Using individual scale de novo assembly to characterize the genetic basis of a sexually dimorphic locus in the medfly (Ceratitis capitata) genetic sexing strain

The Mediterranean fruit fly (medfly) is an important agricultural pest of many fruit and vegetable species. To protect the mainland United States from this pest, the sterile insect technique (SIT) is employed, involving release of tens of millions of sterile male medfly into the Los Angeles basin of California weekly. These flies have several mutations making them amenable to mass release. Due to a chromosomal translocation between the 5th chromosome and the male Y chromosome, females are homozygous recessive for both a temperature sensitive lethal mutation and a white pupal mutation, allowing straightforward separation of male and female flies and generation of male only release strains. Heterozygosity for these loci is maintained in males through the chromosomal translocation, linking wild-type phenotype with the sex chromosome. While the relative position of these mutations is known (5th chromosome), the genes and specific mutation causing the traits are not known. To address this, we developed a crossing scheme to isolate these mutations from the SIT line in the background of an inbred lab line . This cross allowed QTL analysis to identify regions of the genome that are strongly linked to these traits. To identify causative mutations, we performed whole genome sequencing of individual F4 flies resulting from this cross which included individuals segregating for the pupal color phenotype.