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Series GSE3490 Query DataSets for GSE3490
Status Public on Oct 22, 2005
Title Comparison of Transcript Profiles in Wild-type and o2 Maize Endosperm in Different Genetic Backgrounds
Organism Zea mays
Experiment type Expression profiling by array
Summary Mutations in the Opaque2 (O2) gene of maize (Zea Mays L.) improve the nutritional value of maize by reducing the level of zeins in the kernel. The phenotype of o2 grain is controlled by many modifier genes and is therefore strongly dependent on the genetic background. We sought to distinguish between two hypotheses to explain differences in phenotypic severity: 1. Differences in phenotypic severity are due to genotype specific differentially expressed genes and 2. Differences in phenotypic severity are due to differences in the degree of differential expression of a set of differentially expressed genes. Eight pairs of inbred lines and their o2 counterparts were characterized for phenotypes controlled by o2 (lysine content, kernel density, seed weight and shoot to root ratio of seedlings). The inbred line B46 was identified as having severe o2 effects while the line M14 was identified as having minimal o2 effects. Transcripts that were differentially expressed between the wild-type and o2 versions of these two lines were identified by microarray hybridization. While genotype specific differentially expressed transcripts were identified, many transcripts were identified with reduced degree of differential expression in M14 relative to B46. Thus, a combination of genotype specific transcripts and degree of differential expression of transcripts can explain differences in phenotypic severity in these two genetic backgrounds. To identify the transcripts most likely to be differentially expressed in a given genetic background, we used RNA from eight genotype pools in microarray hybridization. By averaging across genotypes in this way, genotype-specific changes are minimized.
Keywords: Genetic modification
 
Overall design A triplicate dye-swap design was used for each comparison (B46/o2, M14/o2, and mixed w.t./mixed o2). For each single dye-swap experiment two slides were used. Three pairs of independent samples were used in each comparison.
 
Contributor(s) Jia H, Nettleton D, Vazquez-Carrillo G, Peterson J, Scott P
Citation Jia, H., D. Nettleton, J.M. Peterson, G. Vazquez-Carrillo, J.-L. Jannink, and M.P. Scott. 2007. Comparison of Transcript Profiles in Wild-Type and o2 Maize Endosperm in Different Genetic Backgrounds. Crop Sci 47:S-45-59.
Submission date Oct 20, 2005
Last update date Mar 16, 2012
Contact name Hongwu Jia
E-mail(s) jiahongwu@yahoo.com
Organization name Iowa State University
Department Agronomy
Lab Paul Scott
Street address 1407 Agronomy Hall
City Ames
State/province IA
ZIP/Postal code 50010
Country USA
 
Platforms (1)
GPL2984 Maize Unigene 1-02-01
Samples (18)
GSM78575 B46/o2 dye-swap rep1 array1
GSM78597 B46/o2 dye-swap rep1 array2
GSM78598 B46/o2 dye-swap rep2 array1
Relations
BioProject PRJNA93311

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