Quantification of Arbuscular Mycorrhizal Symbiosis by Molecular and Gene Expression Analysis (qRT-PCR)

Arbuscular mycorrhizas (AMs) represent one of the most widespread and extensively studied symbiotic associations between plants and beneficial microorganisms. Over 80% of terrestrial plant species, including the majority of agricultural and horticultural crops, are capable of establishing this mutualistic relationship with arbuscular mycorrhizal fungi (AMF). Through this symbiosis, the fungus aids the plant in the uptake of water and mineral nutrients, particularly under stress conditions. Beyond nutrient acquisition, AM symbiosis also influences key ecological and agronomic traits, including plant architecture, flowering, fruit quality, and tolerance to both biotic and abiotic stresses.As such, AMF hold significant potential as biofertilizers and bioprotective agents within sustainable agriculture. However, to fully leverage these benefits, a well-established and functional symbiosis is essential.Accurate quantification of AM colonization is thus crucial not only for research purposes, but also from an agronomic applications. In this context, gene expression analysis emerges as a powerful tool in biological research. In AM symbiosis, the expression patterns of specific genes provide insight into underlying regulatory networks and offer information on the extent and effectiveness of nutrient and water acquisition by the plant. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is particularly valuable for profiling a wide range of actively expressed genes, providing a molecular snapshot of the plant's physiological state. Nonetheless, to accurately identify expressed genes differentially, it is essential to implement appropriate controls that minimize nonspecific variation stemming from technical factors. In this chapter, we outline several histological and molecular methodologies for the accurate quantification and analysis of AM colonization in plant roots.