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Molecular variability of a Minnesota population of Phoma medicaginis var. medicaginis, the causal agent of spring black stem and leaf spot of alfalfa

Spring black stem and leaf spot of alfalfa (Medicago sativa) caused by Phoma medicaginis var. medicaginis is an important disease of alfalfa in temperate regions of the United States, causing yield losses and decreasing forage quality. Isolates of the fungus vary in morphological and cultural characteristics, as well as aggressiveness on alfalfa. The sequence of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (rDNA) and amplified fragment length polymorphism (AFLP) fingerprinting were used to characterize the diversity of P. medicaginis var. medicaginis isolates collected from leaves and stems of alfalfa plants from northern and southern areas of Minnesota. Sequences of the ITS1-5.8S-ITS2 regions of the rDNA repeats from 14 isolates were highly conserved. AFLP analysis of 121 isolates with eight primer pair combinations revealed a moderate amount of variation as measured by the Dice coefficient (55%) and a gene diversity index of H = 0.23. Molecular polymorphisms were not correlated with geographic locations or plant organs from which the isolates were isolated. Analysis of molecular variance tests revealed a very low level of population subdivision between northern and southern isolates (FST = 0.02) and between isolates collected from leaves and stems (FST = 0.01). AFLP fingerprinting was successful in detecting polymorphisms among P. medicaginis var. medicaginis isolates, whereas the utility of ITS region may be restricted to taxonomic or phylogenetic studies.