Dataset Information

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering.

ABSTRACT: BACKGROUND:Drought stress is a major abiotic factor that affects rapeseed (Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs' response to drought stress is still lacking, especially in the case of B. napus. In order to further understand the molecular mechanism of the response of B. napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) responding drought stress and rehydration treatment at the seedling stage. RESULTS:A total of 5546 down-regulated and 6997 up-regulated mRNAs were detected in Q2 compared with 7824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up- regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. LncRNA-mRNA interaction network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. We further identified 34 transcription factors (TFs) corresponding to 126 differentially expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differentially expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes. Notably, some lncRNAs were co-expressed with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs co-located with XLOC_052298, XLOC_094954 and XLOC_012868 were mainly categorized as signal transport and defense/stress response. CONCLUSIONS:The results of this study increased our understanding of expression characterization of rapeseed lncRNAs in response to drought stress and re-watering, which would be useful to provide a reference for the further study of the function and action mechanisms of lncRNAs under drought stress and re-watering.

SUBMITTER: Tan X

PROVIDER: S-EPMC7032001 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering.

Tan Xiaoyu X Li Su S Hu Liyong L Zhang Chunlei C

BMC plant biology 20200219 1

<h4>Background</h4>Drought stress is a major abiotic factor that affects rapeseed (Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs' response to drought stress is still lacking, especially in the case of B. napus. In order to further understand the molecular mechanism of the response of B. napus to drought stress, we compared ...[more]

PMID: 32075594

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Project description:Abiotic stresses such as drought and salt stresses have a negative effect on the growth and productivity of plants. Improvement of stress tolerance through genetic engineering in plants has been reported in intense studies. Transcription factors play vital roles in plant adaptation to stresses by regulating expression of a great deal of target genes. A family of Arabidopsis basic region leucine zipper (bZIP) transcription factors that can recognize and bind to the abscisic acid (ABA)-responsive elements (ABREs) in promoter is named as ABRE binding factors (ABFs)/ABRE binding proteins (AREBs). They play a key role in the regulation of expression of downstream stress-responsive genes in ABA signalling. Genetic transformation of ABF/ABRE transcription factors has been suggested to be an effective approach for engineering stress-tolerant plants. However, whether the ABF/ABRE transcription factors are able to be used for generating stress-tolerant rapeseed plants has not yet been studied.BnaABF2, encoding a bZIP transcription factor, was cloned from rapeseed in this study. Subcellular localization and transactivation analyses showed that BnaABF2 was localized to the nucleus with transactivation activity in plant cells. BnaABF2 gene expression was induced by drought and salt stresses and BnaABF2 positively functions in ABA signalling during the vegetative stage. Overexpression of BnaABF2 was found to render drought and salt tolerance to Arabidopsis plants. The resistance of the BnaABF2-expressing transgenic plants to drought and salt stresses is due to reduced water-loss rate and expression of stress-responsive genes such as RD29B, RAB18 and KIN2. The expression of RD29B, RAB18 and KIN2 regulated by BnaABF2 is involved in an ABA-dependent stress signalling.Identification of the positive role of rapeseed BnaABF2 in plant tolerance to drought and salt provides evidence for ability of engineering stress-tolerant rapeseed plants by genetic transformation of BnaABF2.

Dataset Information

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering.

Publications

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering.

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