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Li X, Lin C, Lan C, Tao Z. Genetic and epigenetic basis of phytohormonal control of floral transition in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4180-4194. [PMID: 38457356 DOI: 10.1093/jxb/erae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/06/2024] [Indexed: 03/10/2024]
Abstract
The timing of the developmental transition from the vegetative to the reproductive stage is critical for angiosperms, and is fine-tuned by the integration of endogenous factors and external environmental cues to ensure successful reproduction. Plants have evolved sophisticated mechanisms to response to diverse environmental or stress signals, and these can be mediated by hormones to coordinate flowering time. Phytohormones such as gibberellin, auxin, cytokinin, jasmonate, abscisic acid, ethylene, and brassinosteroids and the cross-talk among them are critical for the precise regulation of flowering time. Recent studies of the model flowering plant Arabidopsis have revealed that diverse transcription factors and epigenetic regulators play key roles in relation to the phytohormones that regulate floral transition. This review aims to summarize our current knowledge of the genetic and epigenetic mechanisms that underlie the phytohormonal control of floral transition in Arabidopsis, offering insights into how these processes are regulated and their implications for plant biology.
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Affiliation(s)
- Xiaoxiao Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chuyu Lin
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenghao Lan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeng Tao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Xie H, Li X, Sun Y, Lin L, Xu K, Lu H, Cheng B, Xue S, Cheng D, Qiang S. DNA Methylation of the Autonomous Pathway Is Associated with Flowering Time Variations in Arabidopsis thaliana. Int J Mol Sci 2024; 25:7478. [PMID: 39000585 PMCID: PMC11242178 DOI: 10.3390/ijms25137478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
Plant flowering time is affected by endogenous and exogenous factors, but its variation patterns among different populations of a species has not been fully established. In this study, 27 Arabidopsis thaliana accessions were used to investigate the relationship between autonomous pathway gene methylation, gene expression and flowering time variation. DNA methylation analysis, RT-qPCR and transgenic verification showed that variation in the flowering time among the Arabidopsis populations ranged from 19 to 55 days and was significantly correlated with methylation of the coding regions of six upstream genes in the autonomous pathway, FLOWERING LOCUS VE (FVE), FLOWERING LOCUS Y (FY), FLOWERING LOCUS D (FLD), PEPPER (PEP), HISTONE DEACETYLASE 5 (HAD5) and Pre-mRNA Processing Protein 39-1 (PRP39-1), as well as their relative expression levels. The expression of FVE and FVE(CS) was modified separately through degenerate codon substitution of cytosine and led to earlier flowering of transgenic plants by 8 days and 25 days, respectively. An accurate determination of methylated sites in FVE and FVE(CS) among those transgenic plants and the recipient Col-0 verified the close relationship between the number of methylation sites, expression and flowering time. Our findings suggest that the methylation variation of these six key upstream transcription factors was associated with the gene expression level of the autonomous pathway and flowering time in Arabidopsis. The FVE(CS) and FVE genes in transgenic plants tended to be hypermethylated, which could be a protective mechanism for plants. However, modification of gene sequences through degenerate codon substitution to reduce cytosine can avoid hypermethylated transferred genes in transgenic plants. It may be possible to partially regulate the flowering of plants by modified trans-epigenetic technology.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sheng Qiang
- Weed Research Laboratory, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; (H.X.); (X.L.); (Y.S.); (L.L.); (K.X.); (H.L.); (B.C.); (S.X.); (D.C.)
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Wang M, Li J, Li T, Kang S, Jiang S, Huang J, Tang H. Light Supplementation in Pitaya Orchards Induces Pitaya Flowering in Winter by Promoting Phytohormone Biosynthesis. Int J Mol Sci 2024; 25:4794. [PMID: 38732009 PMCID: PMC11083671 DOI: 10.3390/ijms25094794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
The interaction between light and phytohormones is crucial for plant growth and development. The practice of supplementing light at night during winter to promote pitaya flowering and thereby enhance yield has been shown to be crucial and widely used. However, it remains unclear how supplemental winter light regulates phytohormone levels to promote flowering in pitaya. In this study, through analyzing the transcriptome data of pitaya at four different stages (NL, L0, L1, L2), we observed that differentially expressed genes (DEGs) were mainly enriched in the phytohormone biosynthesis pathway. We further analyzed the data and found that cytokinin (CK) content first increased at the L0 stage and then decreased at the L1 and L2 stages after supplemental light treatment compared to the control (NL). Gibberellin (GA), auxin (IAA), salicylic acid (SA), and jasmonic acid (JA) content increased during the formation of flower buds (L1, L2 stages). In addition, the levels of GA, ethylene (ETH), IAA, and abscisic acid (ABA) increased in flower buds after one week of development (L2f). Our results suggest that winter nighttime supplemental light can interact with endogenous hormone signaling in pitaya, particularly CK, to regulate flower bud formation. These results contribute to a better understanding of the mechanism of phytohormone interactions during the induction of flowering in pitaya under supplemental light in winter.
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Affiliation(s)
- Meng Wang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (M.W.); (J.L.); (T.L.); (S.K.); (S.J.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Jiaxue Li
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (M.W.); (J.L.); (T.L.); (S.K.); (S.J.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Tao Li
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (M.W.); (J.L.); (T.L.); (S.K.); (S.J.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Shaoling Kang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (M.W.); (J.L.); (T.L.); (S.K.); (S.J.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Senrong Jiang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (M.W.); (J.L.); (T.L.); (S.K.); (S.J.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Jiaquan Huang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (M.W.); (J.L.); (T.L.); (S.K.); (S.J.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Hua Tang
- Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (M.W.); (J.L.); (T.L.); (S.K.); (S.J.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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Du X, Gao Y, Zhang H, Xu X, Li Y, Zhao L, Luo M, Wang H. HDA6 modulates Arabidopsis pavement cell morphogenesis through epigenetic suppression of ROP6 GTPase expression and signaling. THE NEW PHYTOLOGIST 2024; 241:2523-2539. [PMID: 38214469 DOI: 10.1111/nph.19532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/13/2024]
Abstract
The transcriptional regulation of Rho-related GTPase from plants (ROPs), which determine cell polarity formation and maintenance during plant development, still remains enigmatic. In this study, we elucidated the epigenetic mechanism of histone deacetylase HDA6 in transcriptional repression of ROP6 and its impact on cell polarity and morphogenesis in Arabidopsis leaf epidermal pavement cells (PCs). We found that the hda6 mutant axe1-4 exhibited impaired jigsaw-shaped PCs and convoluted leaves. This correlated with disruptions in the spatial organizations of cortical microtubules and filamentous actin, which is integral to PC indentation and lobe formation. Further transcriptional analyses and chromatin immunoprecipitation assay revealed that HDA6 specifically represses ROP6 expression through histone H3K9K14 deacetylation. Importantly, overexpression of dominant negative-rop6 in axe1-4 restored interdigitated cell morphology. Our study unveils HDA6 as a key regulator in Arabidopsis PC morphogenesis through epigenetic suppression of ROP6. It reveals the pivotal role of HDA6 in the transcriptional regulation of ROP6 and provides compelling evidence for the functional interplay between histone deacetylation and ROP6-mediated cytoskeletal arrangement in the development of interdigitated PCs.
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Affiliation(s)
- Xiaojuan Du
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingmiao Gao
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Zhang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoyu Xu
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Li
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lifeng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Wang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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Hou H, Wu C, Huo J, Liu N, Jiang Y, Sui S, Li Z. Integrated transcriptome and proteome analysis provides insights into CpFPA1 for floral induction in Chimonanthus praecox (Magnoliidae) without FLC in genome. PLANT CELL REPORTS 2024; 43:66. [PMID: 38341387 DOI: 10.1007/s00299-024-03145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/31/2023] [Indexed: 02/12/2024]
Abstract
KEY MESSAGE We used transcriptomic and proteomic association analysis to reveal the critical genes/proteins at three key flower bud differentiation stages and overexpression of CpFPA1 in Arabidopsis resulted in earlier flowering. Wintersweet (Chimonanthus praecox), a rare winter-flowering woody plant, is well known for its unique blooming time, fragrance and long flowering period. However, the molecular mechanism of flowering in C. praecox remains poorly unclear. In this study, we used transcriptomic and proteomic association analysis to reveal the critical genes/proteins at three key flower bud (FB) differentiation stages (FB.Apr, FB.May and FB.Nov) in C. praecox. The results showed that a total of 952 differential expressed genes (DEGs) and 40 differential expressed proteins (DEPs) were identified. Gene ontology (GO) enrichment revealed that DEGs in FB.Apr/FB.May comparison group were mainly involved in metabolic of biological process, cell and cell part of cellular component and catalytic activity of molecular function. In the EuKaryotic Orthologous Groups (KOG) functional classification, DEPs were predicted mainly in the function of general function prediction only (KOG0118), post-translational modification, protein turnover and chaperones. The autonomous pathway genes play an essential role in the floral induction. Based on transcriptome and proteome correlation analysis, six candidate genes associated with the autonomous pathway were identified, including FPA1, FPA2a, FPA2b, FCA, FLK, FY. Furthermore, CpFPA1 was isolated and functionally characterized, and ectopic expression of CpFPA1 in Arabidopsis Columbia (Col-0) resulted in earlier flowering. These data could contribute to understand the function of CpFPA1 for floral induction and provide information for further research on the molecular mechanisms of flowering in wintersweet.
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Affiliation(s)
- Huifang Hou
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Chunyu Wu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Juntao Huo
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Ning Liu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Yingjie Jiang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Shunzhao Sui
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Zhineng Li
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
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Yuan C, Hu Y, Liu Q, Xu J, Zhou W, Yu H, Shen L, Qin C. MED8 regulates floral transition in Arabidopsis by interacting with FPA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1234-1247. [PMID: 37565662 DOI: 10.1111/tpj.16419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/04/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Success in plant reproduction is highly dependent on the correct timing of the floral transition, which is tightly regulated by the flowering pathways. In the model plant Arabidopsis thaliana, the central flowering repressor FLOWERING LOCUS C (FLC) is precisely regulated by multiple flowering time regulators in the vernalization pathway and autonomous pathway, including FPA. Here we report that Arabidopsis MEDIATOR SUBUNIT 8 (MED8) promotes floral transition in Arabidopsis by recruiting FPA to the FLC locus to repress FLC expression. Loss of MED8 function leads to a significant late-flowering phenotype due to increased FLC expression. We further show that MED8 directly interacts with FPA in the nucleus and recruits FPA to the FLC locus. Moreover, MED8 is indispensable for FPA's function in controlling flowering time and regulating FLC expression. Our study thus reveals a flowering mechanism by which the Mediator subunit MED8 represses FLC expression by facilitating the binding of FPA to the FLC locus to ensure appropriate timing of flowering for reproductive success.
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Affiliation(s)
- Chen Yuan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yikai Hu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qinggang Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jingya Xu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Wei Zhou
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Hao Yu
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 117543, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Cheng Qin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
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Rehman S, Bahadur S, Xia W. An overview of floral regulatory genes in annual and perennial plants. Gene 2023; 885:147699. [PMID: 37567454 DOI: 10.1016/j.gene.2023.147699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
The floral initiation in angiosperms is a complex process influenced by endogenous and exogenous signals. With this approach, we aim to provide a comprehensive review to integrate this complex floral regulatory process and summarize the regulatory genes and their functions in annuals and perennials. Seven primary paths leading to flowering have been discovered in Arabidopsis under several growth condition that include; photoperiod, ambient temperature, vernalization, gibberellins, autonomous, aging and carbohydrates. These pathways involve a series of interlinked signaling pathways that respond to both internal and external signals, such as light, temperature, hormones, and developmental cues, to coordinate the expression of genes that are involved in flower development. Among them, the photoperiodic pathway was the most important and conserved as some of the fundamental loci and mechanisms are shared even by closely related plant species. The activation of floral regulatory genes such as FLC, FT, LFY, and SOC1 that determine floral meristem identity and the transition to the flowering stage result from the merging of these pathways. Recent studies confirmed that alternative splicing, antisense RNA and epigenetic modification play crucial roles by regulating the expression of genes related to blooming. In this review, we documented recent progress in the floral transition time in annuals and perennials, with emphasis on the specific regulatory mechanisms along with the application of various molecular approaches including overexpression studies, RNA interference and Virus-induced flowering. Furthermore, the similarities and differences between annual and perennial flowering will aid significant contributions to the field by elucidating the mechanisms of perennial plant development and floral initiation regulation.
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Affiliation(s)
- Shazia Rehman
- Sanya Nanfan Research Institution, Hainan University, Haikou 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Saraj Bahadur
- College of Forestry, Hainan University, Haikou 570228 China
| | - Wei Xia
- Sanya Nanfan Research Institution, Hainan University, Haikou 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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Wang J, Zhang B, Guo H, Chen L, Han F, Yan C, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Zhang Y. Transcriptome Analysis Reveals Key Genes and Pathways Associated with the Regulation of Flowering Time in Cabbage ( Brassica oleracea L. var. capitata). PLANTS (BASEL, SWITZERLAND) 2023; 12:3413. [PMID: 37836153 PMCID: PMC10574337 DOI: 10.3390/plants12193413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/17/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023]
Abstract
Flowering time is an important agronomic trait in cabbage (Brassica oleracea L. var. capitata), but the molecular regulatory mechanism underlying flowering time regulation in cabbage remains unclear. In this study, transcriptome analysis was performed using two sets of cabbage materials: (1) the early-flowering inbred line C491 (P1) and late-flowering inbred line B602 (P2), (2) the early-flowering individuals F2-B and late-flowering individuals F2-NB from the F2 population. The analysis revealed 9508 differentially expressed genes (DEGs) common to both C491_VS_ B602 and F2-B_VS_F2-NB. The Kyoto Encyclopedia of Genes and Genomes (KEGGs) analysis showed that plant hormone signal transduction and the MAPK signaling pathway were mainly enriched in up-regulated genes, and ribosome and DNA replication were mainly enriched in down-regulated genes. We identified 321 homologues of Arabidopsis flowering time genes (Ft) in cabbage. Among them, 25 DEGs (11 up-regulated and 14 down-regulated genes) were detected in the two comparison groups, and 12 gene expression patterns closely corresponded with the different flowering times in the two sets of materials. Two genes encoding MADS-box proteins, Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), showed significantly reduced expression in the late-flowering parent B602 compared with the early-flowering parent C491 via qRT-PCR analysis, which was consistent with the RNA-seq data. Next, the expression levels of Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2) were analyzed in two other groups of early-flowering and late-flowering inbred lines, which showed that their expression patterns were consistent with those in the parents. Sequence analysis revealed that three and one SNPs between B602 and C491 were identified in Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), respectively. Therefore, BoSEP2-1 and BoSEP2-2 were designated as candidates for flowering time regulation through a potential new regulatory pathway. These results provide new insights into the molecular mechanisms underlying flowering time regulation in cabbage.
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Affiliation(s)
- Jiao Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China;
| | - Bin Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Huiling Guo
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Li Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Chao Yan
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China;
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Mu Zhuang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.W.); (B.Z.); (H.G.); (L.C.); (F.H.); (L.Y.); (M.Z.); (H.L.); (J.J.); (Y.W.)
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9
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Heidari B, Nemie-Feyissa D, Lillo C. Distinct Clades of Protein Phosphatase 2A Regulatory B'/B56 Subunits Engage in Different Physiological Processes. Int J Mol Sci 2023; 24:12255. [PMID: 37569631 PMCID: PMC10418862 DOI: 10.3390/ijms241512255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is a strongly conserved and major protein phosphatase in all eukaryotes. The canonical PP2A complex consists of a catalytic (C), scaffolding (A), and regulatory (B) subunit. Plants have three groups of evolutionary distinct B subunits: B55, B' (B56), and B''. Here, the Arabidopsis B' group is reviewed and compared with other eukaryotes. Members of the B'α/B'β clade are especially important for chromatid cohesion, and dephosphorylation of transcription factors that mediate brassinosteroid (BR) signaling in the nucleus. Other B' subunits interact with proteins at the cell membrane to dampen BR signaling or harness immune responses. The transition from vegetative to reproductive phase is influenced differentially by distinct B' subunits; B'α and B'β being of little importance, whereas others (B'γ, B'ζ, B'η, B'θ, B'κ) promote transition to flowering. Interestingly, the latter B' subunits have three motifs in a conserved manner, i.e., two docking sites for protein phosphatase 1 (PP1), and a POLO consensus phosphorylation site between these motifs. This supports the view that a conserved PP1-PP2A dephosphorelay is important in a variety of signaling contexts throughout eukaryotes. A profound understanding of these regulators may help in designing future crops and understand environmental issues.
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Affiliation(s)
| | | | - Cathrine Lillo
- IKBM, Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4036 Stavanger, Norway; (B.H.); (D.N.-F.)
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10
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Jiang M, Zhang Y, Yang X, Li X, Lang H. Brassica rapa orphan gene BR1 delays flowering time in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1135684. [PMID: 36909380 PMCID: PMC9998908 DOI: 10.3389/fpls.2023.1135684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Orphan genes are essential to the emergence of species-specific traits and the process of evolution, lacking sequence similarity to any other identified genes. As they lack recognizable domains or functional motifs, however, efforts to characterize these orphan genes are often difficult. Flowering is a key trait in Brassica rapa, as premature bolting can have a pronounced adverse impact on plant quality and yield. Bolting resistance-related orphan genes, however, have yet to be characterized. In this study, an orphan gene designated BOLTING RESISTANCE 1 (BR1) was identified and found through gene structural variation analyses to be more highly conserved in Chinese cabbage than in other available accessions. The expression of BR1 was increased in bolting resistant Chinese cabbage and decreased in bolting non-resistant type, and the expression of some mark genes were consist with bolting resistance phenotype. BR1 is primarily expressed in leaves at the vegetative growth stage, and the highest BR1 expression levels during the flowering stage were observed in the flower buds and silique as compared to other tissue types. The overexpression of BR1 in Arabidopsis was associated with enhanced bolting resistance under long day (LD) conditions, with these transgenic plants exhibiting significant decreases in stem height, rosette radius, and chlorophyll content. Transcriptomic sequencing of WT and BR1OE plants showed the association of BR1 with other bolting resistance genes. Transcriptomic sequencing and qPCR revealed that six flowering integrator genes and one chlorophyll biosynthesis-related gene were downregulated following BR1 overexpression. Six key genes in photoperiodic flowering pathway exhibited downward expression trends in BR1OE plants, while the expression of floral repressor AtFLC gene was upregulated. The transcripts of these key genes were consistent with observed phenotypes in BR1OE plants, and the results indicated that BR1 may function through vernalization and photoperiodic pathway. Instead, the protein encoded by BR1 gene was subsequently found to localize to the nucleus. Taken together, we first propose that orphan gene BR1 functions as a novel regulator of flowering time, and these results suggested that BR1 may represent a promising candidate gene to support the selective breeding of Chinese cabbage cultivars with enhanced bolting resistance.
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Affiliation(s)
- Mingliang Jiang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
| | - Yuting Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiaolong Yang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hong Lang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
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Liang C, Liu L, Zhang Z, Ze S, Pei L, Feng L, Ji M, Yang B, Zhao N. Transcriptome analysis of critical genes related to flowering in Mikania micrantha at different altitudes provides insights for a potential control. BMC Genomics 2023; 24:14. [PMID: 36627560 PMCID: PMC9832669 DOI: 10.1186/s12864-023-09108-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mikania micrantha is a vine with strong invasion ability, and its strong sexual reproduction ability is not only the main factor of harm, but also a serious obstacle to control. M. micrantha spreads mainly through seed production. Therefore, inhibiting the flowering and seed production of M. micrantha is an effective strategy to prevent from continuing to spread. RESULT The flowering number of M. micrantha is different at different altitudes. A total of 67.01 Gb of clean data were obtained from nine cDNA libraries, and more than 83.47% of the clean reads were mapped to the reference genome. In total, 5878 and 7686 significantly differentially expressed genes (DEGs) were found in E2 vs. E9 and E13 vs. E9, respectively. Based on the background annotation and gene expression, some candidate genes related to the flowering pathway were initially screened, and their expression levels in the three different altitudes in flower bud differentiation showed the same trend. That is, at an altitude of 1300 m, the flower integration gene and flower meristem gene were downregulated (such as SOC1 and AP1), and the flowering inhibition gene was upregulated (such as FRI and SVP). Additionally, the results showed that there were many DEGs involved in the hormone signal transduction pathway in the flower bud differentiation of M. micrantha at different altitudes. CONCLUSIONS Our results provide abundant sequence resources for clarifying the underlying mechanisms of flower bud differentiation and mining the key factors inhibiting the flowering and seed production of M. micrantha to provide technical support for the discovery of an efficient control method.
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Affiliation(s)
- Chen Liang
- grid.412720.20000 0004 1761 2943College of Life Sciences, Southwest Forestry University, Kunming, 650224 China
| | - Ling Liu
- grid.464490.b0000 0004 1798 048XYunnan Academy of Forestry and Grassland, Kunming, 650201 China
| | - Zhixiao Zhang
- grid.464490.b0000 0004 1798 048XYunnan Academy of Forestry and Grassland, Kunming, 650201 China
| | - Sangzi Ze
- Yunnan Forestry and Grassland Pest Control and Quarantine Bureau, Kunming, 650051 China
| | - Ling Pei
- grid.412720.20000 0004 1761 2943College of Life Sciences, Southwest Forestry University, Kunming, 650224 China
| | - Lichen Feng
- grid.412720.20000 0004 1761 2943College of Life Sciences, Southwest Forestry University, Kunming, 650224 China
| | - Mei Ji
- grid.464490.b0000 0004 1798 048XYunnan Academy of Forestry and Grassland, Kunming, 650201 China
| | - Bin Yang
- grid.412720.20000 0004 1761 2943Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, 650224 China
| | - Ning Zhao
- grid.412720.20000 0004 1761 2943College of Life Sciences, Southwest Forestry University, Kunming, 650224 China ,grid.412720.20000 0004 1761 2943Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, 650224 China
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12
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Hao JF, Wang C, Gu CR, Xu DX, Zhang L, Zhang HG. Anatomical observation and transcriptome analysis of buds reveal the association between the AP2 gene family and reproductive induction in hybrid larch (Larix kaempferi × Larix olgensis). TREE PHYSIOLOGY 2023; 43:118-129. [PMID: 36150026 PMCID: PMC9833870 DOI: 10.1093/treephys/tpac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Hybrid larch is an excellent afforestation species in northern China. The instability of seed yield is an urgent problem to be solved. The biological characteristics related to seed setting in larch are different from those in angiosperms and other gymnosperms. Studying the developmental mechanism of the larch sporophyll can deepen our understanding of conifer reproductive development and help to ensure an adequate supply of seeds in the seed orchard. The results showed that the formation of microstrobilus primordia in hybrid larch could be observed in anatomical sections collected in the middle of July. The contents of endogenous gibberellin 3 (GA3) and abscisic acid (ABA) were higher and the contents of GA4, GA7, jasmonic acid and salicylic acid were lower in multiseeded larch. Transcriptome analysis showed that transcription factors were significantly enriched in the AP2 family. There were 23 differentially expressed genes in the buds of the multiseeded and less-seeded types, and the expression of most of these genes was higher in the buds than in the needles. We conclude that mid-July is the early stage of reproductive organ development in hybrid larch and is suitable for the study of reproductive development. GA3 and ABA may be helpful for improving seed setting in larch, and 23 AP2/EREBP family genes are involved in the regulation of reproductive development in larch.
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Affiliation(s)
- Jun-Fei Hao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Chen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Chen-Rui Gu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Dai-Xi Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Han-Guo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51 Hexing Road, Xiangfang District, Harbin 150040, China
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13
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Waheed S, Liang F, Zhang M, He D, Zeng L. High-Throughput Sequencing Reveals Novel microRNAs Involved in the Continuous Flowering Trait of Longan ( Dimocarpus longan Lour.). Int J Mol Sci 2022; 23:15565. [PMID: 36555206 PMCID: PMC9779457 DOI: 10.3390/ijms232415565] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
A major determinant of fruit production in longan (Dimocarpus longan Lour.) is the difficulty of blossoming. In this study, high-throughput microRNA sequencing (miRNA-Seq) was carried out to compare differentially expressed miRNAs (DEmiRNAs) and their target genes between a continuous flowering cultivar 'Sijimi' (SJ), and a unique cultivar 'Lidongben' (LD), which blossoms only once in the season. Over the course of our study, 1662 known miRNAs and 235 novel miRNAs were identified and 13,334 genes were predicted to be the target of 1868 miRNAs. One conserved miRNA and 29 new novel miRNAs were identified as differently expressed; among them, 16 were upregulated and 14 were downregulated. Through the KEGG pathway and cluster analysis of DEmiRNA target genes, three critical regulatory pathways, plant-pathogen interaction, plant hormone signal transduction, and photosynthesis-antenna protein, were discovered to be strongly associated with the continuous flowering trait of the SJ. The integrated correlation analysis of DEmiRNAs and their target mRNAs revealed fourteen important flowering-related genes, including COP1-like, Casein kinase II, and TCP20. These fourteen flowering-related genes were targeted by five miRNAs, which were novel-miR137, novel-miR76, novel-miR101, novel-miR37, and csi-miR3954, suggesting these miRNAs might play vital regulatory roles in flower regulation in longan. Furthermore, novel-miR137 was cloned based on small RNA sequencing data analysis. The pSAK277-miR137 transgenic Arabidopsis plants showed delayed flowering phenotypes. This study provides new insight into molecular regulation mechanisms of longan flowering.
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Affiliation(s)
| | | | | | | | - Lihui Zeng
- Institute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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14
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Ouyang Y, Zhang X, Wei Y, He Y, Zhang X, Li Z, Wang C, Zhang H. AcBBX5, a B-box transcription factor from pineapple, regulates flowering time and floral organ development in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1060276. [PMID: 36507446 PMCID: PMC9729951 DOI: 10.3389/fpls.2022.1060276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Flowering is an important factor to ensure the success of plant reproduction, and reasonable flowering time is crucial to the crop yield. BBX transcription factors can regulate several growth and development processes. However, there is little research on whether BBX is involved in flower formation and floral organ development of pineapple. In this study, AcBBX5, a BBX family gene with two conserved B-box domains, was identified from pineapple. Subcellular localization analysis showed that AcBBX5 was located in the nucleus. Transactivation analysis indicated that AcBBX5 had no significant toxic effects on the yeast system and presented transcriptional activation activity in yeast. Overexpression of AcBBX5 delayed flowering time and enlarged flower morphology in Arabidopsis. Meanwhile, the expression levels of AtFT, AtSOC1, AtFUL and AtSEP3 were decreased, and the transcription levels of AtFLC and AtSVP were increased in AcBBX5-overexpressing Arabidopsis, which might lead to delayed flowering of transgenic plants. Furthermore, transcriptome data and QRT-PCR results showed that AcBBX5 was expressed in all floral organs, with the high expression levels in stamens, ovaries and petals. Yeast one-hybrid and dual luciferase assay results showed that AcBBX5 bound to AcFT promoter and inhibited AcFT gene expression. In conclusion, AcBBX5 was involved in flower bud differentiation and floral organ development, which provides an important reference for studying the functions of BBX and the molecular regulation of flower.
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Affiliation(s)
- Yanwei Ouyang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Sanya Nanfan Research Institute, Hainan University, Haikou, China
| | - Xiumei Zhang
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Yongzan Wei
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Yukun He
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Sanya Nanfan Research Institute, Hainan University, Haikou, China
| | - Xiaohan Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Sanya Nanfan Research Institute, Hainan University, Haikou, China
| | - Ziqiong Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Sanya Nanfan Research Institute, Hainan University, Haikou, China
| | - Can Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Sanya Nanfan Research Institute, Hainan University, Haikou, China
| | - Hongna Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Sanya Nanfan Research Institute, Hainan University, Haikou, China
- Key Laboratory of Ministry of Agriculture for Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
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15
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Mutation of an Essential 60S Ribosome Assembly Factor MIDASIN 1 Induces Early Flowering in Arabidopsis. Int J Mol Sci 2022; 23:ijms23126509. [PMID: 35742952 PMCID: PMC9223865 DOI: 10.3390/ijms23126509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
Ribosome biogenesis is tightly associated with plant growth and reproduction. Mutations in genes encoding ribosomal proteins (RPs) or ribosome biogenesis factors (RBFs) generally result in retarded growth and delayed flowering. However, the early-flowering phenotype resulting from the ribosome biogenesis defect is rarely reported. We previously identified that the AAA-ATPase MIDASIN 1 (MDN1) functions as a 60S RBF in Arabidopsis. Here, we found that its weak mutant mdn1-1 is early-flowering. Transcriptomic analysis showed that the expression of FLOWERING LOCUS C (FLC) is down-regulated, while that of some autonomous pathway genes and ABSCISIC ACID-INSENSITIVE 5 (ABI5) is up-regulated in mdn1-1. Phenotypic analysis revealed that the flowering time of mdn1-1 is severely delayed by increasing FLC expression, suggesting that the early flowering in mdn1-1 is likely associated with the downregulation of FLC. We also found that the photoperiod pathway downstream of CONSTANTS (CO) and FLOWERING LOCUS T (FT) might contribute to the early flowering in mdn1-1. Intriguingly, the abi5-4 allele completely blocks the early flowering in mdn1-1. Collectively, our results indicate that the ribosome biogenesis defect elicited by the mutation of MDN1 leads to early flowering by affecting multiple flowering regulation pathways.
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16
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Bernardi Y, Ponso MA, Belén F, Vegetti AC, Dotto MC. MicroRNA miR394 regulates flowering time in Arabidopsis thaliana. PLANT CELL REPORTS 2022; 41:1375-1388. [PMID: 35333960 DOI: 10.1007/s00299-022-02863-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
miR394 regulates Arabidopsis flowering time in a LCR-independent manner. Arabidopsis plants harboring mutations in theMIR394 genes exhibit early flowering, lower expression of floral repressor FLC and higher expression of floral integrators FT and SOC1. Plant development occurs throughout its entire life cycle and involves a phase transition between vegetative and reproductive phases, leading to the flowering process, fruit formation and ultimately seed production. It has been shown that the microRNA394 (miR394) regulates the accumulation of the transcript coding for LEAF CURLING RESPONSIVENESS, a member of a family of F-Box proteins. The miR394 pathway regulates several processes including leaf morphology and development of the shoot apical meristem during embryogenesis, as well as having been assigned a role in the response to biotic and abiotic stress in Arabidopsis thaliana and other species. Here, we characterized plants harboring mutations in MIR394 precursor genes and demonstrate that mir394a mir394b double mutants display an early flowering phenotype which correlates with a lower expression of FLOWERING LOCUS C earlier in development and higher expression of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1. Consequently, mutant plants produce fewer branches and exhibit lower seed production. Our work reveals previously unknown developmental aspects regulated by the miR394 pathway, in an LCR-independent manner, contributing to the characterization of the multiple roles of this versatile plant regulatory miRNA.
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Affiliation(s)
- Yanel Bernardi
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
- Instituto Tecnológico de Chascomús (INTECH, CONICET-UNSAM), Chascomús, Argentina
| | - María Agustina Ponso
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
- Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB, UNVM-CONICET). Instituto de Ciencias Básicas, Villa María, Córdoba, Argentina
| | - Federico Belén
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
| | - Abelardo C Vegetti
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
| | - Marcela C Dotto
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina.
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17
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Zhang X, Nomoto M, Garcia-León M, Takahashi N, Kato M, Yura K, Umeda M, Rubio V, Tada Y, Furumoto T, Aoyama T, Tsuge T. CFI 25 Subunit of Cleavage Factor I is Important for Maintaining the Diversity of 3' UTR Lengths in Arabidopsis thaliana (L.) Heynh. PLANT & CELL PHYSIOLOGY 2022; 63:369-383. [PMID: 35016226 DOI: 10.1093/pcp/pcac002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/28/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Cleavage and polyadenylation at the 3' end of the pre-mRNA is essential for mRNA function, by regulating its translatability, stability and translocation to the cytoplasm. Cleavage factor I (CFI) is a multi-subunit component of the pre-mRNA 3' end processing machinery in eukaryotes. Here, we report that plant CFI 25 subunit of CFI plays an important role in maintaining the diversity of the 3' ends of mRNA. The genome of Arabidopsis thaliana (L.) Heynh. contained four genes encoding three putative CFI subunits (AtCFI 25, AtCFI 59 and AtCFI 68), orthologous to the mammalian CFI subunits. There were two CFI 25 paralogs (AtCFI 25a and AtCFI 25b) that shared homology with human CFI 25. Two null alleles of AtCFI 25a displayed smaller rosette leaves, longer stigmatic papilla, smaller anther, earlier flowering and lower fertility compared to wild-type plants. Null alleles of AtCFI 25b, as well as, plants ectopically expressing full-length cDNA of AtCFI 25a, displayed no obvious morphological defects. AtCFI 25a was shown to interact with AtCFI 25b, AtCFI 68 and itself, suggesting various forms of CFI in plants. Furthermore, we show that AtCFI 25a function was essential for maintaining proper diversity of the 3' end lengths of transcripts coding for CFI subunits, suggesting a self-regulation of the CFI machinery in plants. AtCFI 25a was also important to maintain 3' ends for other genes to different extent. Collectively, AtCFI 25a, but not AtCFI 25b, seemed to play important roles during Arabidopsis development by maintaining proper diversity of the 3' UTR lengths.
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Affiliation(s)
- Xiaojuan Zhang
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Nagoya, Aichi, 464-8601 Japan
| | - Marta Garcia-León
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Naoki Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan
| | - Mariko Kato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, 162-0041 Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo, Tokyo, 112-8610 Japan
- Center for Interdisciplinary AI and Data Science, Ochanomizu University, Bunkyo, Tokyo, 112-8610 Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan
| | - Vicente Rubio
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, Aichi, 464-8601 Japan
| | - Tsuyoshi Furumoto
- Department of Plant Life Science, Graduate School of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194 Japan
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011 Japan
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18
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Xu X, Xu J, Yuan C, Hu Y, Liu Q, Chen Q, Zhang P, Shi N, Qin C. Characterization of genes associated with TGA7 during the floral transition. BMC PLANT BIOLOGY 2021; 21:367. [PMID: 34380420 PMCID: PMC8359562 DOI: 10.1186/s12870-021-03144-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 07/14/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND The TGACG-binding (TGA) family has 10 members that play vital roles in Arabidopsis thaliana defense responses and development. However, their involvement in controlling flowering time remains largely unknown and requires further investigation. RESULTS To study the role of TGA7 during floral transition, we first investigated the tga7 mutant, which displayed a delayed-flowering phenotype under both long-day and short-day conditions. We then performed a flowering genetic pathway analysis and found that both autonomous and thermosensory pathways may affect TGA7 expression. Furthermore, to reveal the differential gene expression profiles between wild-type (WT) and tga7, cDNA libraries were generated for WT and tga7 mutant seedlings at 9 days after germination. For each library, deep-sequencing produced approximately 6.67 Gb of high-quality sequences, with the majority (84.55 %) of mRNAs being between 500 and 3,000 nt. In total, 325 differentially expressed genes were identified between WT and tga7 mutant seedlings. Among them, four genes were associated with flowering time control. The differential expression of these four flowering-related genes was further validated by qRT-PCR. CONCLUSIONS Among these four differentially expressed genes associated with flowering time control, FLC and MAF5 may be mainly responsible for the delayed-flowering phenotype in tga7, as TGA7 expression was regulated by autonomous pathway genes. These results provide a framework for further studying the role of TGA7 in promoting flowering.
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Affiliation(s)
- Xiaorui Xu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Jingya Xu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Chen Yuan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Yikai Hu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Qinggang Liu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Qianqian Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China.
| | - Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China.
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19
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Li F, Hu Q, Chen F, Jiang JF. Transcriptome analysis reveals Vernalization is independent of cold acclimation in Arabidopsis. BMC Genomics 2021; 22:462. [PMID: 34154522 PMCID: PMC8218483 DOI: 10.1186/s12864-021-07763-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
Background Through vernalization, plants achieve flowering competence by sensing prolonged cold exposure (constant exposure approximately 2-5 °C). During this process, plants initiate defense responses to endure cold conditions. Here, we conducted transcriptome analysis of Arabidopsis plants subjected to prolonged cold exposure (6 weeks) to explore the physiological dynamics of vernalization and uncover the relationship between vernalization and cold stress. Results Time-lag initiation of the two pathways and weighted gene co-expression network analysis (WGCNA) revealed that vernalization is independent of cold acclimation. Moreover, WGCNA revealed three major networks involving ethylene and jasmonic acid response, cold acclimation, and chromatin modification in response to prolonged cold exposure. Finally, throughout vernalization, the cold stress response is regulated via an alternative splicing-mediated mechanism. Conclusion These findings illustrate a comprehensive picture of cold stress- and vernalization-mediated global changes in Arabidopsis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07763-3.
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Affiliation(s)
- Fei Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jia Fu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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20
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Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22115716. [PMID: 34071961 PMCID: PMC8198774 DOI: 10.3390/ijms22115716] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Flowering is one of the most critical developmental transitions in plants’ life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny’s success. In Arabidopsis thaliana, seven flowering genetic pathways have been described under specific growth conditions. However, the evidence condensed here suggest that these pathways are tightly interconnected in a complex multilevel regulatory network. In this review, we pursue an integrative approach emphasizing the molecular interactions among the flowering regulatory network components. We also consider that the same regulatory network prevents or induces flowering phase change in response to internal cues modulated by environmental signals. In this sense, we describe how during the vegetative phase of development it is essential to prevent the expression of flowering promoting genes until they are required. Then, we mention flowering regulation under suboptimal growing temperatures, such as those in autumn and winter. We next expose the requirement of endogenous signals in flowering, and finally, the acceleration of this transition by long-day photoperiod and temperature rise signals allowing A. thaliana to bloom in spring and summer seasons. With this approach, we aim to provide an initial systemic view to help the reader integrate this complex developmental process.
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21
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Qin F, Yu B, Li W. Heat shock protein 101 (HSP101) promotes flowering under nonstress conditions. PLANT PHYSIOLOGY 2021; 186:407-419. [PMID: 33561259 PMCID: PMC8154077 DOI: 10.1093/plphys/kiab052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 01/10/2021] [Indexed: 05/13/2023]
Abstract
Heat shock proteins (HSPs) are stress-responsive proteins that are conserved across all organisms. Heat shock protein 101 (HSP101) has an important role in thermotolerance owing to its chaperone activity. However, if and how it functions in development under nonstress conditions is not yet known. By using physiological, molecular, and genetic methods, we investigated the role of HSP101 in the control of flowering in Arabidopsis (Arabidopsis thaliana (L.) Heynh.) under nonstress conditions. Knockout and overexpression of HSP101 cause late and early flowering, respectively. Late flowering can be restored by rescue of HSP101. HSP101 regulates the expression of genes involved in the six known flowering pathways; the most negatively regulated genes are FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP); downstream integrators of the flowering pathways are positively regulated. The late-flowering phenotype of loss-of-HSP101 mutants is suppressed by both the mutations of FLC and SVP. The responses of flowering time to exogenous signals do not change in HSP101 mutants. HSP101 is also found in nonspecific regions according to subcellular localization. We found that HSP101 promotes flowering under nonstress conditions and that this promotion depends on FLC and SVP. Our data suggest that this promotion could occur through a multiple gene regulation mechanism.
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Affiliation(s)
- Feng Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Buzhu Yu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Yuxi Normal University, Yuxi 653100, China
| | - Weiqi Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Author for communication:
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22
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Dutta S, Deb A, Biswas P, Chakraborty S, Guha S, Mitra D, Geist B, Schäffner AR, Das M. Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering. Sci Rep 2021; 11:7849. [PMID: 33846519 PMCID: PMC8041875 DOI: 10.1038/s41598-021-87491-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 03/26/2021] [Indexed: 02/01/2023] Open
Abstract
Bamboos, member of the family Poaceae, represent many interesting features with respect to their fast and extended vegetative growth, unusual, yet divergent flowering time across species, and impact of sudden, large scale flowering on forest ecology. However, not many studies have been conducted at the molecular level to characterize important genes that regulate vegetative and flowering habit in bamboo. In this study, two bamboo FD genes, BtFD1 and BtFD2, which are members of the florigen activation complex (FAC) have been identified by sequence and phylogenetic analyses. Sequence comparisons identified one important amino acid, which was located in the DNA-binding basic region and was altered between BtFD1 and BtFD2 (Ala146 of BtFD1 vs. Leu100 of BtFD2). Electrophoretic mobility shift assay revealed that this alteration had resulted into ten times higher binding efficiency of BtFD1 than BtFD2 to its target ACGT motif present at the promoter of the APETALA1 gene. Expression analyses in different tissues and seasons indicated the involvement of BtFD1 in flower and vegetative development, while BtFD2 was very lowly expressed throughout all the tissues and conditions studied. Finally, a tenfold increase of the AtAP1 transcript level by p35S::BtFD1 Arabidopsis plants compared to wild type confirms a positively regulatory role of BtFD1 towards flowering. However, constitutive expression of BtFD1 had led to dwarfisms and apparent reduction in the length of flowering stalk and numbers of flowers/plant, whereas no visible phenotype was observed for BtFD2 overexpression. This signifies that timely expression of BtFD1 may be critical to perform its programmed developmental role in planta.
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Affiliation(s)
- Smritikana Dutta
- grid.412537.60000 0004 1768 2925Department of Life Sciences, Presidency University, Kolkata, India
| | - Anwesha Deb
- grid.412537.60000 0004 1768 2925Department of Life Sciences, Presidency University, Kolkata, India
| | - Prasun Biswas
- grid.412537.60000 0004 1768 2925Department of Life Sciences, Presidency University, Kolkata, India ,grid.411826.80000 0001 0559 4125Department of Botany, Kalna College, Kalna, West Bengal India
| | - Sukanya Chakraborty
- grid.412537.60000 0004 1768 2925Department of Life Sciences, Presidency University, Kolkata, India
| | - Suman Guha
- grid.412537.60000 0004 1768 2925Department of Statistics, Presidency University, Kolkata, India
| | - Devrani Mitra
- grid.412537.60000 0004 1768 2925Department of Life Sciences, Presidency University, Kolkata, India
| | - Birgit Geist
- grid.4567.00000 0004 0483 2525Institute of Biochemical Plant Pathology, Department of Environmental Sciences, Helmholtz Zentrum München, München, Germany
| | - Anton R. Schäffner
- grid.4567.00000 0004 0483 2525Institute of Biochemical Plant Pathology, Department of Environmental Sciences, Helmholtz Zentrum München, München, Germany
| | - Malay Das
- grid.412537.60000 0004 1768 2925Department of Life Sciences, Presidency University, Kolkata, India
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23
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Zhou L, Lu Y, Huang J, Sha Z, Mo W, Xue J, Ma S, Shi W, Yang Z, Gao J, Bian M. Arabidopsis CIB3 regulates photoperiodic flowering in an FKF1-dependent way. Biosci Biotechnol Biochem 2021; 85:765-774. [PMID: 33686404 DOI: 10.1093/bbb/zbaa120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/22/2020] [Indexed: 01/29/2023]
Abstract
Arabidopsis cryptochrome 2 (CRY2) and FLAVIN-BINDING, KELCH REPEAT, and F-BOX 1 (FKF1) are blue light receptors mediating light regulation of growth and development, such as photoperiodic flowering. CRY2 interacts with a basic helix-loop-helix transcription factor CIB1 in response to blue light to activate the transcription of the flowering integrator gene FLOWERING LOCUS T (FT). CIB1, CIB2, CIB4, and CIB5 function redundantly to promote flowering in a CRY2-dependent way and form various heterodimers to bind to the noncanonical E-box sequence in the FT promoter. However, the function of CIB3 has not been described. We discovered that CIB3 promotes photoperiodic flowering independently of CRY2. Moreover, CIB3 does not interact with CRY2 but interacts with CIB1 and functions synergistically with CIB1 to promote the transcription of the GI gene. FKF1 is required for CIB3 to promote flowering and enhances the CIB1-CIB3 interaction in response to blue light.
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Affiliation(s)
- Lianxia Zhou
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Yi Lu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Jie Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Zhiwei Sha
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Weiliang Mo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Jiayi Xue
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China.,Humen Foreign Language School, Dongguan, China
| | - Shuodan Ma
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Wuliang Shi
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Zhenming Yang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Jie Gao
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Mingdi Bian
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
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24
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Xu D, Liu Q, Chen G, Yan Z, Hu H. Aldehyde dehydrogenase ALDH3F1 involvement in flowering time regulation through histone acetylation modulation on FLOWERING LOCUS C. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1080-1092. [PMID: 31829514 DOI: 10.1111/jipb.12893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/05/2019] [Indexed: 06/10/2023]
Abstract
Flowering time regulation is one of the most important processes in the whole life of flowering plants and FLOWERING LOCUS C (FLC) is a central repressor of flowering time. However, whether metabolic acetate level affects flowering time is unknown. Here we report that ALDEHYDE DEHYDROGENASE ALDH3F1 plays essential roles in floral transition via FLC-dependent pathway. In the aldh3f1-1 mutant, the flowering time was significant earlier than Col-0 and the FLC expression level was reduced. ALDH3F1 had aldehyde dehydrogenase activity to affect the acetate level in plants, and the amino acids of E214 and C252 are essential for its catalytic activity. Moreover, aldh3f1 mutation reduced acetate level and the total acetylation on histone H3. The H3K9Ac level on FLC locus was decreased in aldh3f1-1, which reduced FLC expression. Expression of ALDH3F1 could rescue the decreased H3K9Ac level on FLC, FLC expression and also the early-flowering phenotype of aldh3f1-1, however ALDH3F1E214A or ALDH3F1C252A could not. Our findings demonstrate that ALDH3F1 participates in flowering time regulation through modulating the supply of acetate for acetyl-CoA, which functions as histone acetylation donor to modulate H3K9Ac on FLC locus.
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Affiliation(s)
- Danyun Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gang Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiqiang Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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25
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Cronk Q, Soolanayakanahally R, Bräutigam K. Gene expression trajectories during male and female reproductive development in balsam poplar (Populus balsamifera L.). Sci Rep 2020; 10:8413. [PMID: 32439903 PMCID: PMC7242425 DOI: 10.1038/s41598-020-64938-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Plant reproductive development from the first appearance of reproductively committed axes through to floral maturation requires massive and rapid remarshalling of gene expression. In dioecious species such as poplar this is further complicated by divergent male and female developmental programs. We used seven time points in male and female balsam poplar (Populus balsamifera L.) buds and catkins representing the full annual flowering cycle, to elucidate the effects of time and sex on gene expression during reproductive development. Time (developmental stage) is dominant in patterning gene expression with the effect of sex nested within this. Here, we find (1) evidence for five successive waves of alterations to the chromatin landscape which may be important in setting the overall reproductive trajectory, regardless of sex. (2) Each individual developmental stage is further characterized by marked sex-differential gene expression. (3) Consistent sexually differentiated gene expression regardless of developmental stage reveal candidates for high-level regulators of sex and include the female-specific poplar ARR17 homologue. There is also consistent male-biased expression of the MADS-box genes PISTILLATA and APETALA3. Our work provides insights into expression trajectories shaping reproductive development, its potential underlying mechanisms, and sex-specific translation of the genome information into reproductive structures in balsam poplar.
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Affiliation(s)
- Quentin Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Raju Soolanayakanahally
- Indian Head Research Farm, Agriculture and Agri-Food Canada, Indian Head, SK, S0G 2K0, Canada
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L 1C6, Canada.
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26
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Golicz AA, Steinfort U, Arya H, Singh MB, Bhalla PL. Analysis of the quinoa genome reveals conservation and divergence of the flowering pathways. Funct Integr Genomics 2020; 20:245-258. [PMID: 31515641 PMCID: PMC7018680 DOI: 10.1007/s10142-019-00711-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 01/09/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a grain crop grown in the Andes renowned as a highly nutritious plant exhibiting tolerance to abiotic stress such as drought, cold and high salinity. Quinoa grows across a range of latitudes corresponding to differing day lengths, suggesting regional adaptations of flowering regulation. Improved understanding and subsequent modification of the flowering process, including flowering time, ensuring high yields, is one of the key factors behind expansion of cultivation zones and goals of the crop improvement programs worldwide. However, our understanding of the molecular basis of flower initiation and development in quinoa is limited. Here, we use a computational approach to perform genome-wide identification and analysis of 611 orthologues of the Arabidopsis thaliana flowering genes. Conservation of the genes belonging to the photoperiod, gibberellin and autonomous pathways was observed, while orthologues of the key genes found in the vernalisation pathway (FRI, FLC) were absent from the quinoa genome. Our analysis indicated that on average each Arabidopsis flowering gene has two orthologous copies in quinoa. Several genes including orthologues of MIF1, FT and TSF were identified as homologue-rich genes in quinoa. We also identified 459 quinoa-specific genes uniquely expressed in the flower and/or meristem, with no known orthologues in other species. The genes identified provide a resource and framework for further studies of flowering in quinoa and related species. It will serve as valuable resource for plant biologists, crop physiologists and breeders to facilitate further research and establishment of modern breeding programs for quinoa.
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Affiliation(s)
- Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - Ursula Steinfort
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Hina Arya
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
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27
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Yan Z, Shi H, Liu Y, Jing M, Han Y. KHZ1 and KHZ2, novel members of the autonomous pathway, repress the splicing efficiency of FLC pre-mRNA in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1375-1386. [PMID: 31701139 PMCID: PMC7031081 DOI: 10.1093/jxb/erz499] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/06/2019] [Indexed: 05/03/2023]
Abstract
As one of the most important events during the life cycle of flowering plants, the floral transition is of crucial importance for plant propagation and requires the precise coordination of multiple endogenous and external signals. There have been at least four flowering pathways (i.e. photoperiod, vernalization, gibberellin, and autonomous) identified in Arabidopsis. We previously reported that two Arabidopsis RNA-binding proteins, KHZ1 and KHZ2, redundantly promote flowering. However, the underlying mechanism was unclear. Here, we found that the double mutant khz1 khz2 flowered late under both long-day and short-day conditions, but responded to vernalization and gibberellin treatments. The late-flowering phenotype was almost completely rescued by mutating FLOWERING LOCUS C (FLC) and fully rescued by overexpressing FLOWERING LOCUS T (FT). Additional experiments demonstrated that the KHZs could form homodimers or interact to form heterodimers, localized to nuclear dots, and repressed the splicing efficiency of FLC pre-mRNA. Together, these data indicate that the KHZs could promote flowering via the autonomous pathway by repressing the splicing efficiency of FLC pre-mRNA.
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Affiliation(s)
- Zongyun Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huiying Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yanan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Meng Jing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuzhen Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
- Correspondence:
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28
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Kim KH, Kim JY, Lim WJ, Jeong S, Lee HY, Cho Y, Moon JK, Kim N. Genome-wide association and epistatic interactions of flowering time in soybean cultivar. PLoS One 2020; 15:e0228114. [PMID: 31968016 PMCID: PMC6975553 DOI: 10.1371/journal.pone.0228114] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/07/2020] [Indexed: 12/02/2022] Open
Abstract
Genome-wide association studies (GWAS) have enabled the discovery of candidate markers that play significant roles in various complex traits in plants. Recently, with increased interest in the search for candidate markers, studies on epistatic interactions between single nucleotide polymorphism (SNP) markers have also increased, thus enabling the identification of more candidate markers along with GWAS on single-variant-additive-effect. Here, we focused on the identification of candidate markers associated with flowering time in soybean (Glycine max). A large population of 2,662 cultivated soybean accessions was genotyped using the 180k Axiom® SoyaSNP array, and the genomic architecture of these accessions was investigated to confirm the population structure. Then, GWAS was conducted to evaluate the association between SNP markers and flowering time. A total of 93 significant SNP markers were detected within 59 significant genes, including E1 and E3, which are the main determinants of flowering time. Based on the GWAS results, multilocus epistatic interactions were examined between the significant and non-significant SNP markers. Two significant and 16 non-significant SNP markers were discovered as candidate markers affecting flowering time via interactions with each other. These 18 candidate SNP markers mapped to 18 candidate genes including E1 and E3, and the 18 candidate genes were involved in six major flowering pathways. Although further biological validation is needed, our results provide additional information on the existing flowering time markers and present another option to marker-assisted breeding programs for regulating flowering time of soybean.
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Affiliation(s)
- Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Ho-Yeon Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Youngbum Cho
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
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Schiessl S. Regulation and Subfunctionalization of Flowering Time Genes in the Allotetraploid Oil Crop Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:605155. [PMID: 33329678 PMCID: PMC7718018 DOI: 10.3389/fpls.2020.605155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/29/2020] [Indexed: 05/03/2023]
Abstract
Flowering is a vulnerable, but crucial phase in building crop yield. Proper timing of this period is therefore decisive in obtaining optimal yields. However, genetic regulation of flowering integrates many different environmental signals and is therefore extremely complex. This complexity increases in polyploid crops which carry two or more chromosome sets, like wheat, potato or rapeseed. Here, I summarize the current state of knowledge about flowering time gene copies in rapeseed (Brassica napus), an important oil crop with a complex polyploid history and a close relationship to Arabidopsis thaliana. The current data show a high demand for more targeted studies on flowering time genes in crops rather than in models, allowing better breeding designs and a deeper understanding of evolutionary principles. Over evolutionary time, some copies of rapeseed flowering time genes changed or lost their original role, resulting in subfunctionalization of the respective homologs. For useful applications in breeding, such patterns of subfunctionalization need to be identified and better understood.
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Affiliation(s)
- Sarah Schiessl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
- *Correspondence: Sarah Schiessl,
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30
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Petit J, Salentijn EMJ, Paulo MJ, Denneboom C, Trindade LM. Genetic Architecture of Flowering Time and Sex Determination in Hemp ( Cannabis sativa L.): A Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2020; 11:569958. [PMID: 33250906 PMCID: PMC7672029 DOI: 10.3389/fpls.2020.569958] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/12/2020] [Indexed: 05/13/2023]
Abstract
Flowering time and sex determination in hemp (Cannabis sativa L.) strongly influence fiber quality and seed production of this crop. The control of these traits is paramount for the breeding of new cultivars. Yet, little is known about the genetics underlying such complex traits and a better understanding requires in depth knowledge of the molecular mechanisms responsible for these traits. In this report, the genetic architecture of flowering time and sex determination in hemp was studied using a Genome-Wide Association Studies (GWAS) approach. Association studies were performed on a panel of 123 hemp accessions, tested in three contrasting environments, using a set of 600 K SNP markers. Altogether, eight QTLs were identified across environments; six for flowering time traits and two for sex determination. These QTLs covered genomic regions with 33 transcripts predicted to be involved in flowering and sex determination as well as a microRNA, miR156. Genes related to perception and transduction of light and transcription factors well-known to regulate flowering were identified in QTLs for flowering time traits. Transcription factors and genes involved in regulating the balance of phytohormones, specially auxins and gibberellic acid, were identified in QTLs for sex determination. Sex determination QTLs were associated with the development of male flowers in female plants and thus with the stability of sex determination in monecious plants. The present study elucidates relevant knowledge on the genetic mechanisms of flowering and sex determination traits in hemp, and provides new tools for hemp breeding.
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Affiliation(s)
- Jordi Petit
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Elma M. J. Salentijn
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Maria-João Paulo
- Biometris, Wageningen University and Research, Wageningen, Netherlands
| | - Christel Denneboom
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Luisa M. Trindade
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Luisa M. Trindade,
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Wang X, Xu X, Mo X, Zhong L, Zhang J, Mo B, Kuai B. Overexpression of TCP8 delays Arabidopsis flowering through a FLOWERING LOCUS C-dependent pathway. BMC PLANT BIOLOGY 2019; 19:534. [PMID: 31795938 PMCID: PMC6889539 DOI: 10.1186/s12870-019-2157-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/21/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Flowering is a key process in the life cycle of plants. The transition from vegetative to reproductive growth is thus under sophisticated regulation by endogenous and environmental signals. The plant-specific Teosinte Branched 1/Cycloidea/Proliferating Cell Factors (TCP) family transcription factors are involved in many biological processes, but their roles in regulating flowering have not been totally elucidated. RESULTS We explored the role of Arabidopsis TCP8 in plant development and, especially, in flowering control. Overexpression of TCP8 significantly delayed flowering under both long-day and short-day conditions and dominant repression by TCP8 led to various growth defects. The upregulation of TCP8 led to more accumulated mRNA level of FLOWERING LOCUS C (FLC), a central floral repressor of Arabidopsis. TCP8 functions in an FLC-dependent manner, as TCP8 overexpression in the flc-6 loss-of-function mutant failed to delay flowering. The vernalization treatment could reverse the late flowering phenotype caused by TCP8 overexpression. CONCLUSIONS Our results provide evidence for a role of TCP8 in flowering control and add to our knowledge of the molecular basis of TCP8 function.
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Affiliation(s)
- Xiaoyan Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Xintong Xu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xiaowei Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Luyao Zhong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Jiancong Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Benke Kuai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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Mackenzie SA, Kundariya H. Organellar protein multi-functionality and phenotypic plasticity in plants. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190182. [PMID: 31787051 PMCID: PMC6939364 DOI: 10.1098/rstb.2019.0182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
With the increasing impact of climate instability on agricultural and ecological systems has come a heightened sense of urgency to understand plant adaptation mechanisms in more detail. Plant species have a remarkable ability to disperse their progeny to a wide range of environments, demonstrating extraordinary resiliency mechanisms that incorporate epigenetics and transgenerational stability. Surprisingly, some of the underlying versatility of plants to adapt to abiotic and biotic stress emerges from the neofunctionalization of organelles and organellar proteins. We describe evidence of possible plastid specialization and multi-functional organellar protein features that serve to enhance plant phenotypic plasticity. These features appear to rely on, for example, spatio-temporal regulation of plastid composition, and unusual interorganellar protein targeting and retrograde signalling features that facilitate multi-functionalization. Although we report in detail on three such specializations, involving MSH1, WHIRLY1 and CUE1 proteins in Arabidopsis, there is ample reason to believe that these represent only a fraction of what is yet to be discovered as we begin to elaborate cross-species diversity. Recent observations suggest that plant proteins previously defined in one context may soon be rediscovered in new roles and that much more detailed investigation of proteins that show subcellular multi-targeting may be warranted. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
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Affiliation(s)
- Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, 362 Frear North Building, University Park, PA 16802, USA
| | - Hardik Kundariya
- Departments of Biology and Plant Science, The Pennsylvania State University, 362 Frear North Building, University Park, PA 16802, USA
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Auge GA, Penfield S, Donohue K. Pleiotropy in developmental regulation by flowering-pathway genes: is it an evolutionary constraint? THE NEW PHYTOLOGIST 2019; 224:55-70. [PMID: 31074008 DOI: 10.1111/nph.15901] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/28/2019] [Indexed: 05/11/2023]
Abstract
Pleiotropy occurs when one gene influences more than one trait, contributing to genetic correlations among traits. Consequently, it is considered a constraint on the evolution of adaptive phenotypes because of potential antagonistic selection on correlated traits, or, alternatively, preservation of functional trait combinations. Such evolutionary constraints may be mitigated by the evolution of different functions of pleiotropic genes in their regulation of different traits. Arabidopsis thaliana flowering-time genes, and the pathways in which they operate, are among the most thoroughly studied regarding molecular functions, phenotypic effects, and adaptive significance. Many of them show strong pleiotropic effects. Here, we review examples of pleiotropy of flowering-time genes and highlight those that also influence seed germination. Some genes appear to operate in the same genetic pathways when regulating both traits, whereas others show diversity of function in their regulation, either interacting with the same genetic partners but in different ways or potentially interacting with different partners. We discuss how functional diversification of pleiotropic genes in the regulation of different traits across the life cycle may mitigate evolutionary constraints of pleiotropy, permitting traits to respond more independently to environmental cues, and how it may even contribute to the evolutionary divergence of gene function across taxa.
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Affiliation(s)
- Gabriela A Auge
- Fundación Instituto Leloir, IIBBA-CONICET, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1405BWE3, Argentina
| | - Steven Penfield
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kathleen Donohue
- Department of Biology, Duke University, Box 90338, Durham , NC 27708-0338, USA
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Jiang S, Xiao L, Huang P, Cheng Z, Chen F, Miao Y, Fu YF, Chen Q, Zhang XM. Nucleoporin Nup98 participates in flowering regulation in a CONSTANS-independent mode. PLANT CELL REPORTS 2019; 38:1263-1271. [PMID: 31236659 DOI: 10.1007/s00299-019-02442-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 06/15/2019] [Indexed: 06/09/2023]
Abstract
Two redundant nucleoporin genes Nup98a and Nup98b bypass the CO-check point in photoperiodic signaling and integrated signals from multiple pathways to directly target FT for flowering control in Arabidopsis. Flowering regulation is an important and widely studied plant development event. Even though nucleoporin Nup98 has been proven to play pivotal roles in the growth and development of mammalian cells and yeast, it is still unknown if Nup98 participates in flowering control in plants. In this study, we investigated the function of two Nup98 homologs, Nup98a and Nup98b, in flowering regulation in Arabidopsis. The results showed that Nup98a and Nup98b redundantly inhibit flowering through multiple pathways including clock, photoperiod, and age pathways. Single mutants of nup98a and nup98b do not show any obvious abnormal phenotypes compared to wild-type plants; however, the nup98a1 nup98b1 double mutant displays early flowering. Significantly, Nup98a/Nup98b gate flowering in a CONSTANS (CO)-independent mode. Therefore, Nup98a/Nup98b bypasses the CO checkpoint in photoperiodic signaling and integrated signals from multiple pathways to directly target FLOWERING LOCUS T (FT) for flowering control. In addition, our results provide a line of genetic evidence for uncoupling the mechanism of flowering and senescence at Nup98a/Nup98b genes in Arabidopsis, which are classically recognized as two coupled developmental events.
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Affiliation(s)
- Shanshan Jiang
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
| | - Long Xiao
- Key Laboratory of Soybean Biology, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Penghui Huang
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
| | - Zhiyuan Cheng
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
| | - Fulu Chen
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China
| | - Yuchen Miao
- Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, Henan University, Kaifeng, 475001, China
| | - Yong-Fu Fu
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China.
| | - Qingshan Chen
- Key Laboratory of Soybean Biology, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin, 150030, China.
| | - Xiao-Mei Zhang
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Nandajie 12, Zhongguancun, Haidian District, Beijing, 100081, China.
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Li Y, Zhang D, An N, Fan S, Zuo X, Zhang X, Zhang L, Gao C, Han M, Xing L. Transcriptomic analysis reveals the regulatory module of apple (Malus × domestica) floral transition in response to 6-BA. BMC PLANT BIOLOGY 2019; 19:93. [PMID: 30841918 PMCID: PMC6402183 DOI: 10.1186/s12870-019-1695-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 02/25/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Insufficient production of flower buds is an intractable problem in 'Fuji' apple orchards. Although cytokinin (CK) promotes flower bud formation in apple trees, little is known about the mechanisms regulating this phenomenon. RESULTS In the present study, high-throughput RNA sequencing (RNA-Seq) of 'Nagafu No. 2' buds was conducted to characterize the transcriptional response to 6-BA treatment during key period of floral transition. A weighted gene co-expression network analysis (WGCNA) of the differentially expressed genes identified hormone signal transduction pathways, totaling 84 genes were highly correlated with the expression pattern of flowering-time genes. The up-regulation of CK signal components and a gibberellin (GA) signal repressor were found to contribute to the promotion of floral transition. In relative comparison to non-treated buds, a series of sugar metabolism- and signal- related genes were associated with relatively high levels of sucrose, fructose, and glucose during floral induction in the 6-BA treated buds. Several transcription factors (i.e. SPLs, SOC1, FD, and COL) that are involved in GA, aging, and photoperiod-regulated flowering pathways were also upregulated by the 6-BA treatment. In addition, potential transcription factors integrating CK signaling to trigger floral induction in apple were also assessed; including PHYTO-CHROME-INTERACTING FACTOR (PIF1,3), WUSCHEL-related homeobox (WOX3,13), and CK response regulators (ARR2). CONCLUSIONS The present study provides insight into the response of flowering and development-related pathways and transcription factors to 6-BA during the period of floral transition in apple. It extends our knowledge of the fundamental mechanisms associated with CK-regulated floral transition in apple trees.
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Affiliation(s)
- Youmei Li
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
| | - Dong Zhang
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
| | - Na An
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
| | - Sheng Fan
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
| | - Xiya Zuo
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
| | - Xin Zhang
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
| | - Lizhi Zhang
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
| | - Cai Gao
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
| | - Mingyu Han
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
| | - Libo Xing
- Department of Horticulture College, Northwest Agriculture & Forestry University, Yangling, 712100 China
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Salentijn EMJ, Petit J, Trindade LM. The Complex Interactions Between Flowering Behavior and Fiber Quality in Hemp. FRONTIERS IN PLANT SCIENCE 2019; 10:614. [PMID: 31156677 PMCID: PMC6532435 DOI: 10.3389/fpls.2019.00614] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/25/2019] [Indexed: 05/05/2023]
Abstract
Hemp, Cannabis sativa L., is a sustainable multipurpose fiber crop with high nutrient and water use efficiency and with biomass of excellent quality for textile fibers and construction materials. The yield and quality of hemp biomass are largely determined by the genetic background of the hemp cultivar but are also strongly affected by environmental factors, such as temperature and photoperiod. Hemp is a facultative short-day plant, characterized by a strong adaptation to photoperiod and a great influence of environmental factors on important agronomic traits such as "flowering-time" and "sex determination." This sensitivity of hemp can cause a considerable degree of heterogeneity, leading to unforeseen yield reductions. Fiber quality for instance is influenced by the developmental stage of hemp at harvest. Also, male and female plants differ in stature and produce fibers with different properties and quality. Next to these causes, there is evidence for specific genotypic variation in fiber quality among hemp accessions. Before improved hemp cultivars can be developed, with specific flowering-times and fiber qualities, and adapted to different geographical regions, a better understanding of the molecular mechanisms controlling important phenological traits such as "flowering-time" and "sex determination" in relation to fiber quality in hemp is required. It is well known that genetic factors play a major role in the outcome of both phenological traits, but the major molecular factors involved in this mechanism are not characterized in hemp. Genome sequences and transcriptome data are available but their analysis mainly focused on the cannabinoid pathway for medical purposes. Herein, we review the current knowledge of phenotypic and genetic data available for "flowering-time," "sex determination," and "fiber quality" in short-day and dioecious crops, respectively, and compare them with the situation in hemp. A picture emerges for several controlling key genes, for which natural genetic variation may lead to desired flowering behavior, including examples of pleiotropic effects on yield quality and on carbon partitioning. Finally, we discuss the prospects for using this knowledge for the molecular breeding of this sustainable crop via a candidate gene approach.
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Eom H, Lee I. Role of TAF15b in transcriptional regulation of autonomous pathway for flowering. PLANT SIGNALING & BEHAVIOR 2018; 13:e1471300. [PMID: 29944459 PMCID: PMC6128682 DOI: 10.1080/15592324.2018.1471300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
The autonomous pathway promotes flowering by repressing a major flowering repressor, FLOWERING LOCUS C (FLC). Approximately 30 genes are involved in this pathway, and several of them are related to RNA processing; however, the molecular basis of the transcriptional regulation of FLC is yet to be understood. Recently, we discovered a new autonomous pathway gene, TATA-binding protein-associated factor 15b (TAF15b), which has a RNA recognition motif (RRM) and represses the level of FLC transcripts. TAF15b regulates the expression of FLC by directly interacting with RNA polymerase II (Pol II) at the transcription start sites on both the sense and antisense strands of the FLC locus. In addition to the transcriptional regulation in the nucleus, TAF15b accumulates in processing bodies (p-bodies), which are cytoplasmic RNA granules involved in translational repression, during heat stress. Here we discuss the implications of our findings and suggest a dual role of TAF15b in both transcriptional and translational regulation.
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Affiliation(s)
- H. Eom
- School of Biological Sciences, Seoul National University, Seoul Korea
- Center for RNA Research, Institute for Basic Science, Seoul, Korea
| | - I. Lee
- School of Biological Sciences, Seoul National University, Seoul Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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Hou X, Guo Q, Wei W, Guo L, Guo D, Zhang L. Screening of Genes Related to Early and Late Flowering in Tree Peony Based on Bulked Segregant RNA Sequencing and Verification by Quantitative Real-Time PCR. Molecules 2018; 23:molecules23030689. [PMID: 29562683 PMCID: PMC6017042 DOI: 10.3390/molecules23030689] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/10/2018] [Accepted: 03/12/2018] [Indexed: 01/13/2023] Open
Abstract
Tree peony (Paeonia suffruticosa Andrews) is a perennial woody shrub bearing large and colorful flowers. However, the flowering period is short and relatively uniform, which to an important extent hinders the cultivation and exploitation of ornamental peonies. In this study, the segregation of an F1 population derived from P. ostti ‘Feng Dan’ (an early-flowering cultivar) × P. suffruticosa ‘Xin Riyuejin’ (a late-flowering cultivar) was used to screen and analyze candidate genes associated with flowering period of the two parents. Extreme early- and late-flowering genotypes of the F1 population at full-bloom stage were sampled to establish an early-flowering mixed pool (T03), a late-flowering mixed pool (T04), a late-flowering male pool (T01), and an early-flowering female pool (T02), using the Sequencing By Synthesis (SBS) technology on the Illumina HiSeq TM2500 platform. A total of 56.51 Gb of clean reads data, comprising at least 87.62% of Quality30 (Q30), was generated, which was then combined into 173,960 transcripts (N50 = 1781) and 78,645 (N50 = 1282) unigenes, with a mean length of 1106.76 and 732.27 base pairs (bp), respectively. Altogether, 58,084 genes were annotated by comparison with public databases, based on an E-value parameter of less than 10−5 and 10−10 for BLAST and HMMER, respectively. In total, 291 unigene sequences were finally screened out by BSR-seq (bulked segregant RNA-seq) association analysis. To validate these unigenes, we finally confirmed seven unigenes that were related to early and late flowering, which were then verified by quantitative real-time PCR (qRT-PCR). This is the first reported study to screen genes associated with early and late flowering of tree peony by the BSA (bulked sample analysis) method of transcriptome sequencing, and to construct a high-quality transcriptome database. A set of candidate functional genes related to flowering time was successfully obtained, providing an important genetic resource for further studies of flowering in peony and the mechanism of regulation of flowering time in tree peony.
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Affiliation(s)
- Xiaogai Hou
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
| | - Qi Guo
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Weiqiang Wei
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
| | - Lili Guo
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
| | - Dalong Guo
- College of Forestry, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
| | - Lin Zhang
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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Dutta S, Biswas P, Chakraborty S, Mitra D, Pal A, Das M. Identification, characterization and gene expression analyses of important flowering genes related to photoperiodic pathway in bamboo. BMC Genomics 2018. [PMID: 29523071 PMCID: PMC5845326 DOI: 10.1186/s12864-018-4571-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background Bamboo is an important member of the family Poaceae and has many inflorescence and flowering features rarely observed in other plant groups. It retains an unusual form of perennialism by having a long vegetative phase that can extend up to 120 years, followed by flowering and death of the plants. In contrast to a large number of studies conducted on the annual, reference plants Arabidopsis thaliana and rice, molecular studies to characterize flowering pathways in perennial bamboo are lacking. Since photoperiod plays a crucial role in flower induction in most plants, important genes involved in this pathway have been studied in the field grown Bambusa tulda, which flowers after 40-50 years. Results We identified several genes from B. tulda, including four related to the circadian clock [LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION1 (TOC1), ZEITLUPE (ZTL) and GIGANTEA (GI)], two circadian clock response integrators [CONSTANS A (COA), CONSTANS B (COB)] and four floral pathway integrators [FLOWERING LOCUS T1, 2, 3, 4 (FT1, 2, 3, 4)]. These genes were amplified from either gDNA and/or cDNA using degenerate as well as gene specific primers based on homologous sequences obtained from related monocot species. The sequence identity and phylogenetic comparisons revealed their close relationships to homologs identified in the temperate bamboo Phyllostachys edulis. While the four BtFT homologs were highly similar to each other, BtCOA possessed a full-length B-box domain that was truncated in BtCOB. Analysis of the spatial expression of these genes in selected flowering and non-flowering tissue stages indicated their possible involvement in flowering. The diurnal expression patterns of the clock genes were comparable to their homologs in rice, except for BtZTL. Among multiple BtCO and BtFT homologs, the diurnal pattern of only BtCOA and BtFT3, 4 were synchronized in the flower inductive tissue, but not in the non-flowering tissues. Conclusion This study elucidates the photoperiodic regulation of bamboo homologs of important flowering genes. The finding also identifies copy number expansion and gene expression divergence of CO and FT in bamboo. Further studies are required to understand their functional role in bamboo flowering. Electronic supplementary material The online version of this article (10.1186/s12864-018-4571-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Smritikana Dutta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Prasun Biswas
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | - Devrani Mitra
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, Kolkata, India
| | - Malay Das
- Department of Life Sciences, Presidency University, Kolkata, India.
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Fudge JB, Lee RH, Laurie RE, Mysore KS, Wen J, Weller JL, Macknight RC. Medicago truncatula SOC1 Genes Are Up-regulated by Environmental Cues That Promote Flowering. FRONTIERS IN PLANT SCIENCE 2018; 9:496. [PMID: 29755488 PMCID: PMC5934494 DOI: 10.3389/fpls.2018.00496] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/03/2018] [Indexed: 05/20/2023]
Abstract
Like Arabidopsis thaliana, the flowering of the legume Medicago truncatula is promoted by long day (LD) photoperiod and vernalization. However, there are differences in the molecular mechanisms involved, with orthologs of two key Arabidopsis thaliana regulators, FLOWERING LOCUS C (FLC) and CONSTANS (CO), being absent or not having a role in flowering time function in Medicago. In Arabidopsis, the MADS-box transcription factor gene, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (AtSOC1), plays a key role in integrating the photoperiodic and vernalization pathways. In this study, we set out to investigate whether the Medicago SOC1 genes play a role in regulating flowering time. Three Medicago SOC1 genes were identified and characterized (MtSOC1a-MtSOC1c). All three MtSOC1 genes, when heterologously expressed, were able to promote earlier flowering of the late-flowering Arabidopsis soc1-2 mutant. The three MtSOC1 genes have different patterns of expression. However, consistent with a potential role in flowering time regulation, all three MtSOC1 genes are expressed in the shoot apex and are up-regulated in the shoot apex of plants in response to LD photoperiods and vernalization. The up-regulation of MtSOC1 genes was reduced in Medicago fta1-1 mutants, indicating that they are downstream of MtFTa1. Insertion mutant alleles of Medicago soc1b do not flower late, suggestive of functional redundancy among Medicago SOC1 genes in promoting flowering.
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Affiliation(s)
- Jared B. Fudge
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Robyn H. Lee
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Rebecca E. Laurie
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Kirankumar S. Mysore
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, United States
| | - Jiangqi Wen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, United States
| | - James L. Weller
- School of Biological Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Richard C. Macknight
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- New Zealand Institute for Plant and Food Research Ltd., University of Otago, Dunedin, New Zealand
- *Correspondence: Richard C. Macknight,
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