- Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage ( Brassica rapa L.) during vernalization. - We performed RNA sequencing of gradient-vernalization in order to explore the reasons for the different bolting process of two Chinese cabbage accessions during vernalization.. - Results: There was considerable variation in gene expression between different-bolting Chinese cabbage accessions during vernalization. - Comparative transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were performed for different-bolting Chinese cabbage during different vernalization periods. - and leaf senescence and carbohydrate metabolism enrichment were found in the two Chinese cabbage-related modules, indicating that these pathways may be related to bolting and flowering. - PAO and NAC029 (plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions.. - In addition, the candidate pathways and hub genes related to vernalization identified here will serve as a reference for breeders in the regulation of Chinese cabbage production.. - This indicates that the demand for Chinese cabbage throughout the year is slowly in- creasing. - Previously, Yui and Yoshikawa [6] ob- served the phenomenon of low temperature promoting Chinese cabbage bolting and flowering. - The vernalization of Chinese cabbage also involves the expression of VIN3, VRN2, and VRN1 [11]. - [20] used an RNA- Seq technology to obtain information including the DEGs, functional annotations, and variable shear, of Chinese cabbage samples before and after vernalization.. - As an important flowering crop, it is necessary to ex- plore the underlying molecular mechanisms of flowering induction in Chinese cabbage.. - Spring Chinese cabbage lose their commercial value after premature bolting as a result of low-temperature effects. - Therefore, the ef- fects of vernalization on Chinese cabbage are worth dis- secting and exploring. - In this study, the gradient vernalization of two different bolting Chinese cabbage accessions were used to analyze the transcriptome pat- tern of Chinese cabbage during vernalization. - Chinese cabbage during vernalization were identified in order to find the reasons for the different bolting.. - The gen- erated cluster dendrogram was used to observe the overall correlation of the transcriptomes of the 2 Chinese cabbage accessions at different time periods (Fig. - After analyzing the transcriptome data of each treat- ment period of 2 Chinese cabbage accessions, low abun- dance and low variability genes were filtered out. - A total of 5748 genes of ‘JWW’ and 5527 genes of ‘XBJ’ were screened out. - Different modules related to ‘ JWW ’ and ‘ XBJ ’ in different periods. - 0.7 were selected as representa- tives of the 2 Chinese cabbage accessions for further analysis. - Five modules were selected for both ‘JWW’ and. - The correlations between different modules of the 2 Chinese cabbage accessions were further investigated.. - In ‘JWW’, MEdarkturquoise was positively correlated with. - c Number of transcripts in the 2 Chinese cabbage accessions, based on the FPKM of different samples. - Expression gene displays were performed for each Chinese cabbage processing stage and corresponded with each module (Fig. - The biological functional terms enriched in ‘JWW’. - In the Brassica database, ‘JWW’ MEbrown and ‘XBJ’ MEtur- quoise were enriched together with photosynthesis,. - 2 WGCNA of gene expression in ‘ JWW ’ (a) and ‘ XBJ ’ (b) during vernalization. - 3 Co-expression modules for ‘ JWW. - 4 Co-expression modules for ‘ XBJ. - 5 Gene expression levels in ‘ JWW ’ (a) and ‘ XBJ ’ (b) with their corresponding log 2 FPKM module values. - In the Arabidopsis Data- base, photosynthesis was the most enriched functional term in ‘JWW’ MEbrown and ‘XBJ’ MEturquoise. - ‘JWW’ MEgreenyellow and ‘XBJ’ MEpurple were. - In ‘JWW’. - At 25 DAT, rapid flowering in ‘XBJ’. - 6 Significant GO terms and ontological relationships (annotated from ClueGO) in ‘ JWW. - vernalization period and may be the key biological func- tions that explain the transformation of late-bolting Chinese cabbage flowering.. - ‘XBJ’ MEblack was enriched in functional terms related to. - Additionally, leaf senescence was positively regulated in ‘XBJ’ MEblack at 50 DAT, indicating that the leaf senescence of Chinese cabbage after vernalization may also signal bolting and flowering promotion. - Hub gene selection for the ‘ JWW ’ and ‘ XBJ ’ co-expression networks. - In the MEgreenyellow of ‘JWW’, genes related to carbohydrate transport and metabol- ism pathways were also enriched, and the expression levels were notably higher than that of the control treatment, indicating that carbohydrate transport and metabolism may play an important role in the vernalization of Chinese cabbage. - 8 Hub genes and expression profiles of ‘ JWW. - 9 Hub genes and expression profiles of ‘ XBJ. - The expression of TSF and BBX32 in ‘XBJ’ at 25 DAT and 50 DAT were higher than in ‘JWW’.. - Formation of specific co-expression networks using two bolting Chinese cabbage accessions and the WGCNA method. - In this experiment, 2 Chinese cabbage accessions con- tained 21 RNA-Seq sample data points, respectively.. - The goal was to uncover the response mechanism of Chinese cabbage across different vernalization time periods and identify key genes. - To our knowledge, there are no reports on the gene interaction networks of Chinese cabbage vernalization across different time periods. - Therefore, based on the WGCNA gene co-expression network in this study, the responses of the 2 Chinese cabbage acces- sions to different vernalization stages were systematically analyzed at the transcriptome level.. - Enrichment of different modules based on the transcriptomic differences of two Chinese cabbage accessions. - Based on the functions predicted by the modules of genes with known biological functions, the characteristics of the 2 Chinese cabbage accessions under vernalization and con- trol treatments were analyzed and determined in order to find the reasons for their different bolting processes.. - Photosynthesis, chlorophyll biosynthetic, cytokinin, and karrikin-responsive biological functional terms were enriched in the two most highly correlated modules of the 2 Chinese cabbage accessions at 0 DAT: MEbrown and MEturquoise. - At 0 DAT, the 2 Chinese cabbage accessions were in the vege- tative growth stage, thus, they exhibited obvious and consistent performance in terms of photosynthesis, chlorophyll biosynthetic, cytokinin, and karrikin. - Using the vernalization of two Chinese cabbage accessions at 0 DAT as a starting period, the different performances of the two could be better analyzed and the reasons for their different bolting performances explored.. - of ‘JWW’. - in ‘XBJ’, which requires polysaccharides to regulate the. - These biological func- tional terms were enriched in MEdarkgrey in ‘JWW’ and may be the key determinants of late-bolting Chinese cabbage floral transition.. - With this finding, we speculated that leaf senes- cence was also a signal that promoted bolting and flowering of Chinese cabbage. - In summary, we tried to find the biological function of two different bolting Chinese cabbage accessions during the vernalization process: the early-bolting ‘ XBJ ’ could bolt and flower faster at 25 DAT, which was promoted by the shoot system morphogenesis and polysaccharide and sugar metabolism, while late-bolting ‘ JWW ’ enriched chitin, ABA, and ethylene-activated signaling pathways at 35 DAT, indicating that these regulatory. - pathways may promote bolting resistance in Chinese cabbage. - An interesting finding was that the regulation of leaf senescence was found in the 2 Chinese cabbage- related modules, indicating that leaf senescence may be related to bolting and flowering.. - Analysis of hub genes enriched in two Chinese cabbage accessions during vernalization. - WGCNA was used to construct the gene co-expression networks of 2 Chinese cabbage accessions and analyze the modules that were highly related to their vernalization periods. - The top 20 hub genes with the highest correlation relationships among these modules were identified to further analyze key candidate vernalization genes for Chinese cabbage with different bolting performances.. - of ‘JWW’ MEdarkgrey. - of ‘XBJ’ MEblack. - A separate study demonstrated that BrBBX32 binds to BrAGL24 in Chinese cabbage through the B-box do- main, which regulates flowering time [50]. - In this study, BBX32 was enriched in ‘JWW’ at 35 DAT, indicating that vernalization induced BBX32 expression and pro- moted the flowering transition of Chinese cabbage. - In this study, vernalization induced SUS1 levels, indicating that SUS1 can be used as a candidate gene for Chinese cabbage vernalization. - In this study, the expression of PAO reached its max- imum level at 50 DAT in both Chinese cabbage acces- sions, indicating that Chinese cabbage was gradually aged during vernalization. - In this study, under the vernalization treatment, the expression of NAC029 in both Chinese cabbage accessions increased and was significantly up- regulated in ‘XBJ’. - and leaf sen- escence and carbohydrate metabolism pathways were found to be enriched in the two Chinese cabbage-related modules, indicating that these may be related to bolting and flowering. - The find- ings of this study provide a comprehensive overview of vernalization-related gene networks in Chinese cabbage and uncovered candidate hub genes in the vernalization process that can be utilized in future breeding research.. - Chinese cabbage accessions. - Two Chinese cabbage accessions, the late-bolting Jin Wawa (JWW) and early-bolting Xiao Baojian (XBJ), were provided by the Chinese Academy of Agricultural Sciences located in Beijing, China. - From ‘JWW’, 5748 co-constructed genes were screened out. - Pearson’s correlation coefficients were used to calculate the correlation be- tween the module characteristic genes and the degree of vernalization of the two Chinese cabbage accessions. - 11 a Treatment process of two Chinese cabbage accessions: (a), (b), and (c) are ‘ JWW. - (d), (c), and (f) are ‘ XBJ. - Log 2 FPKM values of the 5748 variable genes in ‘ JWW ’ (J for ‘ JWW. - Log 2 FPKM values of the 5527 variable genes in ‘ XBJ ’ (X for ‘ XBJ. - Annotation information of the hub genes of each module in ‘ JWW. - Annotation information of the hub genes of each module in ‘ XBJ. - Agrobiological Particularities of Chinese Cabbage: Brassica rapa L. - Research concerning the bolting of Chinese cabbage (Brassica campestris var. - https://doi.org/10.1016/S . - Bolting resistant breeding of Chinese cabbage. - Molecular cloning, characterization and expression analysis of bolting-associated genes in flowering Chinese cabbage. - https://doi.. - https://doi.org/10.1038/s . - Cloning and characterization of the LFY homologue from Chinese cabbage (Brassica rapa subsp. - https://doi.org/10.1007/s . - https://doi.org/10.1186/s x.. - https://doi.org/10.1186/s . - https://doi.org . - https://doi.org/10.1016/S X.. - BBX32 interacts with AGL24 involved in flowering time control in Chinese cabbage (Brassica rapa L. - https://doi.org/10.1111/. - https://doi.org/10.1093/
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