FCM gene flow in agricultural environments

Many different tools have been employed to measure dispersal in insects, with many studies focusing on traditional mark-release-recapture methods (MRR). These MRR studies are often limited due to the scale at which insects can be released and the size of the trapping grid. In recent years the use of molecular tools has gained traction since it can provide high-resolution answers across large spatial scales. Various molecular markers have been used to explore gene flow in insects, one of which is, Single Nucleotide Polymorphism (SNP) markers. A SNP (pronounced "snip") is an alteration in a single nucleotide (one of the four letters of the alphabet of DNA) in the genome of an organism that results in variation in the DNA sequence. Occurring naturally throughout an organism's genome, SNPs are readily used to track inheritance and gene flow.

Recently, SNPs were employed to investigate the gene flow of FCM across SA, specifically looking at the possibility of host races and fine-scale movement pathways between different sampling locations. Several sampling locations were included from the Western Cape, Eastern Cape, Mpumalanga and Limpopo Provinces and FCM were collected from multiple hosts including Citrus, Prunus and Punica. SNP genotypes were produced using DArT-Seq™ technology, which is a sequencing system that employs Next Generation Sequencing (NGS) platforms to produce detailed genome characterisation in a cost-effective way by removing less informative (repetitive) regions in the genome before sequencing.

Based on the results, it seems there is no indication of a crop-specific genotype of FCM in SA (Figure 1) which means that moths disperse freely between different host types. In addition, FCM is capable of dispersal over large distances and a proportion of this dispersal can likely be human mediated through the transport of fruit in the formal and informal fruit trade. These results firstly highlight the importance of consistent monitoring and the systems approach to ensure control of FCM on various levels. Moreover, it is critical to include alternative or wild hosts adjacent to orchards or vineyards in management practices and to carefully consider the scale (single orchards/vineyards vs. area-wide) at which specific management practices are employed to ensure population suppression.

Next steps include statistical analyses of the significance of potential correlations between genotype and sub-location or crop type. These results will be used to fine-tune our understanding of the genetic structure in FCM populations and shed light on the movement patterns of FCM between different geographic locations and host types. Future work should focus on identifying “successful” genotypes (i.e. genotypes that show high virulence or are wide-spread) and investigate informative genes such as insecticide resistance or chemosensory capabilities in these genotypes with the aid of the recently completed whole genome of FCM.