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Series GSE29132 Query DataSets for GSE29132
Status Public on May 09, 2011
Title Corn under weed, low nitrogen, and shade stress
Organism Zea mays
Experiment type Expression profiling by array
Summary This study was designed to identify changes in gene expression when corn was placed under various related stresses including being grown with a competing weed (canola) to the V4 or V8 stage, or when 40% shade cloth was present to the V4 or V8 stage, or under low nitrogen (no added nitrogen fertilizer), or under weed/shade free fertilized control conditions. In all 5 treatments and the control, samples were harvested at V8.
Mechanisms underlying early season weed stress on crop growth are not well described. Corn vegetative growth and development, yield, and gene expression response to nitrogen (N), light (40% shade), and weed stresses were compared with the response of nonstressed plants. Vegetative parameters, including leaf area and biomass, were measured from V2 toV12 corn stages. Transcriptome (2008) or quantitative Polymerase Chain Reaction (q PCR) (2008/09) analyses examined differential gene expression in stressed versus nonstressed corn at V8. Vegetative parameters were impacted minimally by N stress although grain yield was 40% lower. Shade, present until V2, reduced biomass and leaf area > 50% at V2 and, at V12, recovering plants remained smaller than nonstressed plants. Grain yields of shade-stressed plants were similar to nonstressed controls, unless shade remained until V8. Growth and yield reductions due to weed stress in 2008 were observed when weeds remained until V6. In 2009, weed stress at V2 reduced vegetative growth, and weed stress until V4 or later reduced yield. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than to nonstressed or low N stressed tissues. Weed-stressed corn had 630 differentially expressed genes compared with the nonstressed control. Of these genes, 259 differed and 82 were shared with shade-stressed plants. Corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants. Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Although shade and weed stress clustered most tightly together, only three ontologies were shared by these stresses, O-methyltransferase activity (lignification processes), Poly U binding activity (post-transcriptional gene regulation), and stomatal movement. Based on both morphologic and genomic observations, results suggest that shade, N, and weed stresses to corn are regulated by both different and overlapping mechanisms.
 
Overall design three biological replicates for each treatment and the control were collected and the resulting labeled cDNA was hybridized to the 46,000-element maize microarray chip developed by the University of Arizona using their protocol (International Microarray Workshop Handbook, 2009Gardiner et al. 2005). The hybridization scheme was a dual hybridization using a rolling circle balanced dye swap design. Thus we had thre biological replicates for each growth condition amd two technical replicates for each biological sample.
 
Contributor(s) Moralis J, Hansen S, Horvath D, Clay D, Clay S
Citation Janet Moriles, Stephanie Hansen, David P. Horvath, Graig Reicks, David E. Clay, and Sharon A. Clay (2012) Microarray and Growth Analyses Identify Differences and Similarities of Early Corn Response to Weeds, Shade, and Nitrogen Stress. Weed Science: April-June 2012, Vol. 60, No. 2, pp. 158-166. doi: http://dx.doi.org/10.1614/WS-D-11-00090.1
Submission date May 08, 2011
Last update date Sep 21, 2012
Contact name David Horvath
E-mail(s) david.horvath@ars.usda.gov
Phone 701-239-1255
Organization name US Dept. Agriculture
Department Agr. Research Service
Lab Bioscience Research Lab
Street address 1605 Albrecht Blvd
City Fargo
State/province ND
ZIP/Postal code 58105
Country USA
 
Platforms (1)
GPL6438 Maize oligonucleotide array 46K version
Samples (36)
GSM721235 shade removed at V8 rep 1 and control rep 1 [Alexa 555]
GSM721236 canola removed at V4 rep 1 and low nitrogen rep 1 [Alexa 555]
GSM721237 canola removed at V8 rep 1 and Canola removed at V4 rep 1 [Alexa 555]
Relations
BioProject PRJNA140449

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE29132_RAW.tar 230.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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