Integrative Methylome and Transcriptome Analysis of DNA Methylation and Sex-Biased Gene Expression in Northern Pike (Esox lucius)

Abstract

Simple Summary Northern pike is an important fish species in aquaculture, with females growing significantly larger and faster than males. Understanding why females grow bigger could help farmers produce more female fish for market. In this study, we examined both the genetic activity (which genes are turned on or off) and the chemical modifications to DNA that control gene activity in female and male northern pike. We found that these DNA modifications, called methylation, work differently between the sexes. In females, certain regions of DNA that control gene activity were linked to higher gene expression, while this pattern was not seen in males. We identified 508 genes whose activity was associated with these DNA modifications, including 13 key candidate genes. Several important biological pathways involved in sex development were affected by these modifications. Our findings indicate that DNA methylation shows patterns that are linked to sex differentiation, and these patterns may also relate to how fast the fish grows, though this potential link to growth requires further investigation using growth-related data. This knowledge could eventually help aquaculture farmers develop strategies to raise more female northern pike, which grow larger and are more valuable for food production.