Molecular Markers for the Identification and Diversity Analysis of Arbuscular Mycorrhizal Fungi (AMF)

Abstract

Molecular markers are the fragments of DNA sequences associated with the genome that are used to identify particular DNA sequence. Markers are very much useful in the identification of microorganisms and in determining plant microbe interactions. This chapter deals with the molecular markers used in the diagnosis of Arbuscular Mycorrhizal Fungi (AMF). Conventional methods of AMF identification and classification have been done with the spore characters such as size, colour, spore wall layer, spore-hyphal attachment and spore germination. However, the problem associated with the availability of well-trained taxonomist and the difficulties in distinguishing the minor differences in the spore wall layers mislead the identification. Nowadays, with the explosive growth of genetic research and marker development improved our knowledge on AMF identity, diversity, role in the ecosystem functioning and plant growth promotion. Molecular markers may be grouped into non-PCR and PCR based approaches. Each of them has their advantages and disadvantages. Therefore, different markers are needed for the identification of AMF. It has been reported that combining two or more genetic markers to identify or classify AMF are more reliable than using single marker. Many molecular markers are biased, as some of the primers used to detect only parts of the community and the level of taxonomic resolution in most cases are uncertain. Species-level community analyses based on rDNA regions should be feasible, but no single molecular marker or DNA barcode is yet suitable for species-level resolution of all AMF genera. Discovery of new molecular markers (DNA or non-DNA based), in the field of AMF identification and plant-AMF interactions are very much desirable.