The seed beetle Callosobruchus maculatus shows pronounced sexual dimorphism, with females being approximately twice the size of males. Due to the XY sex determination, the only genomic region exclusive to males is the Y chromosome, and past research has uncovered two segregating Y-haplotypes in the population that cause a variation in male body size. The goal of this project is to use differential expression analysis to better understand how the genetic variation on the Y chromosome causes the phenotypic variation we observe in the males, which could give insight on how male body size can be regulated independent of females in general. We have generated RNAseq data from three time points in late larval development (where individuals start to show their size differences) for both male haplotypes and females of the same population. Prototype-sequencing has found high rRNA contamination in the data, so we have decided to sequence at a greater depth than usual to ensure that after filtering the rRNA reads there is still enough mRNA data left to ensure sufficient statistical power for differential expression analysis. The planned workflow is to do trim the data, filter the rRNA contamination with a pre-existing custom reference library, map to an also pre-existing reference assembly and perform differential expression analysis. This project will contribute to work done in the larger storage project NAISS 2024/6-73.