The FCM Genome – Completing the puzzle

Many new and emerging tools based on genetic technology and gene sequencing have become available in recent years, that can be used to assist with insect pest management. These include diagnostic tools for rapid species identification, population genetics to investigate relatedness between species or individuals, and movement patterns across the agricultural landscape to inform management strategies. In the past, many of these have been employed for FCM, including identification (Timm et al., 2007, 2008; Mgocheki et al., 2016; Rizzo et al., 2021) and population connectivity (Timm et al., 2009).

Knowing the degree of connectivity between populations allows the identification and setup of management units for effective control. Subsequently, the development of Next Generation Sequencing (NGS) technologies has made it possible for researchers to sequence the entire genome of organisms.

The genome contains the genetic makeup, better known as the DNA (deoxyribonucleic acid) of the organism. It consists of a four-letter alphabet (nucleotides) of which the order determines some functional role in the organism. Therefore, sequencing the genome of an organism simply means determining the order of the nucleotides in the DNA of the organism, by assembling several overlapping segments – like building a jigsaw puzzle – to piece together the uninterrupted genetic code.

The genome is essentially an information guide and is the first step in developing genomic resources to answer important questions relating to pest control (e.g. insecticide resistance, mating and reproduction, chemo-sensation, sex determination and development). In addition, it offers the opportunity for solution-driven research to develop novel FCM control strategies.

Recently, the genome of FCM was sequenced and assembled, based on a single male moth. The project was initiated in 2018 by the Applied Physiological Ecology Lab under the leadership of Prof John Terblanche and Dr Minette Karsten, who was a postdoctoral research associate at the time (but has been a researcher at Hortgro since 2021), in the Department of Conservation Ecology and Entomology (Stellenbosch University). The project was brought to completion to the lab group in 2020 by the addition of Dr Anandi Bierman, a postdoctoral research associate with a strong bioinformatics and genomics background.

In total, the final FCM genome assembly is 1283.41Mb in size, comparable to that of codling moth (Cydia pomonella) and other important Lepidopteran agricultural pests (Wan et al., 2019). Studies focused on the codling moth genome have identified genes linked specifically to insecticide resistance and the olfactory attraction to pheromones and pear ester, which play a role in mating disruption.

For FCM, very little is known about their odour reception ability, which is applicable to the location of oviposition sites, mates and plant host choice (food). In the FCM genome assembly, many similarities to codling moth insecticide resistance genes and odour reception genes were identified. In particular, a genetic variant in the Octopamine receptor (OAR1) gene was found in both codling moth and FCM, shown to confer insecticide resistance against azinphos-methyl and deltamethrin. This implies a potential mechanism for insecticide resistance in FCM.

However, many differences were also found, in particular, the absence of odorant receptor 3 (OR3), responsible for the detection of pear ester. Interestingly, the co-receptor for OR3 is present in FCM, but the gene itself is not. This alludes to the presence of a novel odorant receptor gene that binds to the co-receptor and suggests the attraction of FCM to different volatiles than codling moth.

Genomic information such as that discussed here has the potential to open doors for the development of optimised attractants for use in monitoring of FCM or optimised pheromones for mating disruption. It also provides opportunities for screening of insecticide resistant populations. The next step will be to investigate the effect of genes identified in this study on FCM biology and behaviour in the field.