title: Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi.
abstract: Root systems consist of different root types (RTs) with distinct developmental and functional characteristics. RTs may be individually reprogrammed in response to their microenvironment to maximize adaptive plasticity. Molecular understanding of such specific remodeling--although crucial for crop improvement--is limited. Here, RT-specific transcriptomes of adult rice crown, large and fine lateral roots were assessed, revealing molecular evidence for functional diversity among individual RTs. Of the three rice RTs, crown roots displayed a significant enrichment of transcripts associated with phytohormones and secondary cell wall (SCW) metabolism, whereas lateral RTs showed a greater accumulation of transcripts related to mineral transport. In nature, arbuscular mycorrhizal (AM) symbiosis represents the default state of most root systems and is known to modify root system architecture. Rice RTs become heterogeneously colonized by AM fungi, with large laterals preferentially entering into the association. However, RT-specific transcriptional responses to AM symbiosis were quantitatively most pronounced for crown roots despite their modest physical engagement in the interaction. Furthermore, colonized crown roots adopted an expression profile more related to mycorrhizal large lateral than to noncolonized crown roots, suggesting a fundamental reprogramming of crown root character. Among these changes, a significant reduction in SCW transcripts was observed that was correlated with an alteration of SCW composition as determined by mass spectrometry. The combined change in SCW, hormone- and transport-related transcript profiles across the RTs indicates a previously overlooked switch of functional relationships among RTs during AM symbiosis, with a potential impact on root system architecture and functioning.
authors.affiliation: Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland; Faculty of Biology, Genetics, University of Munich, 82152 Martinsried, Germany; caroline.gutjahr@lmu.de up220@cam.ac.uk.
authors.forename: Caroline
authors.initials: C
authors.lastname: Gutjahr
authors.affiliation: Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland; Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), 36821 Irapuato, Guanajuato, Mexico;
authors.forename: Ruairidh J H
authors.initials: RJ
authors.lastname: Sawers
authors.affiliation: School of Pharmaceutical Sciences, Phytochemistry and Bioactive Natural Products, University of Lausanne and University of Geneva, CH-1211 Geneva 4, Switzerland;
authors.forename: Guillaume
authors.initials: G
authors.lastname: Marti
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), 36821 Irapuato, Guanajuato, Mexico;
authors.forename: Liliana
authors.initials: L
authors.lastname: Andrés-Hernández
authors.affiliation: Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland; Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom; and.
authors.forename: Shu-Yi
authors.initials: SY
authors.lastname: Yang
authors.affiliation: Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland;
authors.forename: Leonardo
authors.initials: L
authors.lastname: Casieri
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
authors.forename: Herbert
authors.initials: H
authors.lastname: Angliker
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Oakeley
authors.affiliation: School of Pharmaceutical Sciences, Phytochemistry and Bioactive Natural Products, University of Lausanne and University of Geneva, CH-1211 Geneva 4, Switzerland;
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Wolfender
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), 36821 Irapuato, Guanajuato, Mexico;
authors.forename: Cei
authors.initials: C
authors.lastname: Abreu-Goodger
authors.affiliation: Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland; Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom; and caroline.gutjahr@lmu.de up220@cam.ac.uk.
authors.forename: Uta
authors.initials: U
authors.lastname: Paszkowski
mesh_terms: D002473:Cell Wall / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D055137:Glomeromycota / Q000502:physiology*; D062385:Hydroxybenzoates / Q000378:metabolism; D008903:Minerals / Q000378:metabolism; D038821:Mycorrhizae / Q000502:physiology*; D012275:Oryza / Q000235:genetics* / Q000382:microbiology* / Q000502:physiology; D010937:Plant Growth Regulators / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000382:microbiology / Q000502:physiology; D013489:Suppression, Genetic; D013559:Symbiosis / Q000235:genetics / Q000502:physiology; D059467:Transcriptome
chemical_list: D062385:Hydroxybenzoates; D008903:Minerals; D010937:Plant Growth Regulators; C017616:phenolic acid
keywords: arbuscular mycorrhizal symbiosis; rice; root system; secondary cell wall; transcriptome