title: Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit.
abstract: Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, <3% (50 genes) of water deficit-responsive genes (1915) were consistently regulated in all tissues, while >75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the cortex of the mature root zone and in the elongation zone. The most prominent functional categories among differentially expressed genes in all tissues were 'transcriptional regulation' and 'hormone metabolism', indicating global reprogramming of cellular metabolism as an adaptation to water deficit. Additionally, the most significant transcriptomic changes in the root tip were associated with cell wall reorganization, leading to continued root growth despite water deficit conditions. This study provides insight into tissue-specific water deficit responses and will be a resource for future genetic analyses and breeding strategies to develop more drought-tolerant maize cultivars.
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany.
authors.forename: Nina
authors.initials: N
authors.lastname: Opitz
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany.
authors.forename: Caroline
authors.initials: C
authors.lastname: Marcon
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Paschold
authors.affiliation: Institute for Crop Science, Biostatistics Unit, University of Hohenheim, D-70599 Stuttgart, Germany.
authors.forename: Waqas Ahmed
authors.initials: WA
authors.lastname: Malik
authors.affiliation: Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Lithio
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany.
authors.forename: Ronny
authors.initials: R
authors.lastname: Brandt
authors.affiliation: Institute for Crop Science, Biostatistics Unit, University of Hohenheim, D-70599 Stuttgart, Germany.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Piepho
authors.affiliation: Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Nettleton
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany hochholdinger@uni-bonn.de.
authors.forename: Frank
authors.initials: F
authors.lastname: Hochholdinger
mesh_terms: D055864:Droughts; D020869:Gene Expression Profiling; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000378:metabolism*; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014867:Water / Q000378:metabolism*; D003313:Zea mays / Q000235:genetics / Q000502:physiology*
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant; D014867:Water
keywords: Drought; RNA-Sequencing (RNA-Seq); expression pattern; low water potential; maize; primary root; tissue specificity; transcriptome; water deficit.