Combined genetic and transcriptomic analysis reveals three major signalling pathways activated by Myc-LCOs in Medicago truncatula

• Published in: The New phytologist 2015-10, Vol.208 (1), p.224-240
• Main Authors: Camps, Céline, Jardinaud, Marie‐Françoise, Rengel, David, Carrère, Sébastien, Hervé, Christine, Debellé, Frédéric, Gamas, Pascal, Bensmihen, Sandra, Gough, Clare
• Format: Article
• Language: English
• Subjects: Alfalfa; arbuscular mycorrhizal (AM) fungi; Arbuscular mycorrhizas; Chitin - analogs & derivatives; Chitin - metabolism; Chitin - pharmacology; common symbiotic signalling pathway (CSSP); Fungal Polysaccharides - metabolism; Fungal Polysaccharides - pharmacology; Fungi; Fungi - metabolism; Gene expression regulation; Gene Expression Regulation, Plant - drug effects; Gene sequencing; Generalized linear models; Genes; Genes, Plant; Genetic analysis; Genetic control; Genomes; Genotype; Genotypes; Identification; Life Sciences; lipo‐chitooligosaccharides (LCOs); Medicago truncatula; Medicago truncatula - drug effects; Medicago truncatula - genetics; Medicago truncatula - metabolism; Medicago truncatula - microbiology; Mutants; Mutation; Myc protein; Mycorrhizae; Nod factors; Nodulation; Nucleic acids; Plant cells; Plant physiology; Plant Proteins - genetics; Plant Proteins - metabolism; Plant roots; Plant Roots - drug effects; Plant Roots - metabolism; Plant Roots - microbiology; Plants; Ribonucleic acid; RNA; RNA sequencing; Sequence Analysis, RNA; Signal Transduction; Signaling; Statistical models; Symbionts; Symbiosis; Symbiosis - genetics; Transcription; Transcription factors; Transcription Factors - metabolism; Transcriptome - drug effects; Transcriptomics; Vegetal Biology
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.13427

Myc-LCOs are newly identified symbiotic signals produced by arbuscular mycorrhizal (AM) fungi. Like rhizobial Nod factors, they are lipo-chitooligosaccharides that activate the common symbiotic signalling pathway (CSSP) in plants. To increase our limited understanding of the roles of Myc-LCOs we aimed to analyse Myc-LCO-induced transcriptional changes and their genetic control. Whole genome RNA sequencing (RNA-seq) was performed on roots of Medicago truncatula wild-type plants, and dmi3 and nsp1 symbiotic mutants affected in nodulation and mycorrhizal signalling. Plants were treated separately with the two major types of Myc-LCOs, sulphated and nonsulphated. Generalized linear model analysis identified 2201 differentially expressed genes and classified them according to genotype and/or treatment effects. Three genetic pathways for Myc-LCO-regulation of transcriptomic reprogramming were highlighted: DMI3- and NSP1-dependent; DMI3-dependent and NSP1-independent; and DMI3- and NSP1-independent. Comprehensive analysis revealed overlaps with previous AM studies, and highlighted certain functions, especially signalling components and transcription factors. These data provide new insights into mycorrhizal signalling mechanisms, supporting a role for NSP1, and specialisation for NSP1-dependent and -independent pathways downstream of DMI3. Our data also indicate significant Myc-LCO-activated signalling upstream of DMI3 and/or parallel to the CSSP and some constitutive activity of the CSSP.