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

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

背景：大黄鱼（Larimichthys crocea）与小黄鱼（Larimichthys polyactis）的种间杂交组合在生长性状上表现出杂种优势，但该现象背后的分子调控机制仍未阐明。DNA甲基化（DNA methylation）在调控基因表达、参与生长发育进程中发挥关键作用。本研究通过整合脑、肝、肌肉组织的转录组（transcriptome）与甲基化组（methylome）数据集，全面解析了复杂的基因调控过程。
结果：本研究共计分析了来自4个群体（LC为大黄鱼、LP为小黄鱼，LPC与LCP为二者的正反交杂交种）的36份组织样本的72组序列数据集，涵盖转录组数据与全基因组DNA甲基化组数据。我们阐明了这四个群体独特的基因表达模式，并探究了其与DNA甲基化的互作关系。研究揭示了多样的DNA甲基化谱特征，且相较于亲本株系，杂交大黄鱼的低甲基化差异区域（hypo-DMRs）数量更多。其中86%~92%的差异甲基化区域（DMRs）位于CG序列背景中。此外，多数DMRs分布于启动子区域、外显子及内含子区域。通过整合DNA甲基化与转录活性的关联分析，本研究共鉴定出1288个差异甲基化表达基因（DMEGs）。功能富集分析显示，多数DMEGs显著富集于蛋白质输出通路、蛋白酶体、萜类骨架生物合成、泛素介导的蛋白水解以及其他自噬通路等通路。本研究还筛选得到stat2、capn2、akt1、mTOR以及mef2aa等候选生长相关基因。其中，capn2、mTOR与akt1的表达水平与DNA甲基化水平呈正相关，而stat2与mef2aa的表达水平则呈负相关。上述结果表明，DNA甲基化模式的改变可通过调控这些基因的表达，进而赋予杂交大黄鱼生长优势。
结论：表观遗传修饰对生长杂种优势相关基因具有差异化调控作用。本研究数据为解析杂交大黄鱼生长相关的表观遗传与转录组改变奠定了基础，从而为阐明生长杂种优势的分子机制提供了初步见解。上述发现对以提升黄花鱼养殖产量为目标的育种工作具有重要指导意义。
总体设计：对大黄鱼、小黄鱼及其正反交杂交种的脑、肝、肌肉组织开展RNA-seq分析。