efficient management programs. However, billbug seasonal biology investigations are currently hindered by our inability to identify the damaging larval stage to species level. DNA barcoding, which involves the use of short DNA sequences that are unique for each species, represents one potential tool that can aid these efforts. By combining DNA-based species identification with morphometric measures capable of serving as a proxy of larval development, it may be possible to gain a more holistic understanding of billbug seasonal biology. In this study, we developed a DNA barcoding reference library using cytochrome oxidase subunit 1 (COI) sequences from morphologically identified adult billbugs collected across Indiana, Missouri, Arizona, and Utah. Next, we applied our reference library for comparison and identification of unknown larval specimens collected across the growing season in Utah and Indiana. We then used a combination of DNA barcoding and larval head capsule diameters acquired from samples collected across a short span of the growing season to produce larval phenology maps. Adult billbug COI sequences varied within species, but the variation was not shaped by geography, indicating that this locus itself could resolve larval species identity. Overlaid with head capsule diameter data from specimens collected across the growing season, a better understanding of billbug species composition and seasonal biology emerged. This knowledge will provide researchers with the tools necessary to fill critical gaps in our understanding of billbug biology thereby improving turfgrass pest management. Using this approach researchers will be able to support efforts to provide growers with the information necessary to develop more prescriptive, location-based management programs and reduce the ecological footprint of turfgrass pest management.

Prosopis spp. are prolific seeders with estimates of seed production reaching from 630,000 to 980,000 seeds per mature tree per annum (Felker 1979; Harding 1988). Prosopis velutina shrubs have been recorded to produce up to 5,000 seeds per year (Glendening and Paulsen

1955). The plant has the ability to establish on disturbed or bare soil and can develop into very dense infestations. The plant often grows on scalded areas devoid of other vegetation and out-competes native herbage for moisture and light.

The plant is armed with long axillary spines; it branches from the base and has long arching stems. Its leaves are not commonly eaten by sheep and bovine breeds. Consequently, it forms dense stands that restrict the movement of stock, particularly around watering points, and this interferes with mustering.

There are many options for control of mesquite with herbicide application being integral in a management suite of mesquite control initiatives. Other control methods, which limit its distribution and spread, include mechanical removal, grazing management, competitive pasture

establishment, biological control, and a burning regime where adequate fuel is available.

The thesis discusses merits of the Prosopis species. Commonly known as mesquite or prickly bush, the Australian pest plant is endemic in the southern United States. The description then turns to how the weed was introduced into Queensland at both Quilpie and Hughenden in the north of the state. Some detail is given to its distribution and the effects on primary producers and the environment, and on the cost of control initiatives conducted through the Queensland Department of Natural Resources and Mines. 

Scientific findings from the research process are considerable given the base knowledge when the mesquite research project was revived in 1989. Initially, a research review of available literature was conducted revealing a large pool of knowledge from the United States of America. Their research findings on foliar applied herbicides have resulted in a high utilization of tank mixes principally containing triclopyr + clopyralid formulations sometimes with hydrocarbon additives. A more comprehensive summary of field research findings for Queensland is compiled as part of this thesis (Chapter 8) and presents some herbicide control options and constraints that may qualify their performance. Basal stem research in North America has produced many adopted recommendations. There have been numerous experiments on controlling mesquite with herbicides with many referred to in Control of Mesquite in the USA (Chapter 1). 

Chapter 2 presents a comparative analysis conducted to determine the different effects of applied herbicides to targeted young mesquite when applied in early summer compared to application in autumn. Formulations of fluroxypyr as well as metsulfuron methyl did not prove

efficacious in this trial. For the first time glyphosate proved to be a valuable herbicide in controlling mesquite when applied in autumn. Triclopyr + picloram and triclopyr alone proved to be more effective following wet conditions when applied in the early summer compared to the autumn application. However, treated plants growing adjacent to continuous paddock ponding were able to recover. Clopyralid exhibited high efficacy in both early summer and autumn treatment applications. 

Following poor control of Prosopis velutina at Quilpie by treatments recommended for control

of Prosopis pallida, a potted plant pilot trial was conducted to determine if the two species responded similarly (Chapter 3). The results indicated that Prosopis velutina was ineffectively controlled by herbicide application, at standard rates, compared to the control of Prosopis pallida. The follow-on replicated trial detail in Chapter 4 indicates a similar response for both

species. The effects of the treatments indicated differing susceptibility between the two species,

with metsulfuron, fluroxypyr, 2,4-D + picloram and triclopyr + picloram demonstrating the most pronounced differences compared to the glyphosate formulations here negligible difference occurred. A re -application of all herbicides to the surviving plants, and to a control

group, indicated that susceptibility can decrease when a follow-up application is in autumn and the time since initial application is short. This trend was particularly noticeable for P. velutina where previous sub -lethal damage prevented effective herbicide action. 

More fieldwork was conducted following this shade -house work as a prolific growth phase occurred in Quilpie mesquite in the early summer of 1999 (Chapter 5). Four glyphosate, and four triclopyr tank mixes and a control set out in each of three habitats made up the 27 plots evaluated in this aerial herbicide experiment. The triclopyr + picloram formulations at 5 and 7 L ha -1 with the addition of paraffinic oil (582 g L-1) and non-ionic surfactants (208 g L-1) produced the most efficacious and uniform results although triclopyr treatment with the addition of 1000 g L-1 alcohol alkoxylate produced similar results. However, the long-term effect was compromised because of the lack of a residual component in this formulation. 

A more manageable result was obtained when larger older plants were foliar overall sprayed using truck -mounted high pressure equipment (Chapter 6). A total of 33 treatments were assessed after each of four assessments of various herbicide mixtures. A blocking factor was plant density. Glyphosate tank formulations were consistently more efficient than other treatments, at all densities, except in combination with metsulfuron methyl. In the low density plots flumetsulam 0.10 g L-1 + glyphosate 3.60 g L-1 tank mix performed significantly better

than other treatments between the second and third applications and the third and fourth applications. Treatments containing clopyralid also showed high efficacy.  

A further experiment using the most common method of control (basal stem application technology) was conducted using dieseline as the herbicide carrier in March 1995 (Chapter 7).

The higher strength treatments with dicamba and triclopyr formulations showed the most activity irrespective of plant size (> 1.5 m or < 1.5 m) or water availability with the higher strength of each formulation, dichloromethoxybenzoic amine @ 10 g a.i. L-1 and triclopyr butoxyethyl ester 10 g a.i. L-1, being the most efficacious and not showing significant differenc from each other. 

In conclusion a three-year cycle planner was developed incorporating best control strategies researched within this thesis (Chapter 8). Suggestions were also put forward covering grazing management to enhance the effect of control strategies.

Pachymetra chaunorhiza is an important soilborne pathogen of sugarcane and is found only in Australia. Pachymetra root rot is managed primarily by growing resistant cultivars, which are chosen for planting based on oospore levels in the soil. This management strategy does not account for differences in virulence among Pachymetra populations, despite previous research demonstrating that two genetically distinct groups of Pachymetra occur, which may differ in pathogenicity. Higher than expected yield losses have been associated with high oospore levels under some cultivars with intermediate resistance to the pathogen. Increased virulence of Pachymetra towards specific cultivars, following long-term exposure to that cultivar, could explain these reports of high yield losses in intermediate cultivars. This research project aimed to deliver knowledge of the genetic and pathogenic variation among Pachymetra populations in different growing regions and following long-term exposure to different cultivars. The level of genetic and pathogenic variation among Pachymetra populations and the factors contributing to pachymetra root rot were investigated in a series of field trials, glasshouse experiments and laboratory molecular analyses. Results from field experiments generally support the current guidelines used for Pachymetra management. No evidence was found to support the hypothesis that planting the same intermediate cultivar over multiple crop cycles could lead to higher than expected yield losses due to pachymetra root rot. Yield losses of 17 percent were associated with continual cropping of Q208A in a field trial near Bundaberg, in the southern Queensland sugarcane-growing region. A range of putative Pachymetra genes were identified which could play a role in pathogenicity. Collectively, the findings from this research supported the conclusion that two genetically distinct groups of Pachymetra occur in growing regions a) north of Townsville and b) south of Townsville, as previously reported. Three potential native hosts of Pachymetra were also identified, including Themeda australis and this finding supports the theory that lighter soil types are conducive to pachymetra root rot.