OsTTG1-dependent gene activation confer chilling tolerance in colored rice
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ABSTRACT:
INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase
SUBMITTER: ChenLi Zhu
PROVIDER: MTBLS9234 | MetaboLights | 2024-07-31
REPOSITORIES: MetaboLights
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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.
2012-12-31 | GSE37940 | GEO
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: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.
2023-11-19 | GSE247749 | GEO
Project description: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.
2020-02-21 | GSE145582 | GEO
Project description:Purpose: In this study, RNA-seq was used to analyzed the molecular mechanism of cold tolerance in rice Methods: Rice 9311 (cold intolerant) and DC907 (cold tolerant) were used as experimental materials for transcriptome sequencing on Illumina HIseq platform. Fastq is used to evaluate the quality of the original data, and NGS QC Toolkit is used to filter the original data to obtain clean reads. Clean reads were compared to the rice 9311 reference genome using HISAT2 software. Put the genome mapping results of all sequenced reads data together, assemble them with cufflinks, and then compare them with known gene models with cuffcompare. The gene expression level of each sample was analyzed by HTSeq software. All treatments were analyzed for differential expression using DEseq. Results: A total of 36 samples were used for RNA sequencing analysis, with three biological replicates per treatment. Each sample generates at least 2G data. The genes regulated by cold stress treatment (1,3 days) and recovery treatment (1,3 days) were determined by comparative analysis.
2022-04-06 | GSE182563 | GEO
Project description:We analyzed expression change of the genes which involved in anthocyanin and pro-anthocyanin biosynthesis to search an origin of black rice.
2015-04-18 | GSE67987 | 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:We analyzed expression change of the genes which involved in anthocyanin and pro-anthocyanin biosynthesis to search an origin of black rice. The submitted samples were transcriptome data in black and red rice pericarps. Rice pericarps were harvested in 7 and 14 days after heading, respectively.
2015-04-18 | E-GEOD-67987 | biostudies-arrayexpress
Project description:Improvement of chilling tolerance is a key strategy to face potential menace from abnormal temperature in rice production, which depends on the signaling network triggered by receptors. However, little is known about the QTL genes encoding membrane complexes for sensing cold. Here, Chilling-tolerance in Gengdao/japonica rice 1 (COG1) was isolated from a chromosome segment substitution line containing a QTL (qCS11-jap) for chilling sensitivity. The major gene COG1 was found to confer chilling tolerance in japonica rice. In natural rice populations, only the haplogroup1 encoded a functional COG1. Evolutionary analysis showed that COG1 originated from Chinese O. Rufipogon and was fixed in japonica rice during domestication. COG1, a membrane-localized LRR-RLP, targeted and activated the kinase OsSERL2 in a cold-induced manner, promoting chilling tolerance. Furthermore, the cold signal transmitted by COG1-OsSERL2 activates OsMAPK3 in the cytoplasm. Our findings reveal a cold-sensing complex, which mediates signaling network for the chilling defense in rice.
2023-06-18 | PXD042294 | Pride
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