DNA methylation profiling and transcriptome sequencing reveal the molecular mechanism of the high-carbohydrate diet on muscle growth of grass carp (Ctenopharyngodon idella)

To investigate the effects of a high-carbohydrate (HC) diet on the growth, serum biochemistry, and DNA methylation and gene transcription profiles of muscle tissue of grass carp (Ctenopharyngodon idella), fish with initial body weight (27.87 ± 0.40) g were fed with a control diet (CON, containing 330 g kg−1 carbohydrate) and an HC diet (containing 490 g kg−1 carbohydrate) for 8 weeks. The results showed that the HC diet had side-effects on muscle growth and health, and caused excessive fat accumulation in the tissues of grass carp. A total of 3135 differentially methylated regions (DMRs) and 530 differentially expressed genes (DEGs) in muscle were screened by bisulfite sequencing and transcriptome sequencing analysis. Twenty-seven DMRs were negatively correlated with DEGs, and eleven DMRs were located in the promoters of DEGs. The methylation level of promoter regions of seven target genes decreased and their transcription levels increased, including FOX protein, diacylglycerol kinase (DGKZ), proto-myosin regulatory protein (tmod1), Notch2, DnaJ homolog (dnajc1), von Willebrand factor D and EGF domains (vwde), and zgc:77838. The methylation level of promoter regions of four target genes increased and their transcription levels decreased, including epidermal growth factor-like domain 6 (EGFL6), estrogen receptor alpha (Erα), cohesin subunit SA-1-like, and LOC795573. These eleven essential genes were mainly involved in GO terms containing cell differentiation, muscle contraction, lipid phosphorylation, PI3K/Akt signaling pathway, and Notch signaling pathway. This study provides a new research direction for the molecular mechanism of the HC diet on muscle growth of grass carp.