Co-extraction of Small RNAs and Total RNA from Arbuscular Mycorrhizal Roots Using Laser Microdissection

Understanding gene expression at the cellular level is essential for dissecting plant-microbe interactions. Laser microdissection (LMD) is a powerful approach for isolating specific plant cell types without the need for molecular markers, enabling the recovery of nucleic acids from defined cellular populations. In plant systems, LMD has been widely applied to study cell-type-specific transcriptomes, including those involved in arbuscular mycorrhizal (AM) symbiosis, where cellular heterogeneity limits bulk tissue analyses. Recent evidence highlights the role of small RNAs (sRNAs) as key regulators of plant-microbe interactions, including cross-kingdom RNA interference. In this chapter, we describe a detailed LMD-based methodology for the co-extraction of sRNAs and mRNAs from AM-colonized root cells, enabling the characterization of plant and fungal sRNAs and the identification of their potential targets, thus providing a framework for studying cell-specific regulatory mechanisms in AM symbiosis.