title: Transcription profile analyses identify genes and pathways central to root cap functions in maize.
abstract: Affymetrix GeneChips arrayed with about one-half (~23K) of the rice genes were used to profile gene transcription activity in three tissues comprising the maize root tip; the proximal meristem (PM), the quiescent center (QC), and the root cap (RC). Here we analyze the gene transcription profile of the RC, compared to both the PM and the QC, from three biological replicates. In the RC, a total of 669 genes were identified as being differentially upregulated, and 365 differentially downregulated. Real-time quantitative RT-PCR analysis was used to confirm upregulated genes in the RC. In addition, using the technique of laser microdissection (LMD) we localized upregulated gene expression to the lateral RC cells. Taken as a whole, transcription profile analyses revealed the upregulation in the maize RC of clusters of genes linked to major metabolic processes and pathways, including: (1) transport, both the export of carbohydrates and the uptake of nutrients; (2) sensing and responding to (often stressful) biotic and abiotic environmental stimuli; (3) integrating the responses of at least 3 major growth regulators (auxin, ethylene, jasmonic acid); (4) processing the large amount of carbohydrate transported into the RC. Although the profile data are derived using heterologous rice GeneChips, with about half of the total rice gene set, this study, nevertheless, provides a genomic scale characterization of the entire RC, and serves as a new platform from which to advance studies of the network of pathways operating in the maize RC.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
authors.forename: Keni
authors.initials: K
authors.lastname: Jiang
authors.forename: Shibo
authors.initials: S
authors.lastname: Zhang
authors.forename: Stanley
authors.initials: S
authors.lastname: Lee
authors.forename: George
authors.initials: G
authors.lastname: Tsai
authors.forename: Kyungpil
authors.initials: K
authors.lastname: Kim
authors.forename: Haiyan
authors.initials: H
authors.lastname: Huang
authors.forename: Charles
authors.initials: C
authors.lastname: Chilcott
authors.forename: Tong
authors.initials: T
authors.lastname: Zhu
authors.forename: Lewis J
authors.initials: LJ
authors.lastname: Feldman
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001692:Biological Transport; D050260:Carbohydrate Metabolism; D002241:Carbohydrates / Q000737:chemistry; D002462:Cell Membrane / Q000378:metabolism; D003517:Cyclopentanes / Q000378:metabolism; D018076:DNA, Complementary / Q000378:metabolism; D015536:Down-Regulation; D005030:Ethylenes / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D018506:Gene Expression Regulation, Plant; D006728:Hormones / Q000378:metabolism; D020407:Internet; D007834:Lasers; D042282:Microdissection; D008954:Models, Biological; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics; D054883:Oxylipins; D018521:Plant Physiological Phenomena; D018517:Plant Roots / Q000235:genetics*; D012313:RNA / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction; D013997:Time Factors; D014158:Transcription, Genetic; D015854:Up-Regulation; D003313:Zea mays / Q000235:genetics* / Q000502:physiology
chemical_list: D002241:Carbohydrates; D003517:Cyclopentanes; D018076:DNA, Complementary; D005030:Ethylenes; D006728:Hormones; D054883:Oxylipins; D012333:RNA, Messenger; D012313:RNA; C011006:jasmonic acid; C036216:ethylene