E-GEOD-47665 - Comprehensive analysis of genic male sterility-related genes in Brassica rapa using Brassica rapa 300k microarray v2.0

Status
Released on 22 October 2013, last updated on 3 May 2014
Organism
Brassica rapa subsp. pekinensis
Samples (14)
Array (1)
Protocols (6)
Description
To identify genes associated with genic male sterility (GMS) that could be useful for hybrid breeding in Chinese cabbage (Brassica rapa ssp. pekinensis), floral bud transcriptome analysis was carried out using a B. rapa microarray with 300,000 probes (Br300K). Among 47,548 clones deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region, a total of 10,622 genes were differentially expressed between fertile and sterile floral buds; 4,774 and 5,848 genes were up-regulated over 2-fold in fertile and sterile buds, respectively. However, the expression of 1,413 and 199 genes showed fertile and sterile bud-specific features, respectively. Genes expressed specifically in fertile buds, possibly GMS-related genes, included homologs of several Arabidopsis male sterility-related genes, genes associated with the cell wall and synthesis of its surface proteins, pollen wall and coat components, signaling components, and nutrient supplies. However, most early genes for pollen development, genes for primexine and callose formation, and genes for pollen maturation and anther dehiscence showed no difference in expression between fertile and sterile buds. Some of the known genes associated with Arabidopsis pollen development showed similar expression patterns to those seen in this study, while others did not. BrbHLH89 and BrMYP99 are putative GMS genes. Additionally, 17 novel genes identified only in B. rapa were specifically and highly expressed only in fertile buds, implying the possible involvement in male fertility. All data suggest that Chinese cabbage GMS might be controlled by genes acting in post-meiotic tapetal development that are different from those known to be associated with Arabidopsis male sterility. A total of 14 chips were used for the microarray experiment. Experiments were performed with two biological replicates.
Experiment type
transcription profiling by array 
Contacts
Yeon-Ki Kim <kim750a11@gmail.com>, Dong Xiangshu, Yoon K Hur
Citation
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-47665.idf.txt
Sample and data relationshipE-GEOD-47665.sdrf.txt
Raw data (2)E-GEOD-47665.raw.1.zip, E-GEOD-47665.raw.2.zip
Processed data (1)E-GEOD-47665.processed.1.zip
Array designA-GEOD-17248.adf.txt
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