Crop Protection

Key Areas

This programme develops integrated management strategies that minimise the effects of pests and diseases on crop production in a sustainable manner.

Research in this Key Area focuses on:

  • Development of proactive threat specific counter-measures and biosecurity incursions plans;
  • Generation of knowledge of the biology, pathogenicity and epidemiology of pathogens posing potential incursion threats to the industry, as well as the agroecology, behaviour and reproductive biology of new potential pests; and
  • Development of improved procedures and diagnostic technologies to ensure that varieties released or propagated into the industry, or imported via the industry Quarantine Facility, are free of pathogens and pests. The information and knowledge gained in this Key Research Area are applied towards the development of Integrated Management tactics for potential new pathogen and pest incursions into the industry.

Research in this Key Area focuses on:

  • Investigation of the biology and ecology of the primary pathogens and pests of the industry with a view to the development of integrated management tactics and knowledge exchange with the grower community; and
  • Assessment of the impact on crop yield of the primary and emerging pathogens and pests in the industry to facilitate grower decision-making regarding the implementation of management tactics. The information and knowledge gained in this Key Performance Area are applied to the development of integrated management tactics for the major pathogens and pests in the industry.

Research in this Key Area seeks to develop knowledge regarding the biological basis of sugarcane resistance to pathogens and pests in order to develop approaches, resources and technologies to enhance resistance breeding in Commercial Breeding.

Research in this Key Area seeks to develop cost-effective technologies that permit the establishment of sugarcane agro-ecological environments in which pathogens and pests are suppressed to low levels by benign biological or ecological means.

Several complementary habitat management technologies are considered, including:

  • Push-pull technology
  • Biodiversity management, including wetland, riparian zone and vegetation corridor restoration;
  • Crop husbandry, including crop rotation, use of fallow crops, nutrient management and crop residue management;
  • The Sterile Insect Technique; and
  • Parasitoid and entomo-pathogen release.

Investigations in this Key Research Area focus on the development of a suite of effective pathogen and pest control agents that are agriculturally, environmentally, ecologically and economically sustainable.

Research focuses on a series of technologies, including:

  • Development of pheromones and traps to enable monitoring and rational agrochemical application programmes, primarily for eldana;
  • Search for more benign alternative chemistries; and
  • Development of superior application tactics and product formulations.
  • Download list of agricultural remedies registered for use in South Africa.

Dr Stuart Rutherford

Programme Manager: Crop Protection


Programme Manager: Crop Protection

Tel: 031 508 7400 (Switchboard)
Tel: 031 508 7529 (Direct)

Role & Overall Purpose

As a programme leader, I am responsible for coordinating and managing research within the Crop Protection Research Programme at SASRI. In this role I am involved in the development of the annual programme of work through encouraging focus, innovation and collaboration in research. As a scientist, my role is to initiate, conduct and supervise research leading to best management practices for sugarcane crop protection in South Africa. I am also currently a National Research Foundation (NRF)-rated scientist.


Plant Pathology, Entomology, Integrated Pest Management, Soil Science, Physiology & Biochemistry, Molecular Biology.

Research Interests
  • Genomics of pest and disease resistance.
  • Mechanisms of resistance to biotic and abiotic stress.
  • Rapid prediction of pest and disease resistance ratings in sugarcane e.g. using Near Infrared.
  • Primed epigenetic in-vitro mutation breeding for resistance to biotic and abiotic stressors.
  • Plant physiological and priming effects of modern crop protection chemistries.
  • Insect pest, host-plant and microbial interactions. Endophytic Beauveria  and Bacillus for pest control.
  • Application of Chemical Ecology in Integrated Pest Management Systems.
Key Outcomes
  • The development of NIR as a means of phenotyping pest and disease resistance in sugarcane.
  • Herbicide tolerant sugarcane produced by mutagenesis.
  • Fusarium resistant sugarcane produced by mutagenesis having improved resistance to Eldana saccharina.
  • The production of an IPM book on eldana control.
Key Publications

Koetle, M.J., Jacob, R.M., Snyman, S.J. and Rutherford R.S. (2023). Long-term cultivation of adaptable cultivars in different agro-climatic zones influences the epigenetic diversity of South African sugarcane (Saccharum spp.). Sugar Tech. 25: 491–495.

Koetle, M.J., Osborn, C., Snyman, S.J. and Rutherford R.S. (2023). The 5-azacytidine-induced epimutagenesis of sugarcane (Saccharum spp. hybrids) for aluminium tolerance. Biochimica Biophysica Acta. 1867: 130491.

Koetle, M.J., Snyman, S.J. and Rutherford R.S. (2023). Rapid identification of drought tolerant sugarcane epimutants via in vitro chimera dissolution and near infrared screening ex vitro. Plant Stress.

Koetle, M.J., Snyman, S.J. and Rutherford, R.S. (2022). Ex vitro morpho-physiological screening of drought tolerant sugarcane epimutants generated via 5-Azacytidine and imidacloprid treatments. Tropical Plant Biology 15: 288–300.

McFarlane, S.A., Kistan, C.J., Koch, A.C., Naude, A. and Rutherford, R.S. (2022) First report of orange rust caused by Puccinia kuehnii on sugarcane in South Africa. Plant Dis.

Mahlanza, T., Rutherford, R.S., Snyman, S.J. and Watt, M.P. (2019). Methylglyoxal-induced enhancement of somatic embryogenesis and associated metabolic changes in sugarcane (Saccharum spp. hybrids). Plant Cell Tissue & Organ Culture 136: 279-286.

Rutherford, R.S., McFarlane, S., Memela, N. and Snyman, S. (2019). Harnessing the sugarcane microbiome for improved resistance to the stalk borer Eldana saccharina Walker (Lepidoptera: Pyralidae). Proceedings of the International Society of Sugarcane Technologists 30: 1721-1727.

Snyman, S.J., Naidoo, M., Watt, M.P. and Rutherford, R.S. (2019). An in vitro screening system to assess aluminium toxicity in sugarcane (Saccharum spp.). In Vitro Cellular and Developmental Biology – Plant 55: 403-408.

Koetle, M., Evans, D.L., Singh, V., Snyman, S., Rutherford, R.S. and Watt, P. (2018). Agronomic evaluation and molecular characterisation of the acetolactate synthase gene in imazapyr tolerant sugarcane (Saccharum hybrid) genotypes. Plant Cell Reports 37: 1201-1213.

Keeping, M.G., Miles, N. and Rutherford, R.S. (2017). Liming an acid soil treated with diverse silicon sources: effects on silicon uptake by sugarcane (Saccharum spp. hybrids). Journal of Plant Nutrition. 40: 1417-1436.

Martin, L.A., Evans, D.L., Castlebury, L.A., Sifundza, J.T., Comstock, J.C., Rutherford, R.S. and McFarlane, S.A. (2017). Macruropyxis fulva sp. nov., an undescribed rust (Pucciniales) infecting sugarcane in southern Africa. Australasian Plant Pathology 46: 63-74 DOI 10.1007/s13313-016-0460-1

Martin, L.A., Rutherford, R.S. and McFarlane, S.A. (2017). Touchdown PCR assay for the rapid diagnosis of tawny rust caused by Macruropyxis fulva on sugarcane. Australasian Plant Pathology 46: 103-105 DOI 10.1007/s13313-016-0464-x

Naidoo, N., Ghai, M., Moodley, K., Mkhize, L., Martin, L., McFarlane, S. and Rutherford, R.S. (2017). Modified RS-LAMP assay and use of lateral flow devices (LFDs) for rapid detection of Leifsonia xyli subsp. xyli (Lxx). Letters in Applied Microbiology 65: 496-503.

Rutherford, R.S., Maphalala, K.Z., Koch, A.C., Snyman, S.J. and Watt, M.P. (2017). Field and laboratory assessments of sugarcane mutants selected in vitro for resistance to the imidazolinone herbicide imazapyr. Crop Breeding and Applied Biotechnology, 17: 107-114.

Keeping, M.G., Rutherford, R.S., Sewpersad, C. and Miles, N. (2015) Provision of nitrogen as ammonium rather than nitrate increases silicon uptake in sugarcane. AoB PLANTS 7: plu080; doi:10.1093/aobpla/plu080

Mahlanza, T., Rutherford, R.S., Snyman, S.J. and Watt, M.P. (2015) Potential of Fusarium sacchari-tolerant mutants in controlling Eldana saccharina and borer-associated Fusarium stem rot in sugarcane. European Journal of Plant Pathology 141: online.

Way, M.J., Conlong, D.E., Martin, L.A., McFarlane, S.A., Stranack, R., Keeping, M.G. and Rutherford, R.S. (2015). First record of yellow sugarcane aphid, Sipha flava (Homoptera: Aphididae), in the South African sugarcane industry. International Sugar Journal, 117: 654-656.

Ghai, M., Singh, V., Martin, L.A., McFarlane, S.A., van Antwerpen, T. and Rutherford, R.S. (2014) A rapid and visual loop-mediated isothermal amplification assay to detect Leifsonia xyli subsp. xyli targeting a transposase gene. Lett. Appl. Microbiol. 59: 648-657.

Mahlanza, T., Rutherford, R.S., Snyman, S.J. and Watt, M.P. (2014) Eldana saccharina (Lepidoptera: Pyralidae) resistance in sugarcane (Saccharum sp.): Effects of Fusarium spp., stalk rind, fibre and nitrogen content. Afr. Entomol. 22: 810-822.

Rhodes, R., Berry, S.D., Ramouthar, P.V. and Rutherford, R.S. (2014) Evaluation of Desmodium uncinatum, Fagopyrum esculentumand Brachiaria humidicola as potential green manure crops for nematode management in sugarcane. S Afr. J. Plant Soil. 31: 25–33.

Rutherford, R.S. (2014) Mechanisms of Resistance to Pests and Pathogens in Sugarcane and Related Species. In F.C. Botha & P.H. Moore (Eds.), Sugarcane Physiology, Biochemistry, and Functional Biology. Wiley-Blackwell. ISBN: 978-0-8138-2121-4.

Rutherford, R.S., Snyman, S.J. and Watt, M.P. (2014) In vitro studies on somaclonal variation and induced mutagenesis: Progress and prospects in sugarcane (Saccharum spp.) – a review. J.Hort. Sci. & Biotech. 89: 1-16.

Sabatier, D.R., Moon, C.M., Mhora, T.T., Rutherford, R.S. and Laing, M.D. (2014) Near-infrared reflectance (NIR) spectroscopy as a high-throughput screening tool for pest and disease resistance in a sugarcane breeding programme. Int. Sugar J. 116: 580-583.

Mahlanza, T., Rutherford, R.S., Snyman, S.J. and Watt, M.P. (2013) In vitro generation of somaclonal variant plants of sugarcane for tolerance to Fusarium sacchari. Plant Cell Rep. 32: 249-262.

Munsamy, A., Rutherford, R.S., Snyman, S.J. and Watt, M.P. (2013). 5-Azacytidine as a tool to induce somaclonal variants with useful traits in sugarcane (Saccharum spp.). Plant Biotech. Rep. 7: 489-502.

Goble, T.A., Costet, L., Robene, I., Nibouche, S., Rutherford, R.S., Conlong, D. and Hill, M. (2012) Beauveria brongniartii epizootics on white grubs attacking sugarcane in South Africa. J. Invert. Pathol. 111: 225-236.

Koch, A.C., Ramgareeb, S., Rutherford, R.S., Snyman, S.J. & Watt, M.P. (2012) An in vitro mutagenesis protocol for the production of sugarcane tolerant to the herbicide imazapyr. In Vitro Cellular Devel.Biol. – Plant 48: 417-427.

Way, M.J., Conlong, D.E. and Rutherford, R.S. (2012) Biosecurity against invasive alien insect pests: A case study of Chilo sacchariphagus (Lepidoptera: Crambidae) in the southern African region. Int. Sugar J. 114: 359-363.

Ramgareeb , S., Snyman, S.J., van Antwerpen, T. and Rutherford, R.S. (2010) Elimination of virus and rapid propagation of disease-free sugarcane (Saccharum spp. cultivar NCo376) using apical meristem culture. Plant Cell, Tissue Organ Cult. 100: 175-181.

Conlong, D.E. and Rutherford, R.S. (2009) Conventional and New Biological and Habitat Interventions for Integrated Pest Management Systems: Review and Case Studies using Eldana saccharina Walker (Lepidoptera: Pyralidae). In R. Peshin & A.K. Dhawan (Eds.), Integrated Pest Management Vol. 1: Innovation-Development Process, Springer, ISBN 978-1-4020-8991-6.

McFarlane, S.A., Govender, P. and Rutherford, R.S. (2009) Interactions between Fusarium species from sugarcane and the stalk borer Eldana saccharina Walker (Lepidoptera: Pyralidae). Ann. Appl. Biol. 155: 349-359

Keeping, M.G., Rutherford, R.S. and Conlong, D.E. (2007) Bt maize as a potential trap crop for management of Eldana saccharina Walker (Lep., Pyralidae) in sugarcane. J. Appl. Entomol. 131: 241-250.

Rutherford R.S. (2007) Sugarcane Diseases, ecology, and control. In D. Pimentel (Ed.), Encyclopaedia of Pest Management Vol 2.pp 643-646. CRC Press, Taylor & Francis. ISBN 13: 978-1-4200-5361-6

Butterfield, M., Rutherford, R., Carson, D. and Huckett, B. (2004) Application of gene discovery to varietal improvement in sugarcane. SA J. Bot. 70: 167-172.

Heinze, B.S., Thokoane, L.N., Williams, N.J., Barnes, J.M. and Rutherford, R.S. (2001) The smut-sugarcane interaction as a model system for the integration of marker discovery and gene isolation. Proc. S. Afr. Sug. Technol. Ass 75: 88-93.

Thokoane, L.N. and Rutherford, R.S. (2001) cDNA-AFLP differential display of sugarcane (Saccharum spp, hybrids) genes induced by challenge with the fungal pathogen Ustilago scitaminea (sugarcane smut). Proc S Afr Sug Technol Ass 75: 104-107.

Rutherford, R.S. (1998) Prediction of resistance in sugarcane to the stalk borer Eldana saccharina Walker by near infrared spectroscopy on crude bud scale extracts. The involvement of chlorogenates and flavonoids. J. Chem. Ecol. 24: 1447-1463

Rutherford, R.S. and van Staden J. (1996) Towards a rapid near infra-red technique for the prediction of resistance to the sugarcane borer Eldana saccharina Walker (Lepidoptera: Pyralidae) using stalk surface wax. J. Chem. Ecol. 22: 681-693.

Rutherford, R.S., Smith, G.S. and van Staden, J. (1994) Development of a meridic diet for the sugarcane borer, Eldana saccharinaWalker (Lepidoptera: Pyralidae). Principles, problems and possible in vivo plant resistance mechanisms. Afr. Entomol. 2: 163-174.


  • Honorary Lecturer – University of KwaZulu-Natal (2012 – Present).
  • BSc Hons (Reading), MBA (Cardiff) PhD (Natal).

Current Projects

Variety Evaluation – Diseases
Additional chemistries and strategies for sugarcane pest and disease control
Sterile Insect Technique for eldana management: Field release trials
X-Ray Irradiation for Eldana SIT
Comparison of diversity and abundance of non-target organisms on Bt and non-Bt sugarcane.
Effect of genetically modified sugarcane in combination with sterile insect releases to control Eldana saccharina
Development of an IRAC laboratory-based Eldana saccharina resistance monitoring protocol
An investigation of insect trap designs and deployment using eldana attractants to monitor eldana infestation in Bt sugarcane
Agronomic assessment of the herbicide tolerance trait in Bt GM sugarcane
Prediction of quantitative resistance to sugarcane pests and diseases by means near infra-red spectroscopy
Spectroscopic determination of YSA-induced stress in sugarcane
A P&D risk model as a precursor to development of an early warning system (EWS)
Yellow sugarcane aphid and thrips varietal susceptibility
The effect of steel slag amendments on yellow sugarcane aphid infestations and cane yields.
An investigation of the population dynamics of yellow sugarcane aphid with a particular emphasis on movement patterns between plants
Biodiversity management and its place in sugarcane agriculture
The eldana microbiome
Use of boron for the control of Eldana saccharina and Fusarium in sugarcane
Determination of sugarcane yellow leaf virus elimination efficiency using molecular techniques
Protection of NovaCane® plantlets against smut and other fungal diseases
Understanding orange rust in the South African context