A pilot study to elucidate effects of artificial selection by size on the zebrafish (Danio rerio) fast skeletal muscle transcriptome.

Fish size is a complex trait determined by the interaction of environmental and genetic factors. While evidence exists that fish final length and size are partially determined by muscle fibre structure. However, the molecular basis behind final body size and muscle fibre composition remains yet to be fully understood. Here we use the fish model zebrafish (Danio rerio) to explore the molecular mechanisms involved in muscle fibre number, muscle growth and their role on animal size determination. In order to do so, we used two lines of zebrafish artificially selected by Amaral and Johnston 2012 for body length to obtain large (L) and small (S) genetic lineages. After selection animals from the L-lineage were significantly larger than individuals from the S-lineage (+6.6%, +6.7% and + 5.5% for standard, total and fork lengths) and had larger and higher number of muscle fibres (+15% and + 24% on average fibre area and fibre number respectively) while individuals from S-lineage showed a higher fibre density (+17%). RNAseq analysis on fast skeletal muscle revealed differences in gene expression, splice variants (SV) abundance and single nucleotide polymorphism (SNPs) retention between lineages, indicating the complexity of the molecular processes involved in the determination of the trait. We found that animals from the L-lineage showed an enrichment in genes related to the dystroglycan complex (GO:0016011) while genes related to the proteasome (GO:0022624), sarcomere (GO:0030017), muscle homeostasis (GO:0046716) and response to stress (GO:0006950) were enriched on the S-lineage. At individual gene level we also found differences in expression, SV or/and SNPs retention for some key genes involved in muscle development such as mef2ca, mef2cb, stac3, map14a and components of the circadian network (per1a, per1b, per3 and cry2b). These preliminary results provide an initial insight of the molecular changes induced by artificial selection for size, that could aid future studies related to determination of fish growth.