Genome analysis of cabbage root fly for targeted pest management

ArticleDetailDownload PDF

Cabbage root fly (Delia radicum) is a devastating root herbivore of important commercial crops such as cabbage, broccoli, and rapeseed. Increased insecticide resistance, and government mandated reduction of environmentally harmful chemicals, leave growers with few options to control an infestation. Dr Nicole M. van Dam, Rebekka Sontowski and Dr Yvonne Poeschl at the German Centre for Integrative Biodiversity Research, sequenced and annotated the full genome of the cabbage root fly to locate possible targets for the development of genetically based insecticides.
Insects have fought to overcome plant host defences for all of evolutionary history. Each time the host develops a new chemical weapon or strategy to stave off potential threats, it is only a matter of time before the herbivores adapt. This constant coevolution produces insect pests which are highly adapted to their preferred host plant, and are able to overcome defences toxic to other species.

One such nuisance is the cabbage root fly, Delia radicum. As its name suggests, this species targets members of the Brassicaceae family, which includes economically important crops such as cabbage, broccoli, radish, pak choi, and rapeseed. Brassicaceae plants defend themselves by producing and storing chemicals called glucosinolates within their cells. When the plant cells are broken, for instance through chewing by herbivores, the enzyme myrosinase is released and converts the glucosinolates into toxic compounds, such as isothiocyanates and nitriles. The glucosinolate-myrosinase defence system, also dubbed the ‘mustard oil bomb’, is present in the shoots as well as the roots.

Cabbage root fly

This defence is highly effective against most herbivores, but cabbage root flies have evolved a way to circumvent it by producing enzymes able to neutralise the toxins within their food. The female fly detects her preferred host plant by its specific odour profile and deposits eggs on the root crown. When the eggs hatch, cabbage root fly larvae (maggots) tunnel down into the soil and feed on the plant roots. The fly’s larvae developed mechanisms to overcome the plant’s defences allowing them to feed on roots, even though they have high levels of glucosinolates. The larvae kill seedlings by restricting the water and nutrient uptake of the roots, and limit the growth of adult plants. A larval infestation on the plant roots has also been shown to reduce seed number and weight, which is particularly devastating for rapeseed harvests.

D. radicum is so highly adapted to its host, it developed molecular mechanisms to overcome the plant’s defences.”

Pesticide solutions

Synthetic pesticides, specifically neonicotinoids, have been the default solution to eradicating cabbage root fly, but they are not a sustainable solution. In an effort to conserve biodiversity and environmental welfare, the European Union aims to reduce all pesticide use to 50% of current applications by 2030. Neonicotinoids in particular have already been banned due to their environmental toxicity. Even if these chemicals were safe to use, the cabbage flies are already acquiring resistance, so there is an ever-growing need for sustainable pest control.

Several alternatives have been explored, but none were as effective as synthetic chemicals. Breeding agricultural crops with wild species which have pest resistance would introduce too many undesirable traits. Other approaches, such as introducing a fungal pathogen which targets the fly reduced the infestation, but it did not eradicate the fly completely.

Cabbage root fly larvae have a pair of mouth hooks (top right) allowing them to feed on the root surface. The resulting damage is visible as brown trenches on the roots (as shown by the arrow).

A genetic approach

In the search for a novel solution toward D. radicum control, Dr Nicole van Dam, Rebekka Sontowski, Dr Yvonne Poeschl and their collaborators sequenced the entire genome of this organism. Their goal was to reveal the genetic foundations of the cabbage root fly’s resistance to specific host defences. To date, the genetic mechanism behind D. radicum host plant adaptation is unknown. By annotating (labelling and functionally describing) the genome, scientists can pinpoint genetic targets for pest control. It was important to examine the genome and transcriptome (gene expression profiles) of the root flies at each stage in their life cycle – egg, larva, pupa, and adult fly – in order to gain a broad picture of how gene expression changed throughout the fly’s lifecycle. The genomic information of related fly species and insect species feeding on the same host plants provided guidance in annotating the newly sequenced genome. Using the genome, researchers can study the function of similar genes found in the cabbage root fly genome.

The genomic information and the sequenced transcriptomes revealed that highly specific clusters of genes were expressed during different life stages. At the egg stage, genes regulating embryonic development and gene regulation were expressed. Genes related to regulation and coordination of organ formation are also highly expressed in egg cells. As the egg grows into a larva, these genes are activated to help synthesise cellular components and organs. The egg and pupal stages shared many gene clusters, as these stages in development are similar in that they don’t involve movement or sensory perception. The larval stage, on the other hand, more frequently expressed genes related to body development, and other cellular structure components. Larvae also had a high expression of metabolic genes, necessary for feeding, growth, and molting. The pupal stage involves the dismantling of many larval structures to form adult wings, eyes, and legs; pupa therefore express catabolic processes, or processes that break down larger structures. Genes responsible for nuclease and peptidase activity, and for building cuticle structures, are more highly expressed in the pupal transcriptome.

This plot connects the position of genes on chromosomes of the genetic model species, Drosophila melanogaster, the fruit fly, with the genes annotated on the Delia radicum chromosomes. This helps us see how similar the chromomosal structure and the location of genes with similar sequence in these two different fly species are.

It was also found that adult flies had a unique transcriptome. Genes involved in light detection, both in the visible and UV spectrum, as well as those involved in taste, odour perception, and temperature detection were expressed only in adult flies. These sensory abilities help the adult flies to find food and locate suitable places to lay eggs.

To study the transcriptomics of insect responses, or the genes expressed when the insects are exposed to certain stimuli, the researchers introduced a group of larvae to high levels of toxic isothiocyanates. These are the compounds resulting from the ‘mustard oil bomb’, which larvae are exposed to when damaging Brassica roots. They compared their gene expression with larvae which were not exposed. For the larvae exposed to isothiocyanates, peptidase genes and genes involved in metabolic and biosynthetic processes were activated. The response demonstrated that the larvae have the ability to quickly metabolise this toxin by activating several genes responsible for synthesising the appropriate peptidases. These genes, located within the cabbage fly genome, were similar to genes annotated in other insect herbivores that are known Brassica pests. They provide important targets for understanding host-plant adaptation and pest control.

It is clear from this analysis that the cabbage root fly larvae and adults are well adapted to their host, efficiently locating it and disarming its defences.

“Many of the genes identified during the whole genome analysis would make excellent targets for RNAi biopesticides.”

Targets of interest

The researchers so far have sequenced, annotated, and described the whole genome of the cabbage root fly. This functional gene annotation highlights important sites within the genome which can potentially be used as targets for RNAi biopesticides. RNAi, or RNA interference, is a biological mechanism which employs double stranded RNA molecules within the cell to suppress genes. It is used by the organism to downregulate gene expression, or to disarm viruses by suppressing the foreign DNA in the cell. RNAi biopesticides are a new technology which selectively targets and disarms a specific gene. We could use the genomic information to design RNAi-based pesticides that specifically disable the maggots’ ability to digest Brassica plants, whilst leaving bees and other non-target organisms unharmed. In countries where this is allowed, plants could be genetically modified to produce the necessary RNAi material. In Europe, where genetically modified plants are not acceptable, an RNAi formulated biopesticide can be sprayed directly onto a non-modified plant as an alternative to using synthetic pesticides.

A visual of the genes expressed in each developmental stage. The coloured ones are specific for a particular stage; the grey/black ones are expressed in all stages. For the larvae, the researchers compared the gene expression with (light green) and without (yellow) isothiocyanates in the diet, to discern which genes are relevant for different stages.

Many of the genes identified during the whole genome analysis would make excellent targets for RNAi biopesticides. Researchers could focus on the sensory genes which enable adult flies to locate or recognise the crop plants, the genes which help maggots digest the plant material, or genes responsible for embryo development within the egg, if they are specific to cabbage root fly.

The whole genome analysis of important agricultural pests, such as D. radicum, undertaken by Dr Nicole van Dam and her team provides novel insight into how belowground herbivores adapt to their host plant defences, but also informs new possibilities for sustainable and targeted pest management which effectively protects our food supply and the environment.

Have RNAi pesticides been developed for other members of Diptera, and if so, can these be used on cabbage root fly?
Based on patents applied for, RNAi biopesticides seems to be most advanced for combating beetles, for example pollen beetles and flea beetles, two above ground rapeseed pests. There is quite some scientific interest in finding RNAi biopesticides against fruit flies and mosquitos.



  • Sontowski, R, Poeschl, Y, Okamura, Y, et al (2022) A high-quality functional genome assembly of Delia radicum L. (Diptera: Anthomiidae) annotated from egg to adult. Molecular Ecology Resources (in press).
  • Zotti, M, Dos Santos, E, Cagliari, D, et al (2018) RNA interference technology in crop protection against arthropod pests, pathogens, and nematodes. Pest Management Science, 74(6), 1239-1250.
  • Crespo, E, Hordijk, C, de Graaf, R, et al (2012) On-line detection of root-induced volatiles in Brassica nigra plants infested with Delia radicum L. root fly larvae. Phytochemistry, 84, 68-77.

Research Objectives

Dr Nicole M. van Dam and her team sequenced the genome of cabbage root fly in order to understand the molecular mechanisms underlying its adaptation to host plant defences, and to facilitate the development of genetically based RNAi biopesticides.


The research presented was supported by the German Research Foundation (Deutsche Forschungsgemeinschaft; DFG). The DFG funded our research project in the Coordinated Research Centre ChemBioSys (SFB 1127, 239748522) as well as the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig (DFG–FZT 118, 202548816).


  • Dr Heiko Vogel & Dr Yu Okamura, Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans‐Knöll‐Str. 8, 07745 Jena, Germany
  • Dr Cervin Guyomar, GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet Tolosan, France
  • Professor Dr Anne-Marie Cortesero, IGEPP, INRAE, Institut Agro, Univ Rennes, 35000, Rennes, France
  • Axel Touw, Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany; Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany


Dr Nicole M. van Dam is full professor at the Friedrich Schiller University, Jena and leads the research group Molecular Interactive Ecology (MIE) at the German Centre for Integrative Biodiversity Research (iDiv), located in Leipzig, Germany. Her research focuses on the molecular and chemical mechanisms of plant-herbivore interactions, particularly root herbivores. She combines metabolomics, transcriptomics and genomics to study plant chemical defences and herbivore adaptations.

Dr Yvonne Poeschl is a Bioinformatician in the MIE group at iDiv. In her research she focuses on the analyses of multi-omics at different levels. This includes the assembly and annotation of new genomes from Next-Generation-Sequencing data to generate new knowledge to understand the mechanisms driving evolutionary relationships between organisms.

Stijn Brouwer (PhD) is a senior researcher at KWR Water Research Institute. His research interests are mainly in customer participation, citizen science, and strategic innovation. Dr Brouwer is the coordinator of the Customer theme group of the Joint Research Programme, and affiliated to the Department of Sociology, University of Antwerp, Belgium.


T: +49-341-9733165/166

Related posts.


Leave a Comment

Your email address will not be published.

Share this article.