Epigenetic patterns associated with size-at-age relationships in the Largemouth Bass complex

Abstract Objective Management efforts for Largemouth Bass Micropterus nigricans, Florida Bass M. salmoides, and resulting hybrid fisheries (hereafter, referred to as the Largemouth Bass complex [LBc]) include the production of robust individuals for commercial and recreational purposes. Epigenetic signals such as cytosine DNA methylation patterns that regulate gene activity and are associated with physiological acclimation have received attention as potential biomarkers of organismal health and growth. Given the complex interactions between sexual dimorphism and environmental variation, identifying molecular signals that predict growth and resulting size-at-age patterns in the LBc would be crucial for stocking efforts aimed at maintaining trophy fisheries. Methods Combined with total lengths, fin clips, and corresponding otolith samples collected by the Texas Parks and Wildlife Department, LBc samples were also collected from Tennessee water bodies proximal to the Oak Ridge National Laboratory in 2023 and 2024, yielding a combined data set of 138 individuals. Individual ages of all bass were estimated using otolith analysis. DNA methylation patterns from extracted fin clip DNA were subsequently assessed, using a final data set containing 2,138,275 cytosine loci from 77 Texas LBc samples (38 males and 39 females) and 61 Tennessee LBc samples (23 males and 38 females). Both the global average DNA methylation and loci-specific patterns that varied with size at age (identified from residuals of a linear mixed-effects model with season as a random effect) were compared. Identified regions were annotated according to cytosine density as well as proximity to genes. To identify physiological patterns impacted by differential methylation signals, enrichment of gene pathways from lists of genes associated with significantly different loci was assessed using the KEGG: Kyoto Encyclopedia of Genes and Genomes functional pathway database. Results Global average DNA methylation decreased as size at age increased in LBc members. We identified 8,247 loci whose methylation states are significantly associated with size-at-age relationships in members of the LBc, as well as 10,963 and 119 loci associated with sexual and environmental factors, respectively. Enrichment of physiological pathways such as MAPK, calcium, mTOR, Wnt, ErbB, GnRH, phosphatidylinositol, and insulin signaling was identified as being impacted by differential methylation of these loci, which corroborates prior results for bass and other teleost species. Conclusions We identified the role of epigenetic patterns on the growth and resulting size-at-age relationships in members of the LBc. Targeting identified regions for assay development in further work may provide valuable resources for aquaculture practices and the management of successful trophy bass fisheries.