Integrative analysis of physiology, biochemistry and transcriptome reveals the mechanism of leaf size formation in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Wang, Lixia; Zhang, Shu; Zhang, Ye; Li, Jingjuan; Zhang, Yihui; Zhou, Dan-Dan; Li, Cheng; He, Lilong; Li, Huayin; Wang, Fengde; Gao, Jianwei

doi:10.3389/fpls.2023.1183398

Cited by 3 publications

(2 citation statements)

References 60 publications

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“…Group 3 actively binds with CDKB1;1, and Group 2 binds with CDKB1;2 [ 9 ], possibly due to the diversity in protein structures among subfamilies. Several studies have confirmed that MSA cis -acting elements regulate G2/M transcription in plants [ 21 , 28 , 29 ]. However, we did not predict MSA elements in this study, possibly because of the strict standards regarding the deletion of MSA elements from non-Brassicaceae species.…”

Section: Discussionmentioning

confidence: 97%

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Genome-Wide Identification and Evolutionary and Expression Analyses of the Cyclin B Gene Family in Brassica napus

Li,

Zhang,

Meng

et al. 2024

Plants

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Cyclin B (CYCB) is a regulatory subunit of cyclin-dependent kinase (CDK), the concentration of which fluctuates to regulate cell cycle progression. Extensive studies have been performed on cyclins in numerous species, yet the evolutionary relationships and biological functions of the CYCB family genes in Brassica napus remain unclear. In this study, we identified 299 CYCB genes in 11 B. napus accessions. Phylogenetic analysis suggests that CYCB genes could be divided into three subfamilies in angiosperms and that the CYCB3 subfamily members may be a newer group that evolved in eudicots. The expansion of BnaCYCB genes underwent segmental duplication and purifying selection in genomes, and a number of drought-responsive and light-responsive cis-elements were found in their promoter regions. Additionally, expression analysis revealed that BnaCYCBs were strongly expressed in the developing seed and silique pericarp, as confirmed by the obviously reduced seed size of the mutant cycb3;1 in Arabidopsis thaliana compared with Col-0. This study provides a comprehensive evolutionary analysis of CYCB genes as well as insight into the biological function of CYCB genes in B. napus.

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Section: Discussionmentioning

confidence: 97%

“…The characterization and contribution of CYCB family genes have been well studied in A. thaliana , O. sativa, and Brassica rapa [ 5 , 6 , 21 ], whereas no research has focused on Brassica napus , one of the most important allopolyploid crops worldwide. Here, we identified CYCB genes across 11 B .…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Evolutionary and Expression Analyses of the Cyclin B Gene Family in Brassica napus

Li,

Zhang,

Meng

et al. 2024

Plants

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Genome-Wide Identification, Expression Analysis and Functional Study of DELLA Genes in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Yuan,

Wang,

Zhao

et al. 2024

Front. Biosci. (Landmark Ed)

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Background: DELLA protein is a crucial factor which played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, little is known about the function and information of DELLA protein in Chinese cabbage. Methods: Using 5 DELLA gene sequences in Arabidopsis Thaliana as probes, 5 DELLA genes in Chinese cabbage were identified by Blast search in Chinese cabbage database (Brassica database (BRAD)). The National Center for Biotechnology Information (NCBI), ExPaSy, SWISS-MODEL, DNAMAN, MEGA 11, PlantCARE were used to identify and analyze the DELLA gene family of Chinese cabbage. Gene expression was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). The function of BraA10gRGL3 was verified by overexpression and phenotypic analysis of BraA10gRGL3 and yeast hybrid. Results: In this study, 5 BraDELLAs homologous to Arabidopsis thaliana were identified and cloned based on the Brassica database, namely, BraA02gRGL1, BraA05gRGL2, BraA10gRGL3, BraA06gRGA and BraA09gRGA. All BraDELLAs contain the DELLA, TVHYNP, and GRAS conserved domains. Cis-element analysis revealed that the promoter regions of these 5 DELLA genes all contain light-responsive elements, TCT motif, I-box, G-box, and box 4, which are associated with GA signaling. Transcriptome analysis results proved that the expression of BraA02gRGL1, BraA05gRGL2, and BraA10gRGL3 in Y2 at different growth stages were lower than them in Y7, which is consistent with the phenotype that Y7 exhibited stronger stress tolerance than Y2. It is worth emphasizing that even through the overexpression of BraA10gRGL3-Y7 in Arabidopsis resulted in smaller leaf size and lower fresh weight compared to the wild type (WT) Arabidopsis: Columbia, a stronger response to abiotic stresses was observed in BraA10gRGL3-Y7. It indicated that BraA10gRGL3-Y7 can improve the stress resistance of plants by inhibiting their growth. Moreover, the yeast two-hybrid experiment confirmed that BraA10gRGL3-Y7 can interacted with BraA05gGID1a-Y7, BraA04gGID1b1, BraA09gGID1b3-Y2, and BraA06gGID1c, whereas BraA10gRGL3-Y2 cannot interact with any BraGID1. Conclusions: Collectively, BraDELLAs play important role in plant development and response to abiotic stress. The differences in amino acid sequences between BraA10gRGL3-Y2 and BraA10gRGL3-Y7 may result in variations in their protein binding sites, thus affecting their interaction with the BraGID1 family proteins. This systematic analysis lays the foundation for further study of the functional characteristics of DELLA genes of Chinese cabbage.

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Exploiting Brassica rapa L. subsp. pekinensis Genome Research

Ritonga,

Gong,

Zhang

et al. 2024

Plants

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Chinese cabbage, Brassica rapa L. subsp. pekinensis is a crucial and extensively consumed vegetable in the world, especially Eastern Asia. The market demand for this leafy vegetable increases year by year, resulting in multiple challenges for agricultural researchers worldwide. Multi-omic approaches and the integration of functional genomics helps us understand the relationships between Chinese cabbage genomes and phenotypes under specific physiological and environmental conditions. However, challenges exist in integrating multi-omics for the functional analysis of genes and for developing potential traits for Chinese cabbage improvement. However, the panomics platform allows for the integration of complex omics, enhancing our understanding of molecular regulator networks in Chinese cabbage agricultural traits. In addition, the agronomic features of Chinese cabbage are significantly impacted by the environment. The expression of these agricultural features is tightly regulated by a combination of signals from both the internal regulatory network and the external growth environment. To comprehend the molecular process of these characteristics, it is necessary to have a prior understanding of molecular breeding for the objective of enhancing quality. While the use of various approaches in Chinese cabbage is still in its early stages, recent research has shown that it has the potential to uncover new regulators both rapidly and effectively, leading to updated regulatory networks. In addition, the utilization of the efficient transformation technique in conjunction with gene editing using CRISPR/Cas9 will result in a reduction in time requirements and facilitate a more precise understanding of the role of the regulators. Numerous studies about Chinese cabbage have been conducted in the past two decades, but a comprehensive review about its genome still limited. This review provides a concise summary of the latest discoveries in genomic research related to Brassica and explores the potential future developments for this species.

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Integrative analysis of physiology, biochemistry and transcriptome reveals the mechanism of leaf size formation in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Cited by 3 publications

References 60 publications

Genome-Wide Identification and Evolutionary and Expression Analyses of the Cyclin B Gene Family in Brassica napus

Genome-Wide Identification and Evolutionary and Expression Analyses of the Cyclin B Gene Family in Brassica napus

Genome-Wide Identification, Expression Analysis and Functional Study of DELLA Genes in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Exploiting Brassica rapa L. subsp. pekinensis Genome Research

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