Ontology highlight
ABSTRACT:
PROVIDER: PRJNA894465 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22046030_1.fastq.gz | Fastqsanger.gz | |||
| SRR22046030_2.fastq.gz | Fastqsanger.gz | |||
| SRR22046031_1.fastq.gz | Fastqsanger.gz | |||
| SRR22046031_2.fastq.gz | Fastqsanger.gz | |||
| SRR22046032_1.fastq.gz | Fastqsanger.gz |
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Project description:Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage resulting in poor growth and yield loss. In general, japonica rice has stronger cold tolerance (CT) than indica rice. However, several favorite alleles for CT exist in indica rice and can be used to enhance CT under japonica background. Genome-wide gene expression profiling is the efficient way to decipher the molecular genetic mechanism of CT enhancement and provide valuable information for the CT improvement in rice molecular breeding. In this study, the transcriptome of a CT introgressed line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanism of K354.Totally 3184 differentially expressed genes (DEGs) including 195 transcription factors were identified in both lines under cold stress, about half of them were commonly regulated, which were involved in the major cold responsive pathways including OsDREB1s regulon. The K354-specific cold-induced DEGs were mainly related to stimulus response, cellular cell wall organization, and microtubule-based movement process compared with commonly cold-induced DEGs by GO analysis. Moreover, 296 constitutive DEGs with significantly different transcription level between C418 and K354 were detected under both control and cold stress conditions. K354-specific cold-regulated and constitutive DEGs jointly account for the CT improvement of K354. Pathway analysis unraveled up-regulation of starch and sucrose metabolism in both genotypes and presumably weaker defense response to stress in K354 than C418 under cold stress. Candidate genes prediction based on previous putative CT genetic networks revealed genotype-dependent CT enhancement mechanism in CT IL K354 vs recurrent parent C418, including Sir2, OsFAD7, OsWAK112d, and PCD related genes, etc.We propose a hypothesis of the CT enhancement mechanism in rice based on the results in present study. Firstly, a number of cold-regulated genes are able to express constitutively at high level or absent under control condition for standing by the arrival of cold stress. Next, under cold stress slower perception of stress signal from the more cold-tolerant membrane can postpone the activation of defensive system which may have possible negative effects on rice growth. Then, PCD will be launched to sacrifice a few cells for maintaining the basal growth of most cells. Finally, the protective responses on multiple aspects of cold damage will be postponed because of delayed several cold-defensive pathways (i.e. OsDREB1C regulon). It might explain why the recovery capacity of K354 from cold stress to control condition is stronger than C418. The CT enhancement mechanism can be regarded as the possible way to improve CT of japonica rice using indica germplasm in rice breeding program. In this study, the specific gene expression patterns of two genotypes (C418 and K354) at 2h, 6h, 12h, 24h and 48h during cold stress treatment (4 C) and control were characterized by using the Affymetrix rice microarray platform.
2012-12-31 | E-GEOD-37940 | biostudies-arrayexpress
Project description:Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage resulting in poor growth and yield loss. In general, japonica rice has stronger cold tolerance (CT) than indica rice. However, several favorite alleles for CT exist in indica rice and can be used to enhance CT under japonica background. Genome-wide gene expression profiling is the efficient way to decipher the molecular genetic mechanism of CT enhancement and provide valuable information for the CT improvement in rice molecular breeding. In this study, the transcriptome of a CT introgressed line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanism of K354.Totally 3184 differentially expressed genes (DEGs) including 195 transcription factors were identified in both lines under cold stress, about half of them were commonly regulated, which were involved in the major cold responsive pathways including OsDREB1s regulon. The K354-specific cold-induced DEGs were mainly related to stimulus response, cellular cell wall organization, and microtubule-based movement process compared with commonly cold-induced DEGs by GO analysis. Moreover, 296 constitutive DEGs with significantly different transcription level between C418 and K354 were detected under both control and cold stress conditions. K354-specific cold-regulated and constitutive DEGs jointly account for the CT improvement of K354. Pathway analysis unraveled up-regulation of starch and sucrose metabolism in both genotypes and presumably weaker defense response to stress in K354 than C418 under cold stress. Candidate genes prediction based on previous putative CT genetic networks revealed genotype-dependent CT enhancement mechanism in CT IL K354 vs recurrent parent C418, including Sir2, OsFAD7, OsWAK112d, and PCD related genes, etc.We propose a hypothesis of the CT enhancement mechanism in rice based on the results in present study. Firstly, a number of cold-regulated genes are able to express constitutively at high level or absent under control condition for standing by the arrival of cold stress. Next, under cold stress slower perception of stress signal from the more cold-tolerant membrane can postpone the activation of defensive system which may have possible negative effects on rice growth. Then, PCD will be launched to sacrifice a few cells for maintaining the basal growth of most cells. Finally, the protective responses on multiple aspects of cold damage will be postponed because of delayed several cold-defensive pathways (i.e. OsDREB1C regulon). It might explain why the recovery capacity of K354 from cold stress to control condition is stronger than C418. The CT enhancement mechanism can be regarded as the possible way to improve CT of japonica rice using indica germplasm in rice breeding program.
2012-12-31 | GSE37940 | GEO
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayM-oM-<M- v1. Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed
2014-10-15 | E-GEOD-57895 | biostudies-arrayexpress
Project description:Low temperature exposure during early vegetative stages limits rice plant’s growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated leaves from two genotypes, cold-tolerant and cold-sensitive, was performed. The cold-tolerant and cold-sensitive genotypes were previously characterized, and are sister lines (derived from the same crossing).
2017-09-06 | GSE103480 | GEO
Project description:RNA-Seq was performed to study the change of gene expression before and after chilling treatment in rice. Different change patterns were identified. We have provided a complete view of transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants.
2016-04-13 | GSE67373 | GEO
Project description:RNA-Seq was performed to study the change of gene expression before and after chilling treatment in rice. Different change patterns were identified. We have provided a complete view of transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The mRNA profiles of 15-day-old rice seedlings with and without chilling treatment (4 °C for 33 h) were generated by deep sequencing using Illumina Hiseq 2000 platform.
2016-04-13 | E-GEOD-67373 | biostudies-arrayexpress
Project description:Cold stress is one of the major abiotic stress factors affecting rice growth and development, leading to great yield loss in the context of global climate change. Exploring superior natural variants that confer cold resistance and the underlying molecular mechanism is the major strategy to breed cold tolerant rice varieties. Here, we identified natural variations of a SIMILAR to RCD ONE (SRO) gene OsSRO1c that confers cold tolerance in rice at both seedling and booting stages. OsSRO1c interacts with transcription factor OsDREB2B and promotes its transcriptional activity by concentrating OsDREB2B into biomolecular condensates in the nucleus. The OsSRO1c-OsDREB2B complex directly sense cold stress through dynamic phase transitions in vivo and in vitro and regulate key cold response gene COLD1. Introgression of an elite haplotype of OsSRO1c into a cold susceptible indica rice can significantly increase its cold resistance ability. Thus, our work revealed a novel cold stress sensing module and provided a promising gene resource for breeding cold tolerant rice varieties.
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Project description:Expression Data of Rice Crown and Growing Point Tissue Under Salt Stress imposed during the Panicle Initiation Stage Experiment Overall Design: Rice Genotypes a sensitive japonica, m103, tolerant japonica agami, sensitive indica ir29 and tolerant indica ir63731 were used for expression anlaysis using the tissue from crown and growing point under control and salt stressed conditions at the sensitive early reproductive stage (panicel initiation).
2008-11-05 | E-GEOD-4438 | biostudies-arrayexpress
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayï¼ v1. Control and treated biological replicates of salt-tolerant cultivar TNG67 (japonica) and salt-sensitive cultivar TCN1 (indica) were analyzed
2016-06-30 | E-GEOD-76613 | biostudies-arrayexpress