Quantification of arbuscular mycorrhizal fungi by quantitative polymerase chain reaction

Problem: Arbuscular mycorrhizal fungal (AMF) root colonization is traditionally measured by microscopy. Roots are first stained and then carefully mounted on a glass slide before examination on the microscope to identify and count fungal structures inside the roots. But microscopy is labor-intensive, and results depend on the observer.

Solution: Methods such as, quantitative polymerase chain reaction (qPCR) can improve quantification and analysis of AMF. This practice abstract provides a short protocol describing qPCR as a method to quantify AMF in plant roots.

Benefits: The qPCR presents a reliable alternative method to quantify AMF root colonization that is less operator-dependent than traditional microscopy and offers scalability to high-throughput analyses. Advantages over microscopy are: 

•          Larger datasets can be analysed/quantified more thoroughly, in a faster amount of time

•          qPCR provides more accurate and precise detection on amplified DNA sequences

•          qPCR is highly specific and sensitive as opposed to visual observations made using microscopy

•          why important for SolACE: to compare novel genotypes in their efficiency to form mycorrhizal symbiosis