title: Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.).
abstract: Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across all root types and highlighted the unique transcriptome of seminal roots. While functions in cell remodeling and cell wall formation were prominent in primary and crown roots, stress-related genes and transcriptional regulators were over-represented in seminal roots, suggesting functional specialization of the different root types. Dynamic expression of lignin biosynthesis genes and histochemical staining suggested diversification of cell wall lignification among the three root types. Our findings highlight a cost-efficient anatomical structure and a unique expression profile of seminal roots of the maize inbred line B73 different from primary and crown roots.
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany.
authors.forename: Huanhuan
authors.identifier: http://orcid.org/0000-0003-1419-7775
authors.initials: H
authors.lastname: Tai
authors.affiliation: Experimental Medicine and Therapy Research, University of Regensburg, D-93053 Regensburg, Germany.
authors.forename: Xin
authors.initials: X
authors.lastname: Lu
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany.
authors.forename: Nina
authors.identifier: http://orcid.org/0000-0003-0776-4890
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.identifier: http://orcid.org/0000-0001-6699-9441
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.identifier: http://orcid.org/0000-0001-6465-2882
authors.initials: A
authors.lastname: Paschold
authors.affiliation: Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Lithio
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.identifier: http://orcid.org/0000-0002-5155-0884
authors.initials: F
authors.lastname: Hochholdinger
mesh_terms: D018517:Plant Roots / Q000033:anatomy & histology / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D003313:Zea mays / Q000033:anatomy & histology* / Q000235:genetics*
chemical_list: D018749:RNA, Plant
keywords: Crown root; RNA-seq; Zea mays.; primary root; root type; seminal root; transcriptome