Transcriptome analysis of developmental stages of cocoa pod borer, Conopomorpha cramerella: A polyphagous insect pest of economic importance in Southeast Asia

Chia Lock Tan, Rosmin Kasran, Wei Wei Lee, Wai Mun Leong

Preprint posted on 1 June 2021

Bitter bites for a chocolate lover. Searching for RNAi targets to fight cocoa crop pests

Selected by Paul Gerald L. Sanchez and Stefano Vianello


 The cocoa tree (Theobroma cacao) is indigenous to the rainforests of central America, yet Indonesia and Malaysia now feature among top cocoa producers amongst South East Asian Nations, with Indonesia having even ranked third amongst top producers in the world.

Despite its present economic importance, the introduction of the cocoa tree to South East Asia (marked and intertwined with the atrocities of Spanish and European colonialism) has come with big consequences: it led to a change of habitat of the moth Conopomorpha cramerella away from rambutan, cola, namnam, and other trees on which it used to live, and onto the pods of the newly introduced cocoa tree. Larvae of this moth (indeed now better known as the Cocoa Pod Borer) dig to the centre of the cocoa pods, feed off the seeds, and chew their way out to emerge, pupate, and transform in the adult. The cocoa pod is ravaged. The economic impact of this pest in South East Asia  is currently enormous, with crop losses up to 80%.

Given that pesticide-based eradication strategies have significant health and environmental impact, the authors discuss recent successes with RNA interference (RNAi) pest control approaches. Successfully employed to fight other crop pests, these strategies involve feeding insects with RNAi constructs that target key genes the pests require for survival. Delivery can either occur by direct feeding, or by genetic modification of the crop these pests are feeding on. Critically, RNAi strategies require knowledge on the best genes to target, yet genetic information on the Cocoa Pod Borer is extremely scarce.


FIGURE 1. Left: adult form of the moth Conopomorpha cramerella (Cocoa Pod Borer). Right: damaged cocoa pods and cocoa leaves (from


Main results

The authors sequence (and make available) the transcriptome of the cocoa pod borer at all of its main stages of development: larva, pupa, and adult. After transcript assembly and gene prediction, they then identify key genes involved in the development, survival, and reproduction of this pest, as well as the overall transcriptional changes marking the transition from one life stage to the other.

Key genes involved in sex determination, spermatogenesis and pheromone binding are are thus identified as potential targets for RNAi-mediated pest-control, given their likelihood of being insecticidal when silenced. Some of the targets highlighted by the authors include:

  • Alcohol dehydrogenases- required for larval survival and regulating genes for moulting and metamorphosis in other species
  • Porin- a male-biased pheromone binding protein
  • Bol- involved in the meiotic division of spermatogenesis in male insects
  • Dsx and Fruitless –  involved in sex determination and involved in sex-specific developmentalmodules

In addition, the authors  identify hundreds of thousands of unknown genes specific to C. cramerella.



The economic impact of the Cocoa Pod Borer (Conopomorpha cramerella) on South East Asian cocoa production is enormous (estimated loss of $ 500 million/year in Indonesia), yet RNAi-based eradication and control strategies require genetic information on the genes to target for maximal insecticidal effect. This is one of the first studies providing such information (characterisation of the transcriptome of the pest at all stages of its life cycle), and to identify candidate targets to deploy RNAi pest control.


 Questions for the authors


  • Could you tell us more about the Malaysian Cocoa Board and its research activities? What is the status of cocoa production in Malaysia, and how deeply is it affected by Conopomorpha cramerella?


  • Do you expect any specific difficulties in deploying RNAi control strategies nationally? Do you expect local growers and smallholders to be able to deploy RNAi pest control?


  • Do you favour delivering RNAi to Conopomorpha cramerella by direct feeding or by modification of cocoa trees?


  • Before the moths moved to cocoa tree, were they also detrimental to rambutan plants and other previous hosts? If not, could properties of resistant hosts be exploited to protect vulnerable crops like the cocoa tree?


  • Are there efficient preventive methods to prevent Conopomorpha cramerella infection in the first place?


  • Does Conopomorpha cramerella have any beneficial role within their ecosystem? Would its elimination possibly have adverse consequences?


Tags: cocoa pod borer, crop pest, rnai, sea

Posted on: 16 June 2021 , updated on: 18 June 2021


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