Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi

Abstract Arbuscular mycorrhiza fungi (AMF) are beneficial soil that can promote the growth of their host plants. Accurate quantification AMF in plant roots is important because level colonization often indicative activity these fungi. Root traditionally measured with microscopy methods which visualize fungal structures inside roots. Microscopy labor-intensive, and results depend on observer. In this study, we present a relative qPCR method to quantify normalized signal gene. First, validated primer pair AMG1F AM1 silico, show primers cover most species without amplifying DNA. Next, compared traditional based greenhouse experiment Petunia plants ranged from very high low levels root colonization. Finally, by sequencing amplicons MiSeq, experimentally confirmed excludes DNA while mostly AMF. Most importantly, our approach was capable discriminating quantitative differences it strongly correlated (Spearman Rho = 0.875) quantifications microscopy. provide balanced discussion about strengths weaknesses methods. conclusion, tested presents reliable alternative less operator-dependent than offers scalability high-throughput analyses.