Context-dependent DNA methylation signatures in animal livestock [WGBS_Lvannamei]

DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting. Overall design: Overall 21 abdominal muscle samples from shrimp were analyzed. The samples were collected from four different locations.

DNA甲基化（DNA methylation）是一类重要的表观遗传修饰（epigenetic modification），广泛保守存在于动物基因组中。学界普遍认为，DNA甲基化模式可随环境变化呈现情境依赖性改变，包括响应动态调整的环境参数。然而，这一现象尚未在家养畜禽中开展系统性研究，而该方向在生物标志物开发领域具备重大潜力。基于此前对克隆纹螯虾（clonal marbled crayfish）种群特异性DNA甲基化的鉴定工作，本研究现已生成大量碱基分辨率的甲基化组（methylome）数据，用于分析位点特异性的DNA甲基化模式。本研究还描述了生物体从一种环境转移至另一环境时，表观遗传特征的时间依赖性转化过程。此外，我们证实了虾类具有养殖体系特异性的甲基化特征、鲑鱼具有河流栖息地特异性特征，以及家鸡具有养殖场特异性特征。综上，本研究为畜禽动物的表观遗传变异提供了详实的研究资源，并提出了通过表观遗传指纹（epigenetic fingerprinting）技术实现动物产品溯源的可能性。整体实验设计：共计分析了21份采自4个不同地点的虾类腹部肌肉样本。