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| Status |
Public on Aug 14, 2013 |
| Title |
Genome-wide expression of transcriptomes under waterlogging stress condition in subtropical maize |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by array
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Thirunavukkarasu N |
| Citation(s) |
23936429 |
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| Submission date |
Dec 20, 2012 |
| Last update date |
Aug 15, 2013 |
| Contact name |
Nepolean Thirunavukkarasu |
| E-mail(s) |
tnepolean@iari.res.in
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| Organization name |
Indian Agricultural Research Institute
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| Department |
Division of Genetics
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| Lab |
maize breeding
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| Street address |
IARI PUSA
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| City |
new delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110012 |
| Country |
India |
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| Platforms (1) |
| GPL4032 |
[Maize] Affymetrix Maize Genome Array |
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| Samples (16)
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| GSM1056294 |
Control HKI1105/Tolerant variety root tissue 28th day after sowing, biological rep1 |
| GSM1056295 |
Control HKI1105/Tolerant variety root tissue 28th day after sowing, biological rep2 |
| GSM1056296 |
Moderate HKI1105/Tolerant variety root tissue 32nd day after sowing, biological rep1 |
| GSM1056297 |
Moderate HKI1105/Tolerant variety root tissue 32nd day after sowing, biological rep2 |
| GSM1056298 |
Recovery HKI1105/Tolerant variety root tissue 42nd day after sowing, biological rep1 |
| GSM1056299 |
Recovery HKI1105/Tolerant variety root tissue 42nd day after sowing, biological rep2 |
| GSM1056300 |
Severe HKI1105/Tolerant variety root tissue 35th day after sowing, biological rep1 |
| GSM1056301 |
Severe HKI1105/Tolerant variety root tissue 35th day after sowing, biological rep2 |
| GSM1056302 |
Control V-372/Susceptible variety root tissue 28th day after sowing, biological rep1 |
| GSM1056303 |
Control V-372/Susceptible variety root tissue 28th day after sowing, biological rep2 |
| GSM1056304 |
Moderate V-372/Susceptible variety root tissue 32nd day after sowing, biological rep1 |
| GSM1056305 |
Moderate V-372/Susceptible variety root tissue 32nd day after sowing, biological rep2 |
| GSM1056306 |
Recovery V-372/Susceptible variety root tissue 42nd day after sowing, biological rep1 |
| GSM1056307 |
Recovery V-372/Susceptible variety root tissue 42nd day after sowing, biological rep2 |
| GSM1056308 |
Severe V-372/Susceptible variety root tissue 35th day after sowing, biological rep1 |
| GSM1056309 |
Severe V-372/Susceptible variety root tissue 35th day after sowing, biological rep2 |
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| Relations |
| BioProject |
PRJNA184371 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE43088_RAW.tar |
34.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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