Transcriptome and DNA methylation analyses provide insight into the heterosis of growth-related traits in hybrid yellow croaker

• DOI: 10.1186/s12864-025-11248-y
• Publication Date: 2025-02-12T16:44:16Z
• Authors: Dan-Dan Guo; Feng Liu; Qing-Ping Xie; Ting Ye; Fu-Liang Wei; Bao-Long Niu; Bao Lou
• Keywords: Larimichthys polyactis; DNA methylation; Growth trait; Genetics; QH426-470; Larimichthys crocea; Transcriptome; Hybrid yellow croaker; TP248.13-248.65; Biotechnology

Interspecific hybrid combinations of Larimichthys crocea × polyactis exhibit heterosis in terms growth traits; however, the molecular regulatory mechanism underlying this phenomenon remains unclear. DNA methylation plays a pivotal role regulating gene expression and is involved development processes. In study, we comprehensively investigated intricate processes by integrating transcriptome methylome datasets from brain, liver, muscle tissues. We analyzed total 72 sequence datasets, including genome-wide data, 36 tissue samples using LC, LP, LPC LCP. elucidated distinct patterns these four populations examined their interactions with methylation. Our findings revealed diverse profiles demonstrated greater number hypo-DMRs yellow croakers than parental lines. The majority (86 ~ 92%) DMRs were observed within CG context. Moreover, found that most located promoter regions as well exons introns. A 1288 DMEGs identified through correlation analysis between transcriptional activity. Functional enrichment significantly enriched pathways related to protein export pathway, proteasome, terpenoid backbone biosynthesis, ubiquitin-mediated proteolysis, autophagy-other pathway. Furthermore, screened candidate growth-related genes, such stat2, capn2, akt1, mTOR, mef2aa. Among these, levels akt1 exhibited positive levels, whereas stat2 mef2aa showed negative correlation. These suggest alterations may promote advantages croaker modulating genes. Epigenetic changes exert influences on genes heterosis. presented data establish foundation for comprehending epigenetic transcriptomic croaker, thereby providing preliminary insights into mechanisms have significant implications breeding programs aimed at enhancing production.