title: Maize maintains growth in response to decreased nitrate supply through a highly dynamic and developmental stage-specific transcriptional response.
abstract: Elucidation of the gene networks underlying the response to N supply and demand will facilitate the improvement of the N uptake efficiency of plants. We undertook a transcriptomic analysis of maize to identify genes responding to both a non-growth-limiting decrease in NO3- provision and to development-based N demand changes at seven representative points across the life cycle. Gene co-expression networks were derived by cluster analysis of the transcript profiles. The majority of NO3--responsive transcription occurred at 11 (D11), 18 (D18) and 29 (D29) days after emergence, with differential expression predominating in the root at D11 and D29 and in the leaf at D18. A cluster of 98 probe sets was identified, the expression pattern of which is similar to that of the high-affinity NO3- transporter (NRT2) genes across the life cycle. The cluster is enriched with genes encoding enzymes and proteins of lipid metabolism and transport, respectively. These are candidate genes for the response of maize to N supply and demand. Only a few patterns of differential gene expression were observed over the entire life cycle; however, the composition of the classes of the genes differentially regulated at individual time points was unique, suggesting tightly controlled regulation of NO3--responsive gene expression.
authors.affiliation: Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.|School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Darren
authors.initials: D
authors.lastname: Plett
authors.affiliation: Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.|School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Ute
authors.initials: U
authors.lastname: Baumann
authors.affiliation: Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.|School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Andreas W
authors.initials: AW
authors.lastname: Schreiber
authors.affiliation: Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.|School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Luke
authors.initials: L
authors.lastname: Holtham
authors.affiliation: Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.|School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Elena
authors.initials: E
authors.lastname: Kalashyan
authors.affiliation: Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.|School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
authors.forename: John
authors.initials: J
authors.lastname: Toubia
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: John
authors.initials: J
authors.lastname: Nau
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: Mary
authors.initials: M
authors.lastname: Beatty
authors.affiliation: DuPont Pioneer, Wilmington, DE, USA.
authors.forename: Antoni
authors.initials: A
authors.lastname: Rafalski
authors.affiliation: DuPont Pioneer, Johnston, IA, USA.
authors.forename: Kanwarpal S
authors.initials: KS
authors.lastname: Dhugga
authors.affiliation: Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
authors.forename: Mark
authors.initials: M
authors.lastname: Tester
authors.affiliation: Australian Centre for Plant Functional Genomics, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.|School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Trevor
authors.initials: T
authors.lastname: Garnett
authors.affiliation: School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia.
authors.forename: Brent N
authors.initials: BN
authors.lastname: Kaiser
mesh_terms: D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects*; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D063990:Gene Ontology; D053263:Gene Regulatory Networks / Q000187:drug effects; D009566:Nitrates / Q000494:pharmacology*; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013997:Time Factors; D014158:Transcription, Genetic / Q000187:drug effects*; D003313:Zea mays / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development*
chemical_list: D009566:Nitrates; D012333:RNA, Messenger
keywords: N use efficiency; NRT2; gene cluster analysis; high-affinity nitrate transporter; lipid metabolism; microarray