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E-GEOD-43088 - Genome-wide expression of transcriptomes under waterlogging stress condition in subtropical maize

Status
Released on 14 August 2013, last updated on 2 June 2014
Organism
Zea mays
Samples (16)
Array (1)
Protocols (7)
Description
Genome-wide transcriptome analysis was performed to understand the expression pattern of transcriptomes in tolerant and susceptible subtropical maize genotypes under waterlogging stress condition. Waterlogging stress causes yield reduction in maize (Zea mays). It is important to dissect the genetic circuits that underlie the plant responses to waterlogging. So, the experiment was designed with the following objectives: to understand the expression pattern of transcriptomes in the tolerant and the susceptible genotypes under waterlogging stress; to identify DEGs functioning in important pathways underlying adaptive traits; to co-map bin locations of the transcriptomes with already known QTLs for waterlogging and find synteny with other species; and to generate gene co-expression networks to study cohorts of genes expressed together in modules and functional cluster, while comparing the two genotypes. Two tropical maize (Zea mays L.) inbred lines, HKI1105 (tolerant) and V-372 (susceptible), were used for our experiment. The genotypes were sown in plastic pots filled with loam soil with sandy texture. The plants were watered daily to soil capacity until the application of stress at 28 days after sowing. To impose waterlogging condition, the perforation in the bottom of the pots (35 cm in height) was sealed and the stress treatment was given by watering the pots (5 cm standing water) for seven continuous days. To allow for recovery from stress, the perforations of the pots were unsealed for proper drainage of excess water. The root samples from both genotypes were collected on the 28th, 32nd, 35th and 42nd day after sowing, which represented control, moderate stress, severe stress and post-stress recovery stages, respectively. Two biological replications were used for each comparison.
Experiment type
transcription profiling by array 
Contacts
Citation
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-43088.idf.txt
Sample and data relationshipE-GEOD-43088.sdrf.txt
Raw data (1)E-GEOD-43088.raw.1.zip
Processed data (1)E-GEOD-43088.processed.1.zip
Array designA-AFFY-77.adf.txt
Links