Time course transcriptomic analysis of cabbage (Brassica oleracea ssp. capitala L.) during vernalization
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ABSTRACT:
ORGANISM(S): Brassica oleracea
PROVIDER: GSE229562 | GEO | 2023/04/17
REPOSITORIES: GEO
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Project description:The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage. Results: The results of whole-transcriptome sequencing showed that 2702 mRNAs, 151 lncRNAs, 16 circRNA, and 233 miRNAs were differentially expressed in vernalized (‘Ver’) and non-vernalized (‘Nor’) seeds of Chinese cabbage. Some transcription factors and regulatory proteins that play important roles in vernalization pathway have been identified, such as the transcription factors of WRKY, MYB, NAC, bHLH, and MADS-box, zinc finger protein CONSTANS like gene and B3 domain protein. We constructed vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA-DEmRNA, 67 DEmiRNA-DElncRNA, and 12 DEmiRNA-DEcircRNA interactions in Chinese cabbage. Meanwhile, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs were identified, which were involved in the regulation of flowering time, floral organ formation, bolting and flowering. Conclusions: The candidate differentially expressed mRNA, miRNA, lncRNA and circRNA for vernalization of Chinese cabbage were identified by the whole-transcriptome sequencing, and the ceRNA network was constructed. This study laid a foundation for further study on the molecular mechanism of vernalization in Chinese cabbage.
2021-11-17 | GSE171708 | GEO
Project description:The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage. Results: The results of whole-transcriptome sequencing showed that 2702 mRNAs, 151 lncRNAs, 16 circRNA, and 233 miRNAs were differentially expressed in vernalized (‘Ver’) and non-vernalized (‘Nor’) seeds of Chinese cabbage. Some transcription factors and regulatory proteins that play important roles in vernalization pathway have been identified, such as the transcription factors of WRKY, MYB, NAC, bHLH, and MADS-box, zinc finger protein CONSTANS like gene and B3 domain protein. We constructed vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA-DEmRNA, 67 DEmiRNA-DElncRNA, and 12 DEmiRNA-DEcircRNA interactions in Chinese cabbage. Meanwhile, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs were identified, which were involved in the regulation of flowering time, floral organ formation, bolting and flowering. Conclusions: The candidate differentially expressed mRNA, miRNA, lncRNA and circRNA for vernalization of Chinese cabbage were identified by the whole-transcriptome sequencing, and the ceRNA network was constructed. This study laid a foundation for further study on the molecular mechanism of vernalization in Chinese cabbage.
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Project description:We investigated the expression profiles and genomic organization of PP2Cs-encoding genes in Brassica oleracea. Analysis of cDNA macroarray transcription profiles for Brassica oleracea and Arabidopsis thaliana revealed significant differences in the expression of a gene encoding protein phosphatase 2C, ABI1, a member of the group A PP2C. To gain insight into the ABA signaling network conservation in a model plant and its crop relatives group A PP2C genes in B. oleracea have been identified and functionally characterized. Twenty homologous sequences were identified as putative members of the group A PP2Cs (BolC.PP2Cs). Phylogenetic analysis revealed that the B. oleracea homologues are closely related to the particular members of the A. thaliana PP2C family. The genetic analysis has corroborated the presence of 2 to 3 copies for almost all of the PP2Cs examined, which corresponded to the unique genes in the A. thaliana genome. Gene expression analyses showed that among 15 PP2Cs-encoding genes studied in B.oleracea, BolC.ABI2, BolC.HAB1, BolC.HAB2.a-c, and BolC.PP2CA.a were drought-induced. However, in contrary to AtPP2Cs, only BolC.ABI1.a-b, BolC.ABI2 and BolC.PP2CA.a were ABA-responsive at the time points tested. Our results indicate that in B. oleracea PP2C-based drought stress signaling has evolved distinctly in comparison to A. thaliana. It is hypothesized that different reactions of particular B. oleracea PP2C genes to the water stress and ABA treatment may indicate lower conservation of their specificity in stress-induced reversible phosphorylation-based protein network operating in B. oleracea and A. thaliana.
2012-10-28 | GSE39753 | GEO
Project description:We investigated the expression profiles and genomic organization of PP2Cs-encoding genes in Brassica oleracea. Analysis of cDNA macroarray transcription profiles for Brassica oleracea and Arabidopsis thaliana revealed significant differences in the expression of a gene encoding protein phosphatase 2C, ABI1, a member of the group A PP2C. To gain insight into the ABA signaling network conservation in a model plant and its crop relatives group A PP2C genes in B. oleracea have been identified and functionally characterized. Twenty homologous sequences were identified as putative members of the group A PP2Cs (BolC.PP2Cs). Phylogenetic analysis revealed that the B. oleracea homologues are closely related to the particular members of the A. thaliana PP2C family. The genetic analysis has corroborated the presence of 2 to 3 copies for almost all of the PP2Cs examined, which corresponded to the unique genes in the A. thaliana genome. Gene expression analyses showed that among 15 PP2Cs-encoding genes studied in B.oleracea, BolC.ABI2, BolC.HAB1, BolC.HAB2.a-c, and BolC.PP2CA.a were drought-induced. However, in contrary to AtPP2Cs, only BolC.ABI1.a-b, BolC.ABI2 and BolC.PP2CA.a were ABA-responsive at the time points tested. Our results indicate that in B. oleracea PP2C-based drought stress signaling has evolved distinctly in comparison to A. thaliana. It is hypothesized that different reactions of particular B. oleracea PP2C genes to the water stress and ABA treatment may indicate lower conservation of their specificity in stress-induced reversible phosphorylation-based protein network operating in B. oleracea and A. thaliana. For each genotype 7 samples were analysed; 4 controls and 3 samples extracted from drought-treated plants. The reliability and reproducibility of the macroarray analyses were ensured by using biological replicates in the experiment.
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