Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Vernalization Periods in Brassica rapa

Dai, Yun; Zhang, Shujiang; Sun, Xiao; Li, Guoliang; Yuan, Lingyun; Li, Fēi; Zhang, Hui; Chen, Guohu; Wang, Chenggang; Sun, Rifei

doi:10.3390/genes11040392

Cited by 13 publications

(15 citation statements)

References 83 publications

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“…After polyploidization in B. rapa, the GA1, DELLA (RGL2) and PIF3 genes were severely down-regulated in autotetraploid B. rapa. Moreover, the up-regulation of ABA associated genes PP2Cs block the generation of some SnRK2 genes causing different growth periods between two B. rapa accessions (Jin Wawa and Xiao Baojian), during continuous vernalization periods [24]. However, in the two plants used in this study, autotetraploid B. rapa exhibited an up-regulation for SnRK2 after polyploidization compared to diploid B. rapa.…”

Section: Degs Changes In Multiple Signal Transduction Pathway Affectmentioning

confidence: 72%

Comparative transcriptome analysis revealed differential gene expression in multiple signaling pathways at flowering in polyploid Brassica rapa

et al. 2021

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Background Polyploidy is widespread in angiosperms and has a significant impact on plant evolution, diversity, and breeding program. However, the changes in the flower development regulatory mechanism in autotetraploid plants remains relatively limited. In this study, RNA-seq analysis was used to investigate changes in signaling pathways at flowering in autotetraploid Brassica rapa. Results The study findings showed that the key genes such as CO, CRY2, and FT which promotes floral formation were down-regulated, whereas floral transition genes FPF1 and FD were up-regulated in autotetraploid B. rapa. The data also demonstrated that the positive regulators GA1 and ELA1 in the gibberellin’s biosynthesis pathway were negatively regulated by polyploidy in B. rapa. Furthermore, transcriptional factors (TFs) associated with flower development were significantly differentially expressed including the up-regulated CIB1 and AGL18, and the down-regulated AGL15 genes, and by working together such genes affected the expression of the down-stream flowering regulator FLOWERING LOCUS T in polyploid B. rapa. Compared with that in diploids autotetrapoid plants consist of differential expression within the signaling transduction pathway, with 13 TIFY gens up-regulated and 17 genes related to auxin pathway down-regulated. Conclusion Therefore, polyploidy is more likely to integrate multiple signaling pathways to influence flowering in B. rapa after polyploidization. In general, the present results shed new light on our global understanding of flowering regulation in polyploid plants during breeding program.

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Section: Degs Changes In Multiple Signal Transduction Pathway Affectmentioning

confidence: 72%

Comparative transcriptome analysis revealed differential gene expression in multiple signaling pathways at flowering in polyploid Brassica rapa

et al. 2021

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“…It has been concluded that increase of activity of FBA enhances photosynthetic capacity, growth, and plant productivity or biomass [ 34 – 36 ], which is consistent with the high-yield of accession Viroflay as reported in the previous studies [ 30 ] and a higher number of DEGs associated with “photosynthesis” term in Viroflay under present study. Among genes involved in carbohydrate metabolism, TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1), which catalyzes the formation of trehalose-6-phosphate (T6P), has been proposed to function as a proxy for carbohydrate status and a signal that coordinates the induction of flowering in plants [ 37 – 39 ]. In this way, Alpha, alpha-trehalose-phosphate synthase (TPS) gene with having important roles in sucrose and starch synthesis [ 37 , 38 ], and TPS1 were highly up-regulated in both vegetative and reproductive stages of accession Kashan, while in Viroflay showed an increase in expression during the transition from vegetative to reproductive growth.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome architecture reveals genetic networks of bolting regulation in spinach

et al. 2021

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Background Bolting refers to the early flowering stem production on agricultural and horticultural crops before harvesting. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components, which cause a large reduction in the quality and productivity of vegetable crops like spinach. However, little is known about the signaling pathways and molecular functions involved in bolting mechanisms in spinach. The genetic information regarding the transition from vegetative growth to the reproductive stage in spinach would represent an advantage to regulate bolting time and improvement of resistant cultivars to minimize performance loss. Results To investigate the key genes and their genetic networks controlling spinach bolting, we performed RNA-seq analysis on early bolting accession Kashan and late-bolting accession Viroflay at both vegetative and reproductive stages and found a significant number of differentially expressed genes (DEGs) ranging from 195 to 1230 in different comparisons. These genes were mainly associated with the signaling pathways of vernalization, photoperiod/circadian clock, gibberellin, autonomous, and aging pathways. Gene ontology analysis uncovered terms associated with carbohydrate metabolism, and detailed analysis of expression patterns for genes of Fructose-1, 6-bisphosphate aldolase, TREHALOSE-6-PHOSPHATE SYNTHASE 1, FLOWERING PROMOTING FACTOR 1, EARLY FLOWERING, GIGANTEA, and MADS-box proteins revealed their potential roles in the initiating or delaying of bolting. Conclusion This study is the first report on identifying bolting and flowering-related genes based on transcriptome sequencing in spinach, which provides insight into bolting control and can be useful for molecular breeding programs and further study in the regulation of the genetic mechanisms related to bolting in other vegetable crops.

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“…Three biological replicates were collected for each sample. The vernalization treatment, sample collection method, RNA-seq period selection, and the detailed methods used for data processing are described in our previous study [ 59 ].…”

Section: Methodsmentioning

confidence: 99%

Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization

et al. 2021

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Background Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. pekinensis), this process causes their commercial value to decline. Clarifying the mechanisms of vernalization is essential for its further application. 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. The biological function analysis and hub gene annotation of highly relevant modules revealed that shoot system morphogenesis and polysaccharide and sugar metabolism caused early-bolting ‘XBJ’ to bolt and flower faster; chitin, ABA and ethylene-activated signaling pathways were enriched in late-bolting ‘JWW’; 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. The high connectivity of hub genes regulated vernalization, including MTHFR2, CPRD49, AAP8, endoglucanase 10, BXLs, GATLs, and WRKYs. Additionally, five genes related to flower development, BBX32 (binds to the FT promoter), SUS1 (increases FT expression), TSF (the closest homologue of FT), PAO and NAC029 (plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions. Conclusion The present work provides a comprehensive overview of vernalization-related gene networks in two different-bolting Chinese cabbages during vernalization. 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.

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Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Vernalization Periods in Brassica rapa

Cited by 13 publications

References 83 publications

Comparative transcriptome analysis revealed differential gene expression in multiple signaling pathways at flowering in polyploid Brassica rapa

Comparative transcriptome analysis revealed differential gene expression in multiple signaling pathways at flowering in polyploid Brassica rapa

Transcriptome architecture reveals genetic networks of bolting regulation in spinach

Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization

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