Epigenetic insights into cottonseed oil biosynthesis: strategies for crop enhancement

Abstract Epigenetic engineering is rapidly emerging as a transformative frontier for unlocking the untapped yield potential of cottonseed oil. This review highlights the role of epigenetic mechanisms, including DNA methylation, histone modifications, and small RNAs, in regulating pathways for oil accumulation in cotton. We discuss epigenomic findings that reveal tissue and developmental stage-specific patterns affecting oil biosynthesis, including distinct regulatory signatures in the embryo versus mitochondrial/nuclear compartments. The application of advanced tools, including CRISPR-based systems and RNA-directed DNA methylation, for precise epigenetic engineering is examined, alongside challenges such as off-target effects and regulatory considerations. Future directions should extend beyond promoter editing to incorporate the regulation of distal enhancer elements. Critical steps include generating high-resolution chromatin interaction maps from developing embryos/endosperms to identify candidate enhancers for key oil genes, which can then be manipulated using CRISPR-dCas9-based activators. Integrating this enhancer biology with non-transgenic approaches, such as pollen priming, bacteriophages and nanoparticle delivery, will be essential for practical applications. We propose a framework that leverages these strategies to address oil-protein trade-offs and develop a holistic epigenetic breeding approach, underscoring the transformative potential of epigenetics for sustainable cottonseed oil yield improvement.