Controlled Assays for Phenotyping the Effects of Strigolactone-Like Molecules on Arbuscular Mycorrhiza Development

Methods Mol Biol. 2021:2309:157-177. doi: 10.1007/978-1-0716-1429-7_13.


Arbuscular mycorrhiza is an ancient symbiosis between most land plants and fungi of the Glomeromycotina, in which the fungi provide mineral nutrients to the plant in exchange for photosynthetically fixed organic carbon. Strigolactones are important signals promoting this symbiosis, as they are exuded by plant roots into the rhizosphere to stimulate activity of the fungi. In addition, the plant karrikin signaling pathway is required for root colonization. Understanding the molecular mechanisms underpinning root colonization by AM fungi, requires the use of plant mutants as well as treatments with different environmental conditions or signaling compounds in standardized cocultivation systems to allow for reproducible root colonization phenotypes. Here we describe how we set up and quantify arbuscular mycorrhiza in the model plants Lotus japonicus and Brachypodium distachyon under controlled conditions. We illustrate a setup for open pot culture as well as for closed plant tissue culture (PTC) containers, for plant-fungal cocultivation in sterile conditions. Furthermore, we explain how to harvest, store, stain, and image AM roots for phenotyping and quantification of different AM structures.

Keywords: Arbuscular mycorrhiza; Brachypodium distachyon; Ink staining; Inoculum; Lotus japonicus; Root length colonization; WGA staining.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Assay*
  • Brachypodium / growth & development
  • Brachypodium / microbiology*
  • Heterocyclic Compounds, 3-Ring / pharmacology*
  • Lactones / pharmacology*
  • Lotus / growth & development
  • Lotus / microbiology*
  • Mycorrhizae / drug effects*
  • Mycorrhizae / growth & development
  • Phenotype
  • Plant Growth Regulators / pharmacology*
  • Plant Roots / growth & development
  • Plant Roots / microbiology*


  • GR24 strigolactone
  • Heterocyclic Compounds, 3-Ring
  • Lactones
  • Plant Growth Regulators