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ABSTRACT: Integrated Metabolome and Transcriptome Profiling Provide Insights into Cold Responses in Rapeseed (Brassica napus L.) Genotypes with Contrasting Cold Stress Sensitivity

PROVIDER: PRJNA890757 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21919087_1.fastq.gz	Fastqsanger.gz
	SRR21919087_2.fastq.gz	Fastqsanger.gz
	SRR21919088_1.fastq.gz	Fastqsanger.gz
	SRR21919088_2.fastq.gz	Fastqsanger.gz
	SRR21919089_1.fastq.gz	Fastqsanger.gz

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RNA-seq of two early-maturing rapeseed varieties treated with different cold stress

Project description:Oil rapeseed (Brassica napus L.) is a typical winter biennial plant, with high cold tolerance during vegetative stage. In recent years, more and more early-maturing rapeseed varieties were planted across China. Unfortunately, the early-maturing rapeseed varieties with low cold tolerance have higher risk of freeze injury in cold winter and spring. Little is known about the molecular mechanisms for coping with different low-temperature stress conditions in rapeseed. In this study, we investigated 47,328 differentially expressed genes (DEGs) of two early-maturing rapeseed varieties with different cold tolerance treated with cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that two conserved (the primary metabolism and plant hormone signal transduction) and two novel (plant-pathogen interaction pathway and circadian rhythms pathway) signaling pathways were significantly enriched with differentially-expressed transcripts. Our results provided a foundation for understanding the low-temperature stress response mechanisms of rapeseed. We also propose new ideas and candidate genes for genetic improvement of rapeseed tolerance to cold stresses.

2020-03-19 | GSE129220 | GEO

Integration of GWAS and transcriptome analysis to identify temperature-dependent genes involved in germination of Brassica napus L.

Project description:Global climate changes on one aspect of extreme temperature records would suddenly reset environmental growth conditions for field-grown crops, which severely affects agronomic and commercial traits. Taking the cold-season preferable crop rapeseed Brassica napus L. for example, low-temperature shocks change endogenous regulatory networks and cause phenotypic damages during most lifespan. Here we screened out two genetic breeding elites with different temperature-dependent germination rates, core germplasms with good germination performance and genetic loci and candidate genes potentially involved in low-temperature tolerant functions for the pre-breeding purpose of cold-tolerant germination. By using the phenotype of the germination index of 273 core germplasms under normal temperature and 10 transcriptomic datasets of cold-tolerant Jia You (JY) 1621 and cold-sensitive JY1605 elite cultivars on three timepoints during germination process, we successfully identified clustered genes of early and late temperature response germination (ETRG and LTRG) genes and several cold-tolerant (CDT) and temperature-insensitive (TPI) candidate regulators. This study performed comprehensive multi-omics research on potential cold-responsive genes for the rapeseed improvement of cold tolerance germination.

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The molecular response of two Brassica napus cultivars to short-term hypoxia in the root zone

Project description:Waterlogging is one major stress for crops and causes multiple problems for plants, for example low gas diffusion, reducing conditions in the soil and accumulation of toxic metabolites. Brassica napus is an important oil crop with high waterlogging sensitivity, which may cause severe yield losses. Its reactions to the stress are not fully understood. In this work the transcriptional response of rapeseed to one aspect of waterlogging, hypoxia in the root zone, was analyzed, including two rapeseed cultivars from different origin, Avatar from Europe and Zhongshuang 9 from Asia. Both cultivars showed a high number of differentially expressed genes in roots after 4 and 24 h of hypoxia. The response included many well-known hypoxia-induced genes such as genes coding for glycolytic and fermentative enzymes. Leaves hardly responded to the root stress after a 24-h-stress treatment, and photosynthesis seemed to be not affected by the stress applied to roots. There was no clear difference in either gene expression or tolerance to waterlogging between the two genotypes used in this study.

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Project description:A critical barrier for improving crops yield is the compensatory effect between seed weight (SW) and seed number (SN), which has been widely reported in several crops including Brassica napus. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction between SW and SN are largely unknown in crops. In this work, we performed a detailed transcriptomic analysis of 48 seed samples obtained from two rapeseed spring genotypes subjected to different source-sink (S-S) ratios in order to modify the relationship between SW and SN under field conditions.

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Project description:Knowledge about molecular mechanisms underlying cold and freezing stress responses in perennial ryegrass is scarce. The current study aims to study cold and freezing stress responses of perennial ryegrass genotypes with contrasting cold tolerances. A panel of 160 genotypes were screened for cold tolerances based on electrolyte leakage % measured after 24 hrs at 12 °C and 24 hrs at 14 °C. Among them, 4 genotypes (2 low EL% and 2 high EL%) were selected to study cold and freezing stress responses. Plants were sampled at 6 timepoints; control (T1), beginning of cold acclimation (T2), 2 weeks into cold acclimation (T3), end of cold cold acclimation (T4), -5°C (T5), -10 °C (T6) followed by RNA extraction and sequencing.

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Project description:Comparative Metabolome and Transcriptome Analysis of Rapeseed (Brassica napus L.) Cotyledons in Response to Cold Stress

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Project description:Compared to ordinary rapeseed, high-oleic acid rapeseed has higher levels of monounsaturated fatty acids and lower levels of saturated fatty acid and polyunsaturated fatty acids, and thus is of high nutritional and health value. In addition, high-oleic acid rapeseed oil imparts cardiovascular protective effects. Based on these properties, high-oleic acid oil crops have been extensively investigated and cultivated. In this study, we employed a microarray analysis with high oleic acid line and low oleic acid line from the developing seeds (27 days after flowering) of Brassica napus.

2018-09-20 | GSE120223 | GEO

Project description:Integrated transcriptomics and metabolomics analyses provide insights into cold stress response in Argyranthemum frutescens

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Project description:genomic and transcriptional variations in rapeseed genotypes with contrasting boron efficiencies

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Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

Project description:Maize is highly sensitive to short term flooding and submergence. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence.

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