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| Status |
Public on Feb 21, 2020 |
| Title |
Cold tolerance in rice plants is partially controlled by root responses |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Rice (Oryza sativa) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the roots of two rice genotypes (CT, cold-tolerant; and CS, cold-sensitive) in response to low temperature stress during the early vegetative stage.
Results: RNAseq analysis revealed that contrasting genotypes present a completely different molecular response to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes that might contribute to rice cold tolerance, including the ones related with cell wall remodeling (glycosyl hydrolase, cellulose synthase, glycosyl transferase, wall-associated kinase, glycine-rich cell wall structural protein), cytoskeleton and growth (microtubule-associated protein 70, kinesin motor domain containing protein, growth regulating factor protein, auxin-independent growth promoter protein, RopGEF7), signaling (receptor-like protein kinase, Rapid Alkalinization Factor 21)), antioxidant system (glutathione peroxidase, metallothionein), lipid metabolism (fatty acid desaturase and phosphatidylinositol transfer protein), and stress response (Tetratricopeptide Repeat-Containing Protein). On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Even though these two genotypes have a similar genetic background (sister lines), some of these genes can probably be involved with cold tolerance or sensitivity and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.
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| Overall design |
Identify and characterize novel genes and metabolic pathways in roots of two indica rice genotypes (CT, cold-tolerant; and CS, cold-sensitive) in response to low temperature stress (10°C for up to 10 days) during the early vegetative stage (three-leaf stage, approximately 30 days).
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| Contributor(s) |
Sperotto RA, Ricachenevsky FK, Fett JP |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Feb 20, 2020 |
| Last update date |
Feb 23, 2020 |
| Contact name |
Raul Antonio Sperotto |
| E-mail(s) |
raulsperotto@gmail.com
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| Organization name |
University of Taquari Valley - Univates
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| Department |
Biological Sciences and Health Center
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| Street address |
Av. Avelino Talini, 171
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| City |
Lajeado |
| ZIP/Postal code |
95914-014 |
| Country |
Brazil |
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| Platforms (1) |
| GPL13160 |
Illumina HiSeq 2000 (Oryza sativa) |
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| Samples (8)
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| GSM4321788 |
Cold-tolerant rice under control solution, biological rep1 |
| GSM4321789 |
Cold-tolerant rice under control solution, biological rep2 |
| GSM4321790 |
Cold-sensitive rice under control solution, biological rep1 |
| GSM4321791 |
Cold-sensitive rice under control solution, biological rep2 |
| GSM4321792 |
Cold-tolerant rice under low temperature stress (10°C for up to 10 days), biological rep1 |
| GSM4321793 |
Cold-tolerant rice under low temperature stress (10°C for up to 10 days), biological rep2 |
| GSM4321794 |
Cold-sensitive rice under low temperature stress (10°C for up to 10 days), biological rep1 |
| GSM4321795 |
Cold-sensitive rice under low temperature stress (10°C for up to 10 days), biological rep2 |
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| Relations |
| BioProject |
PRJNA607661 |
| SRA |
SRP250080 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE145582_STARscVSsf.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE145582_STARscVStc.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE145582_STARsfVStf.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE145582_STARtcVStf.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE145582_readme.txt |
702 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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