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Li YT, Liu DH, Luo Y, Abbas Khan M, Mahmood Alam S, Liu YZ. Transcriptome analysis reveals the key network of axillary bud outgrowth modulated by topping in citrus. Gene 2024; 926:148623. [PMID: 38821328 DOI: 10.1016/j.gene.2024.148623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Topping, an important tree shaping and pruning technique, can promote the outgrowth of citrus axillary buds. However, the underlying molecular mechanism is still unclear. In this study, spring shoots of Citrus reticulata 'Huagan No.2' were topped and transcriptome was compared between axillary buds of topped and untopped shoots at 6 and 11 days after topping (DAT). 1944 and 2394 differentially expressed genes (DEGs) were found at 6 and 11 DAT, respectively. KEGG analysis revealed that many DEGs were related to starch and sucrose metabolism, signal transduction of auxin, cytokinin and abscisic acid. Specially, transcript levels of auxin synthesis, transport, and signaling-related genes (SAURs and ARF5), cytokinin signal transduction related genes (CRE1, AHP and Type-A ARRs), ABA signal responsive genes (PYL and ABF) were up-regulated by topping; while transcript levels of auxin receptor TIR1, auxin responsive genes AUX/IAAs, ABA signal transduction related gene PP2Cs and synthesis related genes NCED3 were down-regulated. On the other hand, the contents of sucrose and fructose in axillary buds of topped shoots were significantly higher than those in untopped shoots; transcript levels of 16 genes related to sucrose synthase, hexokinase, sucrose phosphate synthase, endoglucanase and glucosidase, were up-regulated in axillary buds after topping. In addition, transcript levels of genes related to trehalose 6-phosphate metabolism and glycolysis/tricarboxylic acid (TCA) cycle, as well to some transcription factors including Pkinase, Pkinase_Tyr, Kinesin, AP2/ERF, P450, MYB, NAC and Cyclin_c, significantly responded to topping. Taken together, the present results suggested that topping promoted citrus axillary bud outgrowth through comprehensively regulating plant hormone and carbohydrate metabolism, as well as signal transduction. These results deepened our understanding of citrus axillary bud outgrowth by topping and laid a foundation for further research on the molecular mechanisms of citrus axillary bud outgrowth.
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Affiliation(s)
- Yan-Ting Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dong-Hai Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yin Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Muhammad Abbas Khan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shariq Mahmood Alam
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yong-Zhong Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops / College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China.
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Wang H, Li X, Meng B, Fan Y, Khan SU, Qian M, Zhang M, Yang H, Lu K. Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1897-1912. [PMID: 38386569 PMCID: PMC11182599 DOI: 10.1111/pbi.14309] [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: 12/18/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
Silique number is a crucial yield-related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high-yielding rapeseed.
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Affiliation(s)
- Hui Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Xiaodong Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Boyu Meng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Mingchao Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Minghao Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Haikun Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and BiotechnologySouthwest UniversityBeibeiChongqingP.R. China
- Engineering Research Center of South Upland Agriculture, Ministry of EducationChongqingP.R. China
- Academy of Agricultural SciencesSouthwest UniversityBeibeiChongqingP.R. China
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3
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Hu ZL, Wilson-Sánchez D, Bhatia N, Rast-Somssich MI, Wu A, Vlad D, McGuire L, Nikolov LA, Laufs P, Gan X, Laurent S, Runions A, Tsiantis M. A CUC1/auxin genetic module links cell polarity to patterned tissue growth and leaf shape diversity in crucifer plants. Proc Natl Acad Sci U S A 2024; 121:e2321877121. [PMID: 38905239 PMCID: PMC11214078 DOI: 10.1073/pnas.2321877121] [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: 12/22/2023] [Accepted: 05/08/2024] [Indexed: 06/23/2024] Open
Abstract
How tissue-level information encoded by fields of regulatory gene activity is translated into the patterns of cell polarity and growth that generate the diverse shapes of different species remains poorly understood. Here, we investigate this problem in the case of leaf shape differences between Arabidopsis thaliana, which has simple leaves, and its relative Cardamine hirsuta that has complex leaves divided into leaflets. We show that patterned expression of the transcription factor CUP-SHAPED COTYLEDON1 in C. hirsuta (ChCUC1) is a key determinant of leaf shape differences between the two species. Through inducible genetic perturbations, time-lapse imaging of growth, and computational modeling, we find that ChCUC1 provides instructive input into auxin-based leaf margin patterning. This input arises via transcriptional regulation of multiple auxin homeostasis components, including direct activation of WAG kinases that are known to regulate the polarity of PIN-FORMED auxin transporters. Thus, we have uncovered a mechanism that bridges biological scales by linking spatially distributed and species-specific transcription factor expression to cell-level polarity and growth, to shape diverse leaf forms.
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Affiliation(s)
- Zi-Liang Hu
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - David Wilson-Sánchez
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Neha Bhatia
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Madlen I. Rast-Somssich
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Anhui Wu
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Daniela Vlad
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Liam McGuire
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Lachezar A. Nikolov
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Patrick Laufs
- Université Paris-Saclay, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles78000, France
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Adam Runions
- Department of Computer Science, University of Calgary, Calgary, ABT2N 1N4, Canada
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
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He L, Liu Y, Mao Y, Wu X, Zheng X, Zhao W, Mo X, Wang R, Wu Q, Wang D, Li Y, Yang Y, Bai Q, Zhang X, Zhou S, Zhao B, Liu C, Liu Y, Tadege M, Chen J. GRAS transcription factor PINNATE-LIKE PENTAFOLIATA2 controls compound leaf morphogenesis in Medicago truncatula. THE PLANT CELL 2024; 36:1755-1776. [PMID: 38318972 PMCID: PMC11062474 DOI: 10.1093/plcell/koae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/17/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024]
Abstract
The milestone of compound leaf development is the generation of separate leaflet primordia during the early stages, which involves two linked but distinct morphogenetic events: leaflet initiation and boundary establishment for leaflet separation. Although some progress in understanding the regulatory pathways for each event have been made, it is unclear how they are intrinsically coordinated. Here, we identify the PINNATE-LIKE PENTAFOLIATA2 (PINNA2) gene encoding a newly identified GRAS transcription factor in Medicago truncatula. PINNA2 transcripts are preferentially detected at organ boundaries. Its loss-of-function mutations convert trifoliate leaves into a pinnate pentafoliate pattern. PINNA2 directly binds to the promoter region of the LEAFY orthologue SINGLE LEAFLET1 (SGL1), which encodes a key positive regulator of leaflet initiation, and downregulates its expression. Further analysis revealed that PINNA2 synergizes with two other repressors of SGL1 expression, the BEL1-like homeodomain protein PINNA1 and the C2H2 zinc finger protein PALMATE-LIKE PENTAFOLIATA1 (PALM1), to precisely define the spatiotemporal expression of SGL1 in compound leaf primordia, thereby maintaining a proper pattern of leaflet initiation. Moreover, we showed that the enriched expression of PINNA2 at the leaflet-to-leaflet boundaries is positively regulated by the boundary-specific gene MtNAM, which is essential for leaflet boundary formation. Together, these results unveil a pivotal role of the boundary-expressed transcription factor PINNA2 in regulating leaflet initiation, providing molecular insights into the coordination of intricate developmental processes underlying compound leaf pattern formation.
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Affiliation(s)
- Liangliang He
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ye Liu
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yawen Mao
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyuan Wu
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoling Zheng
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Weiyue Zhao
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xiaoyu Mo
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruoruo Wang
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinq Wu
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongfa Wang
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Youhan Li
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yuanfan Yang
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Quanzi Bai
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xiaojia Zhang
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Shaoli Zhou
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Baolin Zhao
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changning Liu
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Jianghua Chen
- CAS Key Laboratory of Topical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
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Yuan Y, Du Y, Delaplace P. Unraveling the molecular mechanisms governing axillary meristem initiation in plants. PLANTA 2024; 259:101. [PMID: 38536474 DOI: 10.1007/s00425-024-04370-w] [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: 11/25/2023] [Accepted: 02/22/2024] [Indexed: 04/24/2024]
Abstract
MAIN CONCLUSION Axillary meristems (AMs) located in the leaf axils determine the number of shoots or tillers eventually formed, thus contributing significantly to the plant architecture and crop yields. The study of AM initiation is unavoidable and beneficial for crop productivity. Shoot branching is an undoubted determinant of plant architecture and thus greatly impacts crop yield due to the panicle-bearing traits of tillers. The emergence of the AM is essential for the incipient bud formation, and then the bud is dormant or outgrowth immediately to form a branch or tiller. While numerous reviews have focused on plant branching and tillering development networks, fewer specifically address AM initiation and its regulatory mechanisms. This review synthesizes the significant advancements in the genetic and hormonal factors governing AM initiation, with a primary focus on studies conducted in Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.). In particular, by elaborating on critical genes like LATERAL SUPPRESSOR (LAS), which specifically regulates AM initiation and the networks in which they are involved, we attempt to unify the cascades through which they are positioned. We concentrate on clarifying the precise mutual regulation between shoot apical meristem (SAM) and AM-related factors. Additionally, we examine challenges in elucidating AM formation mechanisms alongside opportunities provided by emerging omics approaches to identify AM-specific genes. By expanding our comprehension of the genetic and hormonal regulation of AM development, we can develop strategies to optimize crop production and address global food challenges effectively.
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Affiliation(s)
- Yundong Yuan
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Yanfang Du
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Pierre Delaplace
- Plant Sciences, Gembloux Agro-Bio Tech, TERRA-Teaching and Research Center, Université de Liège, 5030, Gembloux, Belgium
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Chen Y, Ling Q, Li X, Ma Q, Tang S, Yuanzhi P, Liu QL, Jia Y, Yong X, Jiang B. Transcriptome analysis during axillary bud growth in chrysanthemum ( chrysanthemum× morifolium). PeerJ 2023; 11:e16436. [PMID: 38111658 PMCID: PMC10726743 DOI: 10.7717/peerj.16436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/19/2023] [Indexed: 12/20/2023] Open
Abstract
The chrysanthemum DgLsL gene, homologous with tomato Ls, is one of the earliest expressed genes controlling axillary meristem initiation. In this study, the wild-type chrysanthemum (CW) and DgLsL-overexpressed line 15 (C15) were used to investigate the regulatory mechanism of axillary bud development in chrysanthemum. Transcriptome sequencing was carried out to detect the differentially expressed genes of the axillary buds 0 h, 24 h and 48 h after decapitation. The phenotypic results showed that the number of axillary buds of C15 was significantly higher than CW. A total of 9,224 DEGs were identified in C15-0 vs. CW-0, 10,622 DEGs in C15-24 vs. CW-24, and 8,929 DEGs in C15-48 vs. CW-48.GO and KEGG pathway enrichment analyses showed that the genes of the flavonoid, phenylpropanoids and plant hormone pathways appeared to be differentially expressed, indicating their important roles in axillary bud germination. DgLsL reduces GA content in axillary buds by promoting GA2ox expression.These results confirmed previous studies on axillary bud germination and growth, and revealed the important roles of genes involved in plant hormone biosynthesis and signal transduction, aiding in the study of the gene patterns involved in axillary bud germination and growth.
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Affiliation(s)
- Yijun Chen
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Qin Ling
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Xin Li
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Qiqi Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - ShaoKang Tang
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Pan Yuanzhi
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Qing-lin Liu
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Yin Jia
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Xue Yong
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
| | - Beibei Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chendu, Sichuan, China
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Neher WR, Rasmussen CG, Braybrook SA, Lažetić V, Stowers CE, Mooney PT, Sylvester AW, Springer PS. The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth. Development 2023; 150:dev201608. [PMID: 37539661 PMCID: PMC10629682 DOI: 10.1242/dev.201608] [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: 02/05/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023]
Abstract
The maize ligule is an epidermis-derived structure that arises from the preligule band (PLB) at a boundary between the blade and sheath. A hinge-like auricle also develops immediately distal to the ligule and contributes to blade angle. Here, we characterize the stages of PLB and early ligule development in terms of topography, cell area, division orientation, cell wall rigidity and auxin response dynamics. Differential thickening of epidermal cells and localized periclinal divisions contributed to the formation of a ridge within the PLB, which ultimately produces the ligule fringe. Patterns in cell wall rigidity were consistent with the subdivision of the PLB into two regions along a distinct line positioned at the nascent ridge. The proximal region produces the ligule, while the distal region contributes to one epidermal face of the auricles. Although the auxin transporter PIN1 accumulated in the PLB, observed differential auxin transcriptional response did not underlie the partitioning of the PLB. Our data demonstrate that two zones with contrasting cellular properties, the preligule and preauricle, are specified within the ligular region before ligule outgrowth.
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Affiliation(s)
- Wesley R. Neher
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
| | - Carolyn G. Rasmussen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Siobhan A. Braybrook
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, Los Angeles, CA 90095, USA
| | - Vladimir Lažetić
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Claire E. Stowers
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Paul T. Mooney
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Anne W. Sylvester
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Patricia S. Springer
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
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Yuan Y, Khourchi S, Li S, Du Y, Delaplace P. Unlocking the Multifaceted Mechanisms of Bud Outgrowth: Advances in Understanding Shoot Branching. PLANTS (BASEL, SWITZERLAND) 2023; 12:3628. [PMID: 37896091 PMCID: PMC10610460 DOI: 10.3390/plants12203628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023]
Abstract
Shoot branching is a complex and tightly regulated developmental process that is essential for determining plant architecture and crop yields. The outgrowth of tiller buds is a crucial step in shoot branching, and it is influenced by a variety of internal and external cues. This review provides an extensive overview of the genetic, plant hormonal, and environmental factors that regulate shoot branching in several plant species, including rice, Arabidopsis, tomato, and wheat. We especially highlight the central role of TEOSINTE BRANCHED 1 (TB1), a key gene in orchestrating bud outgrowth. In addition, we discuss how the phytohormones cytokinins, strigolactones, and auxin interact to regulate tillering/branching. We also shed light on the involvement of sugar, an integral component of plant development, which can impact bud outgrowth in both trophic and signaling ways. Finally, we emphasize the substantial influence of environmental factors, such as light, temperature, water availability, biotic stresses, and nutrients, on shoot branching. In summary, this review offers a comprehensive evaluation of the multifaced regulatory mechanisms that underpin shoot branching and highlights the adaptable nature of plants to survive and persist in fluctuating environmental conditions.
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Affiliation(s)
- Yundong Yuan
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an 271018, China
| | - Said Khourchi
- Plant Sciences, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Shujia Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfang Du
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an 271018, China
| | - Pierre Delaplace
- Plant Sciences, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
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Yang Q, Yuan C, Cong T, Zhang Q. The Secrets of Meristems Initiation: Axillary Meristem Initiation and Floral Meristem Initiation. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091879. [PMID: 37176937 PMCID: PMC10181267 DOI: 10.3390/plants12091879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023]
Abstract
The branching phenotype is an extremely important agronomic trait of plants, especially for horticultural crops. It is not only an important yield character of fruit trees, but also an exquisite ornamental trait of landscape trees and flowers. The branching characteristics of plants are determined by the periodic initiation and later development of meristems, especially the axillary meristem (AM) in the vegetative stage and the floral meristem (FM) in the reproductive stage, which jointly determine the above-ground plant architecture. The regulation of meristem initiation has made great progress in model plants in recent years. Meristem initiation is comprehensively regulated by a complex regulatory network composed of plant hormones and transcription factors. However, as it is an important trait, studies on meristem initiation in horticultural plants are very limited, and the mechanism of meristem initiation regulation in horticultural plants is largely unknown. This review summarizes recent research advances in axillary meristem regulation and mainly reviews the regulatory networks and mechanisms of AM and FM initiation regulated by transcription factors and hormones. Finally, considering the existing problems in meristem initiation studies and the need for branching trait improvement in horticulture plants, we prospect future studies to accelerate the genetic improvement of the branching trait in horticulture plants.
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Affiliation(s)
- Qingqing Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Cunquan Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tianci Cong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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10
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Yang T, Jiao Y, Wang Y. Stem Cell Basis of Shoot Branching. PLANT & CELL PHYSIOLOGY 2023; 64:291-296. [PMID: 36416577 DOI: 10.1093/pcp/pcac165] [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: 09/24/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
During their postembryonic development, plants continuously form branches to conquer more space and adapt to changing environments. In seed plants, this is achieved by lateral branching, in which axillary meristems (AMs) initiate at the leaf axils to form axillary buds. The developmental potential of AMs to form shoot branches is the same as that of embryonic shoot apical meristems (SAMs). Recent studies in Arabidopsis thaliana have revealed the cellular origin of AMs and have identified transcription factors and phytohormones that regulate sequential steps leading to AM initiation. In particular, a group of meristematic cells detached from the SAM are key to AM initiation, which constitutes an excellent system for understanding stem cell fate and de novo meristem formation.
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Affiliation(s)
- Tingting Yang
- College of Life Sciences, University of Chinese Academy of Sciences, 19A Yuquan Rd., Shijingshan District, Beijing 100049, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Center for Quantitative Biology, Peking University, 5 Summer Palace Rd., Haidian District, Beijing 100871, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, 19A Yuquan Rd., Shijingshan District, Beijing 100049, China
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11
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Sun J, Bie XM, Chu XL, Wang N, Zhang XS, Gao XQ. Genome-edited TaTFL1-5 mutation decreases tiller and spikelet numbers in common wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1142779. [PMID: 36895877 PMCID: PMC9989183 DOI: 10.3389/fpls.2023.1142779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Tillering is a critical agronomic trait of wheat (Triticum aestivum L.) that determines the shoot architecture and affects grain yield. TERMINAL FLOWER 1 (TFL1), encoding a phosphatidylethanolamine-binding protein, is implicated in the transition to flowering and shoot architecture in plant development. However, the roles of TFL1 homologs is little known in wheat development. CRISPR/Cas9-mediated targeted mutagenesis was used in this study to generate a set of wheat (Fielder) mutants with single, double or triple-null tatfl1-5 alleles. The wheat tatfl1-5 mutations decreased the tiller number per plant in the vegetative growth stage and the effective tiller number per plant and spikelet number per spike at maturity in the field. RNA-seq analysis showed that the expression of the auxin signaling-related and cytokinin signaling-related genes was significantly changed in the axillary buds of tatfl1-5 mutant seedlings. The results suggested that wheat TaTFL1-5s were implicated in tiller regulation by auxin and cytokinin signaling.
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12
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Bernal-Gallardo JJ, Zuñiga-Mayo VM, Marsch-Martinez N, de Folter S. Novel Roles of SPATULA in the Control of Stomata and Trichome Number, and Anthocyanin Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2023; 12:596. [PMID: 36771679 PMCID: PMC9919660 DOI: 10.3390/plants12030596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The bHLH transcription factor SPATULA (SPT) has been identified as a regulator during different stages of Arabidopsis development, including the control of leaf size. However, the mechanism via which it performs this function has not been elucidated. To better understand the role of SPT during leaf development, we used a transcriptomic approach to identify putative target genes. We found putative SPT target genes related to leaf development, and to stomata and trichome formation. Furthermore, genes related to anthocyanin biosynthesis. In this work, we demonstrate that SPT is a negative regulator of stomata number and a positive regulator of trichome number. In addition, SPT is required for sucrose-mediated anthocyanin biosynthesis.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Mexico
| | - Victor M. Zuñiga-Mayo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Mexico
- CONACYT, Instituto de Fitosanidad, Colegio de Postgraduados, Campus Montecillo, Texcoco 56230, Mexico
| | - Nayelli Marsch-Martinez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Mexico
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13
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Minow MAA, Coneva V, Lesy V, Misyura M, Colasanti J. Plant gene silencing signals move from the phloem to influence gene expression in shoot apical meristems. BMC PLANT BIOLOGY 2022; 22:606. [PMID: 36550422 PMCID: PMC9783409 DOI: 10.1186/s12870-022-03998-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Small RNAs (sRNA) are potent regulators of gene expression that can diffuse short distances between cells and move long distances through plant vasculature. However, the degree to which sRNA silencing signals can move from the phloem to the shoot apical meristem (SAM) remains unclear. RESULTS Two independent transgenic approaches were used to examine whether phloem sRNA silencing can reach different domains of the SAM and silence SAM-expressed genes. First, the phloem companion-cell specific SUCROSE-PROTON SYMPORTER2 (SUC2) promoter was used to drive expression of an inverted repeat to target the FD gene, an exclusively SAM-localized floral regulator. Second, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) transgene in SAM stem cells. Both phloem silencing signals phenocopied the loss of function of their targets and altered target gene expression suggesting that a phloem-to-SAM silencing communication axis exists, connecting distal regions of the plant to SAM stem cells. CONCLUSIONS Demonstration of phloem-to-SAM silencing reveals a regulatory link between somatic sRNA expressed in distal regions of the plant and the growing shoot. Since the SAM stem cells ultimately produce the gametes, we discuss the intriguing possibility that phloem-to-SAM sRNA trafficking could allow transient somatic sRNA expression to manifest stable, transgenerational epigenetic changes.
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Affiliation(s)
- Mark A. A. Minow
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Viktoriya Coneva
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Victoria Lesy
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Max Misyura
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
| | - Joseph Colasanti
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East Guelph, Ontario, Canada
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14
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Nicolas A, Maugarny-Calès A, Adroher B, Chelysheva L, Li Y, Burguet J, Bågman AM, Smit ME, Brady SM, Li Y, Laufs P. De novo stem cell establishment in meristems requires repression of organ boundary cell fate. THE PLANT CELL 2022; 34:4738-4759. [PMID: 36029254 PMCID: PMC9709991 DOI: 10.1093/plcell/koac269] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/24/2022] [Indexed: 05/27/2023]
Abstract
Stem cells play important roles in animal and plant biology, as they sustain morphogenesis and tissue replenishment following aging or injury. In plants, stem cells are embedded in multicellular structures called meristems. The formation of new meristems is essential for the plastic expansion of the highly branched shoot and root systems. In particular, axillary meristems (AMs) that produce lateral shoots arise from the division of boundary domain cells at the leaf base. The CUP-SHAPED COTYLEDON (CUC) genes are major determinants of the boundary domain and are required for AM initiation. However, how AMs get structured and how stem cells become established de novo remain elusive. Here, we show that two NGATHA-LIKE (NGAL) transcription factors, DEVELOPMENT-RELATED PcG TARGET IN THE APEX4 (DPA4)/NGAL3 and SUPPRESSOR OF DA1-1 7 (SOD7)/NGAL2, redundantly repress CUC expression in initiating AMs of Arabidopsis thaliana. Ectopic boundary fate leads to abnormal growth and organization of the AM and prevents de novo stem cell establishment. Floral meristems of the dpa4 sod7 double mutant show a similar delay in de novo stem cell establishment. Altogether, while boundary fate is required for the initiation of AMs, our work reveals how it is later repressed to allow proper meristem establishment and de novo stem cell niche formation.
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Affiliation(s)
- Antoine Nicolas
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
- Université Paris-Saclay, Orsay, 91405, France
| | - Aude Maugarny-Calès
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
- Université Paris-Saclay, Orsay, 91405, France
| | - Bernard Adroher
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Liudmila Chelysheva
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Yu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jasmine Burguet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Margot E Smit
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
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15
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Ferrari C, Manosalva Pérez N, Vandepoele K. MINI-EX: Integrative inference of single-cell gene regulatory networks in plants. MOLECULAR PLANT 2022; 15:1807-1824. [PMID: 36307979 DOI: 10.1016/j.molp.2022.10.016] [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: 07/01/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 05/26/2023]
Abstract
Multicellular organisms, such as plants, are characterized by highly specialized and tightly regulated cell populations, establishing specific morphological structures and executing distinct functions. Gene regulatory networks (GRNs) describe condition-specific interactions of transcription factors (TFs) regulating the expression of target genes, underpinning these specific functions. As efficient and validated methods to identify cell-type-specific GRNs from single-cell data in plants are lacking, limiting our understanding of the organization of specific cell types in both model species and crops, we developed MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data), an integrative approach to infer cell-type-specific networks in plants. MINI-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons, resulting in networks with increased accuracy. Next, regulons are assigned to different cell types, leveraging cell-specific expression, and candidate regulators are prioritized using network centrality measures, functional annotations, and expression specificity. This embedded prioritization strategy offers a unique and efficient means to unravel signaling cascades in specific cell types controlling a biological process of interest. We demonstrate the stability of MINI-EX toward input data sets with low number of cells and its robustness toward missing data, and show that it infers state-of-the-art networks with a better performance compared with other related single-cell network tools. MINI-EX successfully identifies key regulators controlling root development in Arabidopsis and rice, leaf development in Arabidopsis, and ear development in maize, enhancing our understanding of cell-type-specific regulation and unraveling the roles of different regulators controlling the development of specific cell types in plants.
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Affiliation(s)
- Camilla Ferrari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.
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16
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The NGATHA-like Genes DPA4 and SOD7 Are Not Required for Stem Cell Specification during Embryo Development in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms231912007. [PMID: 36233309 PMCID: PMC9569844 DOI: 10.3390/ijms231912007] [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: 09/16/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 01/09/2023] Open
Abstract
In plants, stem cells are embedded in structures called meristems. Meristems can be formed either during embryogenesis or during the plant's life such as, for instance, axillary meristems. While the regulation of the stem cell population in an established meristem is well described, how it is initiated in newly formed meristems is less well understood. Recently, two transcription factors of the NGATHA-like family, DEVELOPMENT-RELATED PcG TARGET IN THE APEX4 (DPA4)/NGAL3 and SUPPRESSOR OF DA1-1 7 (SOD7)/NGAL2 have been shown to facilitate de novo stem cell initiation in Arabidopsis thaliana axillary meristems. Here, we tested whether the DPA4 and SOD7 genes had a similar role during stem cell formation in embryo shoot apical meristems. Using DPA4 and SOD7 reporter lines, we characterized the expression pattern of these genes during embryo development, revealing only a partial overlap with the stem cell population. In addition, we showed that the expression of a stem cell reporter was not modified in dpa4-2 sod7-2 double mutant embryos compared to the wild type. Together, these observations suggest that DPA4 and SOD7 are not required for stem cell specification during embryo shoot apical meristem initiation. This work stresses the difference in the regulatory network leading to meristem formation during the embryonic and post-embryonic phases.
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17
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Zhang X, Sun Y, Qiu X, Lu H, Hwang I, Wang T. Tolerant mechanism of model legume plant Medicago truncatula to drought, salt, and cold stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:847166. [PMID: 36160994 PMCID: PMC9490062 DOI: 10.3389/fpls.2022.847166] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Legume plants produce one-third of the total yield of primary crops and are important food sources for both humans and animals worldwide. Frequent exposure to abiotic stresses, such as drought, salt, and cold, greatly limits the production of legume crops. Several morphological, physiological, and molecular studies have been conducted to characterize the response and adaptation mechanism to abiotic stresses. The tolerant mechanisms of the model legume plant Medicago truncatula to abiotic stresses have been extensively studied. Although many potential genes and integrated networks underlying the M. truncatula in responding to abiotic stresses have been identified and described, a comprehensive summary of the tolerant mechanism is lacking. In this review, we provide a comprehensive summary of the adaptive mechanism by which M. truncatula responds to drought, salt, and cold stress. We also discuss future research that need to be explored to improve the abiotic tolerance of legume plants.
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Affiliation(s)
- Xiuxiu Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciencess, Beijing, China
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciencess, Changchun, China
| | - Xiao Qiu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hai Lu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Tianzuo Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciencess, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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18
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Zhang L, Fang W, Chen F, Song A. The Role of Transcription Factors in the Regulation of Plant Shoot Branching. PLANTS 2022; 11:plants11151997. [PMID: 35956475 PMCID: PMC9370718 DOI: 10.3390/plants11151997] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022]
Abstract
Transcription factors, also known as trans-acting factors, balance development and stress responses in plants. Branching plays an important role in plant morphogenesis and is closely related to plant biomass and crop yield. The apical meristem produced during plant embryonic development repeatedly produces the body of the plant, and the final aerial structure is regulated by the branching mode generated by axillary meristem (AM) activities. These branching patterns are regulated by two processes: AM formation and axillary bud growth. In recent years, transcription factors involved in regulating these processes have been identified. In addition, these transcription factors play an important role in various plant hormone pathways and photoresponses regulating plant branching. In this review, we start from the formation and growth of axillary meristems, including the regulation of hormones, light and other internal and external factors, and focus on the transcription factors involved in regulating plant branching and development to provide candidate genes for improving crop architecture through gene editing or directed breeding.
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Affiliation(s)
- Lingling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, 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, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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19
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Kusnandar AS, Itoh JI, Sato Y, Honda E, Hibara KI, Kyozuka J, Naramoto S. NARROW AND DWARF LEAF 1, the Ortholog of Arabidopsis ENHANCER OF SHOOT REGENERATION1/DORNRÖSCHEN, Mediates Leaf Development and Maintenance of the Shoot Apical Meristem in Oryza sativa L. PLANT & CELL PHYSIOLOGY 2022; 63:265-278. [PMID: 34865135 DOI: 10.1093/pcp/pcab169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
The molecular basis for leaf development, a major focus in developmental biology, remains unclear in the monocotyledonous grass, rice (Oryza sativa). Here, we performed a mutant screen in rice and identified an AP2-type transcription factor family protein, NARROW AND DWARF LEAF1 (NDL1). NDL1 is the ortholog of Arabidopsis thaliana (subsequently called Arabidopsis) ENHANCER OF SHOOT REGENERATION1 (ESR1)/DORNRÖSCHEN (DRN) and mediates leaf development and maintenance of the shoot apical meristem (SAM). Loss of function of NDL1 results in bladeless leaves and SAMs that are flat, rather than dome-shaped, and lack cell proliferation activity. This loss of function also causes reduced auxin signaling. Moreover, as is the case with Arabidopsis ESR1/DRN, NDL1 plays crucial roles in shoot regeneration. Importantly, we found that NDL1 is not expressed in the SAM but is expressed in leaf primordia. We propose that NDL1 cell autonomously regulates leaf development, but non-cell autonomously regulates SAM maintenance in rice.
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Affiliation(s)
| | - Jun-Ichi Itoh
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Yutaka Sato
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan
| | - Eriko Honda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Ken-Ichiro Hibara
- Graduate School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Hyogo, 656-0484 Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577 Japan
| | - Satoshi Naramoto
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810 Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577 Japan
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20
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Liu W, Sun J, Li J, Liu C, Si F, Yan B, Wang Z, Song X, Yang Y, Zhu Y, Cao X. Reproductive tissue-specific translatome of a rice thermo-sensitive genic male sterile line. J Genet Genomics 2022; 49:624-635. [PMID: 35041992 DOI: 10.1016/j.jgg.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 10/19/2022]
Abstract
Translational regulation, especially tissue- or cell type-specific gene regulation, plays essential roles in plant growth and development. Thermo-sensitive genic male sterile (TGMS) lines have been widely used for hybrid breeding in rice (Oryza sativa). However, little is known about translational regulation during reproductive stage in TGMS rice. Here, we used translating ribosome affinity purification (TRAP) combined with RNA sequencing to investigate the reproductive tissue-specific translatome of TGMS rice expressing FLAG-tagged ribosomal protein L18 (RPL18) from the germline-specific promoter MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1). Differentially expressed genes at the transcriptional and translational levels were enriched in pollen and anther-related formation and development processes. These contained a number of genes reported to be involved in tapetum programmed cell death (PCD) and lipid metabolism during pollen development and anther dehiscence in rice, including several encoding transcription factors and key enzymes, as well as several long non-coding RNAs (lncRNAs) that potentially affect tapetum and pollen-related genes in male sterility. This study represents the first comprehensive reproductive tissue-specific characterization of the translatome in TGMS rice. These results contribute to our understanding of the molecular basis of sterility in TGMS rice and will facilitate further genetic manipulation of TGMS rice in two-line breeding systems.
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Affiliation(s)
- Wei Liu
- College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ji Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuyan Si
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanzhu Yang
- Department of Rice Breeding, Hunan Yahua Seed Scientific Research Institute, Changsha 410119, Hunan, China
| | - Yuxian Zhu
- College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China; Institute for Advanced Studies, Wuhan University, Wuhan 430072, Hubei, China.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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21
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Wang Y. Stem Cell Basis for Fractal Patterns: Axillary Meristem Initiation. FRONTIERS IN PLANT SCIENCE 2021; 12:805434. [PMID: 34975997 PMCID: PMC8718902 DOI: 10.3389/fpls.2021.805434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Whereas stem cell lineages are of enormous importance in animal development, their roles in plant development have only been appreciated in recent years. Several specialized lineages of stem cells have been identified in plants, such as meristemoid mother cells and vascular cambium, as well as those located in the apical meristems. The initiation of axillary meristems (AMs) has recently gained intensive attention. AMs derive from existing stem cell lineages that exit from SAMs and define new growth axes. AMs are in fact additional rounds of SAMs, and display the same expression patterns and functions as the embryonic SAM, creating a fractal branching pattern. Their formation takes place in leaf-meristem boundaries and mainly comprises two key stages. The first stage is the maintenance of the meristematic cell lineage in an undifferentiated state. The second stage is the activation, proliferation, and re-specification to form new stem cell niches in AMs, which become the new postembryonic "fountain of youth" for organogenesis. Both stages are tightly regulated by spatially and temporally interwound signaling networks. In this mini-review, I will summarize the most up-to-date understanding of AM establishment and mainly focus on how the leaf axil meristematic cell lineage is actively maintained and further activated to become CLV3-expressed stem cells, which involves phytohormonal cascades, transcriptional regulations, epigenetic modifications, as well as mechanical signals.
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22
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Luo Z, Janssen BJ, Snowden KC. The molecular and genetic regulation of shoot branching. PLANT PHYSIOLOGY 2021; 187:1033-1044. [PMID: 33616657 PMCID: PMC8566252 DOI: 10.1093/plphys/kiab071] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/22/2021] [Indexed: 05/27/2023]
Abstract
The architecture of flowering plants exhibits both phenotypic diversity and plasticity, determined, in part, by the number and activity of axillary meristems and, in part, by the growth characteristics of the branches that develop from the axillary buds. The plasticity of shoot branching results from a combination of various intrinsic and genetic elements, such as number and position of nodes and type of growth phase, as well as environmental signals such as nutrient availability, light characteristics, and temperature (Napoli et al., 1998; Bennett and Leyser, 2006; Janssen et al., 2014; Teichmann and Muhr, 2015; Ueda and Yanagisawa, 2019). Axillary meristem initiation and axillary bud outgrowth are controlled by a complex and interconnected regulatory network. Although many of the genes and hormones that modulate branching patterns have been discovered and characterized through genetic and biochemical studies, there are still many gaps in our understanding of the control mechanisms at play. In this review, we will summarize our current knowledge of the control of axillary meristem initiation and outgrowth into a branch.
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Affiliation(s)
- Zhiwei Luo
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Bart J Janssen
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
| | - Kimberley C Snowden
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
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23
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Depuydt T, Vandepoele K. Multi-omics network-based functional annotation of unknown Arabidopsis genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1193-1212. [PMID: 34562334 DOI: 10.1111/tpj.15507] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Unraveling gene function is pivotal to understanding the signaling cascades that control plant development and stress responses. As experimental profiling is costly and labor intensive, there is a clear need for high-confidence computational annotation. In contrast to detailed gene-specific functional information, transcriptomics data are widely available for both model and crop species. Here, we describe a novel automated function prediction method, which leverages complementary information from multiple expression datasets by analyzing study-specific gene co-expression networks. First, we benchmarked the prediction performance on recently characterized Arabidopsis thaliana genes, and showed that our method outperforms state-of-the-art expression-based approaches. Next, we predicted biological process annotations for known (n = 15 790) and unknown (n = 11 865) genes in A. thaliana and validated our predictions using experimental protein-DNA and protein-protein interaction data (covering >220 000 interactions in total), obtaining a set of high-confidence functional annotations. Our method assigned at least one validated annotation to 5054 (42.6%) unknown genes, and at least one novel validated function to 3408 (53.0%) genes with computational annotations only. These omics-supported functional annotations shed light on a variety of developmental processes and molecular responses, such as flower and root development, defense responses to fungi and bacteria, and phytohormone signaling, and help fill the information gap on biological process annotations in Arabidopsis. An in-depth analysis of two context-specific networks, modeling seed development and response to water deprivation, shows how previously uncharacterized genes function within the respective networks. Moreover, our automated function prediction approach can be applied in future studies to facilitate gene discovery for crop improvement.
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Affiliation(s)
- Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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24
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Yao FQ, Li XH, Wang H, Song YN, Li ZQ, Li XG, Gao XQ, Zhang XS, Bie XM. Down-expression of TaPIN1s Increases the Tiller Number and Grain Yield in Wheat. BMC PLANT BIOLOGY 2021; 21:443. [PMID: 34592922 PMCID: PMC8482684 DOI: 10.1186/s12870-021-03217-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 09/20/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Tiller number is a factor determining panicle number and grain yield in wheat (Triticum aestivum). Auxin plays an important role in the regulation of branch production. PIN-FORMED 1 (PIN1), an auxin efflux carrier, plays a role in the regulation of tiller number in rice (Oryza sativa); however, little is known on the roles of PIN1 in wheat. RESULTS Nine homologs of TaPIN1 genes were identified in wheat, of which TaPIN1-6 genes showed higher expression in the stem apex and young leaf in wheat, and the TaPIN1-6a protein was localized in the plasma membrane. The down-expression of TaPIN1s increased the tiller number in TaPIN1-RNA interference (TaPIN1-RNAi) transgenic wheat plants, indicating that auxin might mediate the axillary bud production. By contrast, the spikelet number, grain number per panicle, and the 1000-grain weight were decreased in the TaPIN1-RNAi transgenic wheat plants compared with those in the wild type. In summary, a reduction of TaPIN1s expression increased the tiller number and grain yield per plant of wheat. CONCLUSIONS Phylogenetic analysis and protein structure of nine TaPIN1 proteins were analyzed, and subcellular localization of TaPIN1-6a was located in the plasma membrane. Knock-down expression of TaPIN1 genes increased the tiller number of transgenic wheat lines. Our study suggests that TaPIN1s is required for the regulation of grain yield in wheat.
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Affiliation(s)
- Fu Quan Yao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xiao Hui Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - He Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yu Ning Song
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhong Qing Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xing Guo Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xin-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xiao Min Bie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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25
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Post-Embryonic Lateral Organ Development and Adaxial-Abaxial Polarity Are Regulated by the Combined Effect of ENHANCER OF SHOOT REGENERATION 1 and WUSCHEL in Arabidopsis Shoots. Int J Mol Sci 2021; 22:ijms221910621. [PMID: 34638958 PMCID: PMC8508843 DOI: 10.3390/ijms221910621] [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: 08/26/2021] [Revised: 09/19/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
The development of above-ground lateral organs is initiated at the peripheral zone of the shoot apical meristem (SAM). The coordination of cell fate determination and the maintenance of stem cells are achieved through a complex regulatory network comprised of transcription factors. Two AP2/ERF transcription factor family genes, ESR1/DRN and ESR2/DRNL/SOB/BOL, regulate cotyledon and flower formation and de novo organogenesis in tissue culture. However, their roles in post-embryonic lateral organ development remain elusive. In this study, we analyzed the genetic interactions among SAM-related genes, WUS and STM, two ESR genes, and one of the HD-ZIP III members, REV, whose protein product interacts with ESR1 in planta. We found that esr1 mutations substantially enhanced the wus and stm phenotypes, which bear a striking resemblance to those of the wus rev and stm rev double mutants, respectively. Aberrant adaxial–abaxial polarity is observed in wus esr1 at relatively low penetrance. On the contrary, the esr2 mutation partially suppressed stm phenotypes in the later vegetative phase. Such complex genetic interactions appear to be attributed to the distinct expression pattern of two ESR genes because the ESR1 promoter-driving ESR2 is capable of rescuing phenotypes caused by the esr1 mutation. Our results pose the unique genetic relevance of ESR1 and the SAM-related gene interactions in the development of rosette leaves.
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26
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Wang L, Yu P, Lyu J, Hu Y, Han C, Bai MY, Fan M. BZR1 Physically Interacts with SPL9 to Regulate the Vegetative Phase Change and Cell Elongation in Arabidopsis. Int J Mol Sci 2021; 22:ijms221910415. [PMID: 34638756 PMCID: PMC8509050 DOI: 10.3390/ijms221910415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/23/2022] Open
Abstract
As sessile organisms, the precise development phase transitions are very important for the success of plant adaptability, survival and reproduction. The transition from juvenile to the adult phase—referred to as the vegetative phase change—is significantly influenced by numbers of endogenous and environmental signals. Here, we showed that brassinosteroid (BR), a major growth-promoting steroid hormone, positively regulates the vegetative phase change in Arabidopsis thaliana. The BR-deficient mutant det2-1 and BR-insensitive mutant bri1-301 displayed the increased ratio of leaf width to length and reduced blade base angle. The plant specific transcription factors SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) are key masters for the vegetative phase transition in plants. The expression levels of SPL9, SPL10 and SPL15 were significantly induced by BR treatment, but reduced in bri1-116 mutant compared to wild-type plants. The gain-of-function pSPL9:rSPL9 transgenic plants displayed the BR hypersensitivity on hypocotyl elongation and partially suppressed the delayed vegetative phase change of det2-1 and bri1-301. Furthermore, we showed that BRASSINAZOLE-RESISTANT 1 (BZR1), the master transcription factor of BR signaling pathway, interacted with SPL9 to cooperatively regulate the expression of downstream genes. Our findings reveal an important role for BRs in promoting vegetative phase transition through regulating the activity of SPL9 at transcriptional and post-transcriptional levels.
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27
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López H, Schmitz G, Thoma R, Theres K. Super determinant1A, a RAWULdomain-containing protein, modulates axillary meristem formation and compound leaf development in tomato. THE PLANT CELL 2021; 33:2412-2430. [PMID: 34009392 PMCID: PMC8364250 DOI: 10.1093/plcell/koab121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/22/2021] [Indexed: 05/28/2023]
Abstract
Shoot branching and complex leaf development relies on the establishment of boundaries that precedes the formation of axillary meristems (AMs) and leaflets. The tomato (Solanum lycopersicum) super determinant mutant is compromised in both processes, due to a mutation in Sde1A. Sde1A encodes a protein with a RAWUL domain, which is also present in Polycomb Group Repressive Complex 1 (PRC1) RING finger proteins and WD Repeat Domain 48 proteins. Genetic analysis revealed that Sde1A and Bmi1A cooperate, whereas Bmi1C antagonizes both activities, indicating the existence of functionally opposing PRC1 complexes that interact with Sde1A. Sde1A is expressed at early stages of boundary development in a small group of cells in the center of the leaf-axil boundary, but its activity is required for meristem formation at later stages. This suggests that Sde1A and Bmi1A promote AM formation and complex leaf development by safeguarding a pool of cells in the developing boundary zones. Genetic and protein interaction analyses showed that Sde1A and Lateral suppressor (Ls) are components of the same genetic pathway. In contrast to ls, sde1a mutants are not compromised in inflorescence branching, suggesting that Sde1A is a potential target for breeding tomato cultivars with reduced side-shoot formation during vegetative development.
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Affiliation(s)
- Hernán López
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
| | - Gregor Schmitz
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
| | - Rahere Thoma
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
| | - Klaus Theres
- Max Planck Institute for Plant Breeding Research, Cologne D-50931, Germany
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28
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Feng J, Cheng L, Zhu Z, Yu F, Dai C, Liu Z, Guo WW, Wu XM, Kang C. GRAS transcription factor LOSS OF AXILLARY MERISTEMS is essential for stamen and runner formation in wild strawberry. PLANT PHYSIOLOGY 2021; 186:1970-1984. [PMID: 33890635 PMCID: PMC8331164 DOI: 10.1093/plphys/kiab184] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/03/2021] [Indexed: 05/19/2023]
Abstract
Axillary bud development is a major factor that impacts plant architecture. A runner is an elongated shoot that develops from axillary bud and is frequently used for clonal propagation of strawberry. However, the genetic control underlying runner production is largely unknown. Here, we identified and characterized loss of axillary meristems (lam), an ethyl methanesulfonate-induced mutant of the diploid woodland strawberry (Fragaria vesca) that lacked stamens in flowers and had reduced numbers of branch crowns and runners. The reduced branch crown and runner phenotypes were caused by a failure of axillary meristem initiation. The causative mutation of lam was located in FvH4_3g41310, which encodes a GRAS transcription factor, and was validated by a complementation test. lamCR mutants generated by CRISPR/Cas9 produced flowers without stamens and had fewer runners than the wild-type. LAM was broadly expressed in meristematic tissues. Gibberellic acid (GA) application induced runner outgrowth from the remaining buds in lam, but failed to do so at the empty axils of lam. In contrast, treatment with the GA biosynthesis inhibitor paclobutrazol converted the runners into branch crowns. Moreover, genetic studies indicated that lam is epistatic to suppressor of runnerless (srl), a mutant of FveRGA1 in the GA pathway, during runner formation. Our results demonstrate that LAM is required for stamen and runner formation and acts sequentially with GA from bud initiation to runner outgrowth, providing insights into the molecular regulation of these economically important organs in strawberry.
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Affiliation(s)
- Jia Feng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Laichao Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenying Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Feiqi Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunying Kang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Author for communication:
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29
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Tissue folding at the organ-meristem boundary results in nuclear compression and chromatin compaction. Proc Natl Acad Sci U S A 2021; 118:2017859118. [PMID: 33608459 PMCID: PMC7923354 DOI: 10.1073/pnas.2017859118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Artificial mechanical perturbations affect chromatin in animal cells in culture. Whether this is also relevant to growing tissues in living organisms remains debated. In plants, aerial organ emergence occurs through localized outgrowth at the periphery of the shoot apical meristem, which also contains a stem cell niche. Interestingly, organ outgrowth has been proposed to generate compression in the saddle-shaped organ-meristem boundary domain. Yet whether such growth-induced mechanical stress affects chromatin in plant tissues is unknown. Here, by imaging the nuclear envelope in vivo over time and quantifying nucleus deformation, we demonstrate the presence of active nuclear compression in that domain. We developed a quantitative pipeline amenable to identifying a subset of very deformed nuclei deep in the boundary and in which nuclei become gradually narrower and more elongated as the cell contracts transversely. In this domain, we find that the number of chromocenters is reduced, as shown by chromatin staining and labeling, and that the expression of linker histone H1.3 is induced. As further evidence of the role of forces on chromatin changes, artificial compression with a MicroVice could induce the ectopic expression of H1.3 in the rest of the meristem. Furthermore, while the methylation status of chromatin was correlated with nucleus deformation at the meristem boundary, such correlation was lost in the h1.3 mutant. Altogether, we reveal that organogenesis in plants generates compression that is able to have global effects on chromatin in individual cells.
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30
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Xu M, Du Q, Tian C, Wang Y, Jiao Y. Stochastic gene expression drives mesophyll protoplast regeneration. SCIENCE ADVANCES 2021; 7:eabg8466. [PMID: 34380624 PMCID: PMC8357238 DOI: 10.1126/sciadv.abg8466] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/22/2021] [Indexed: 05/06/2023]
Abstract
Cell pluripotency is fundamental to biology. It has long been known that differentiated somatic plant cells may reacquire pluripotency, but the underlying mechanism remains elusive. In many plant species, a single isolated mesophyll protoplast may regenerate into an entire plant, which is widely used in gene transformation. Here, we identified two transcription factors whose ectopic activation promotes protoplast regeneration. Furthermore, we found that their expression was induced by protoplast isolation but at a very low frequency. Using live imaging and single-cell transcriptomics, we show that isolating protoplasts induces enhanced expression variation at the genome level. Isolating protoplasts also leads to genome-wide increases in chromatin accessibility, which promotes stochastic activation of gene expression and enhances protoplast regeneration. We propose that transcriptome chaos with increased expression variability among cells creates a cellular-level evolutionary driver selecting for regenerating cells.
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Affiliation(s)
- Mengxue Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingwei Du
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caihuan Tian
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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31
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Thiel J, Koppolu R, Trautewig C, Hertig C, Kale SM, Erbe S, Mascher M, Himmelbach A, Rutten T, Esteban E, Pasha A, Kumlehn J, Provart NJ, Vanderauwera S, Frohberg C, Schnurbusch T. Transcriptional landscapes of floral meristems in barley. SCIENCE ADVANCES 2021; 7:eabf0832. [PMID: 33910893 PMCID: PMC8081368 DOI: 10.1126/sciadv.abf0832] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/26/2021] [Indexed: 05/02/2023]
Abstract
Organ development in plants predominantly occurs postembryonically through combinatorial activity of meristems; therefore, meristem and organ fate are intimately connected. Inflorescence morphogenesis in grasses (Poaceae) is complex and relies on a specialized floral meristem, called spikelet meristem, that gives rise to all other floral organs and ultimately the grain. The fate of the spikelet determines reproductive success and contributes toward yield-related traits in cereal crops. Here, we examined the transcriptional landscapes of floral meristems in the temperate crop barley (Hordeum vulgare L.) using RNA-seq of laser capture microdissected tissues from immature, developing floral structures. Our unbiased, high-resolution approach revealed fundamental regulatory networks, previously unknown pathways, and key regulators of barley floral fate and will equally be indispensable for comparative transcriptional studies of grass meristems.
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Affiliation(s)
- J Thiel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - R Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - C Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - C Hertig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S Erbe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - M Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - A Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - T Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - E Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - A Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - J Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - N J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - S Vanderauwera
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - C Frohberg
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - T Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
- Martin Luther University Halle-Wittenberg, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
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De Clercq I, Van de Velde J, Luo X, Liu L, Storme V, Van Bel M, Pottie R, Vaneechoutte D, Van Breusegem F, Vandepoele K. Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators. NATURE PLANTS 2021; 7:500-513. [PMID: 33846597 DOI: 10.1038/s41477-021-00894-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in Arabidopsis thaliana, different regulatory input networks capturing complementary information about DNA motifs, open chromatin, TF-binding and expression-based regulatory interactions were combined using a supervised learning approach, resulting in an integrated gene regulatory network (iGRN) covering 1,491 TFs and 31,393 target genes (1.7 million interactions). This iGRN outperforms the different input networks to predict known regulatory interactions and has a similar performance to recover functional interactions compared to state-of-the-art experimental methods. The iGRN correctly inferred known functions for 681 TFs and predicted new gene functions for hundreds of unknown TFs. For regulators predicted to be involved in reactive oxygen species (ROS) stress regulation, we confirmed in total 75% of TFs with a function in ROS and/or physiological stress responses. This includes 13 ROS regulators, previously not connected to any ROS or stress function, that were experimentally validated in our ROS-specific phenotypic assays of loss- or gain-of-function lines. In conclusion, the presented iGRN offers a high-quality starting point to enhance our understanding of gene regulation in plants by integrating different experimental data types.
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Affiliation(s)
- Inge De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
| | - Jan Van de Velde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Xiaopeng Luo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Li Liu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Robin Pottie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dries Vaneechoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
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Ma Y, Xue H, Zhang F, Jiang Q, Yang S, Yue P, Wang F, Zhang Y, Li L, He P, Zhang Z. The miR156/SPL module regulates apple salt stress tolerance by activating MdWRKY100 expression. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:311-323. [PMID: 32885918 PMCID: PMC7868983 DOI: 10.1111/pbi.13464] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/04/2020] [Accepted: 07/17/2020] [Indexed: 05/14/2023]
Abstract
Salt stress dramatically impedes plant growth and development as well as crop yield. The apple production regions are reduced every year, because of the secondary salt damage by improper fertilization and irrigation. To expand the cultivation area of apple (Malus domestica) and select salt-resistant varieties, the mechanism of salt tolerance in apple is necessary to be clarified. The miR156/SPL regulatory module plays key roles in embryogenesis, morphogenesis, life cycle stage transformation, flower formation and other processes. However, its roles in the mechanisms of salt tolerance are unknown. In order to elucidate the mechanism of 156/SPL regulating salt stress in apple, we performed RLM-5' RACE and stable genetic transformation technology to verify that both mdm-MIR156a and MdSPL13 responded to salt stress in apple and that the latter was the target of the former. MIR156a overexpression weakened salt resistance in apple whereas MdSPL13 overexpression strengthened it. A total of 6094 differentially expressed genes relative to nontransgenic apple plants were found by RNA-Seq analysis of MdSPL13OE. Further verification indicated that MdSPL13 targeted the MdWRKY100 gene promoter. Moreover, MdWRKY100 overexpression enhanced salt tolerance in apple. Our results revealed that the miR156/SPL module regulates salt tolerance by up-regulating MdWRKY100 in apple. This study is the first to elucidate the mechanism underlying the miRNA network response to salt stress in apple and provides theoretical and empirical bases and genetic resources for the molecular breeding of salt tolerance in apple.
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Affiliation(s)
- Yue Ma
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Hao Xue
- College of HorticultureShenyang Agricultural UniversityShenyangChina
- College of HorticultureAnhui Agricultural UniversityHefeiChina
| | - Feng Zhang
- College of Bioscience and BiotechnologyShenyang Agricultural UniversityShenyangChina
| | - Qiu Jiang
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Shuang Yang
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Pengtao Yue
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Feng Wang
- College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
| | - Yuanyan Zhang
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Linguang Li
- Shandong Institute of PomologyTaianShandongChina
| | - Ping He
- Shandong Institute of PomologyTaianShandongChina
| | - Zhihong Zhang
- College of HorticultureShenyang Agricultural UniversityShenyangChina
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Zhou Y, Gan X, Viñegra de la Torre N, Neumann U, Albani MC. Beyond flowering time: diverse roles of an APETALA2-like transcription factor in shoot architecture and perennial traits. THE NEW PHYTOLOGIST 2021; 229:444-459. [PMID: 32745288 DOI: 10.1111/nph.16839] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/22/2020] [Indexed: 05/11/2023]
Abstract
Polycarpic perennials maintain vegetative growth after flowering. PERPETUAL FLOWERING 1 (PEP1), the orthologue of FLOWERING LOCUS C (FLC) in Arabis alpina regulates flowering and contributes to polycarpy in a vernalisation-dependent pathway. pep1 mutants do not require vernalisation to flower and have reduced return to vegetative growth as all of their axillary branches become reproductive. To identify additional genes that regulate flowering and contribute to perennial traits we performed an enhancer screen of pep1. Using mapping-by-sequencing, we cloned a mutant (enhancer of pep1-055, eop055), performed transcriptome analysis and physiologically characterised the role it plays on perennial traits in an introgression line carrying the eop055 mutation and a functional PEP1 wild-type allele. eop055 flowers earlier than pep1 and carries a lesion in the A. alpina orthologue of the APETALA2 (AP2)-like gene, TARGET OF EAT2 (AaTOE2). AaTOE2 is a floral repressor and acts upstream of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 5 (AaSPL5). In the wild-type background, which requires cold treatment to flower, AaTOE2 regulates the age-dependent response to vernalisation. In addition, AaTOE2 ensures the maintenance of vegetative growth by delaying axillary meristem initiation and repressing flowering of axillary buds before and during cold exposure. We conclude that AaTOE2 is instrumental in fine tuning different developmental traits in the perennial life cycle of A. alpina.
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Affiliation(s)
- Yanhao Zhou
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, Cologne, 50674, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
- Cluster of Excellence on Plant Sciences, "From Complex Traits towards Synthetic Modules", Düsseldorf, 40225, Germany
| | - Xiangchao Gan
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Natanael Viñegra de la Torre
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, Cologne, 50674, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Ulla Neumann
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, Cologne, 50674, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
- Cluster of Excellence on Plant Sciences, "From Complex Traits towards Synthetic Modules", Düsseldorf, 40225, Germany
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Mallet J, Laufs P, Leduc N, Le Gourrierec J. Photocontrol of Axillary Bud Outgrowth by MicroRNAs: Current State-of-the-Art and Novel Perspectives Gained From the Rosebush Model. FRONTIERS IN PLANT SCIENCE 2021; 12:770363. [PMID: 35173747 PMCID: PMC8841825 DOI: 10.3389/fpls.2021.770363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/13/2021] [Indexed: 05/05/2023]
Abstract
Shoot branching is highly dependent on environmental factors. While many species show some light dependence for branching, the rosebush shows a strict requirement for light to allow branching, making this species an excellent model to further understand how light impinges on branching. Here, in the first part, we provide a review of the current understanding of how light may modulate the complex regulatory network of endogenous factors like hormones (SL, IAA, CK, GA, and ABA), nutrients (sugar and nitrogen), and ROS to control branching. We review the regulatory contribution of microRNAs (miRNAs) to branching in different species, highlighting the action of such evolutionarily conserved factors. We underline some possible pathways by which light may modulate miRNA-dependent regulation of branching. In the second part, we exploit the strict light dependence of rosebush for branching to identify putative miRNAs that could contribute to the photocontrol of branching. For this, we first performed a profiling of the miRNAs expressed in early light-induced rosebush buds and next tested whether they were predicted to target recognized regulators of branching. Thus, we identified seven miRNAs (miR156, miR159, miR164, miR166, miR399, miR477, and miR8175) that could target nine genes (CKX1/6, EXPA3, MAX4, CYCD3;1, SUSY, 6PFK, APX1, and RBOHB1). Because these genes are affecting branching through different hormonal or metabolic pathways and because expression of some of these genes is photoregulated, our bioinformatic analysis suggests that miRNAs may trigger a rearrangement of the regulatory network to modulate branching in response to light environment.
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Affiliation(s)
- Julie Mallet
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Nathalie Leduc
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - José Le Gourrierec
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
- *Correspondence: José Le Gourrierec,
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Jia T, Zhang K, Li F, Huang Y, Fan M, Huang T. The AtMYB2 inhibits the formation of axillary meristem in Arabidopsis by repressing RAX1 gene under environmental stresses. PLANT CELL REPORTS 2020; 39:1755-1765. [PMID: 32970176 DOI: 10.1007/s00299-020-02602-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/13/2020] [Indexed: 05/12/2023]
Abstract
AtMYB2 protein represses the formation of axillary meristems in response to environmental stresses so that plants can undergo a shorter vegetative development stage under environmental stresses. Shoot branching is an important event determined by endogenous factors during the development of plants. The formation of axillary meristem is also significantly repressed by environmental stresses and the underlying mechanism is largely unknown. The REGULATOR OF AXILLARY MERISTEMS (RAX) genes encode the R2R3 MYB transcription factors that have been shown to regulate the formation of axillary meristems in Arabidopsis. The AtMYB2 is also a member of R2R3 MYB gene family whose expression is usually induced by the environmental stresses. In this study, our results showed that AtMYB2 protein plays a pivotal negative regulatory role in the formation of axillary meristem. AtMYB2 is mainly expressed in the leaf axils as that of RAX1. The environmental stresses can increase the expression of AtMYB2 protein which further inhibits the expression of RAX1 gene by binding to its promoter. Therefore, AtMYB2 protein represses the formation of axillary meristems in response to environmental stresses so that plants can undergo a shorter vegetative development stage under environmental stresses.
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Affiliation(s)
- Tianqi Jia
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Kaidian Zhang
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Fan Li
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yifeng Huang
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Manman Fan
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Tao Huang
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
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Poretska O, Yang S, Pitorre D, Poppenberger B, Sieberer T. AMP1 and CYP78A5/7 act through a common pathway to govern cell fate maintenance in Arabidopsis thaliana. PLoS Genet 2020; 16:e1009043. [PMID: 32960882 PMCID: PMC7531801 DOI: 10.1371/journal.pgen.1009043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 10/02/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Higher plants can continuously form new organs by the sustained activity of pluripotent stem cells. These stem cells are embedded in meristems, where they produce descendants, which undergo cell proliferation and differentiation programs in a spatiotemporally-controlled manner. Under certain conditions, pluripotency can be reestablished in descending cells and this reversion in cell fate appears to be actively suppressed by the existing stem cell pool. Mutation of the putative carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) in Arabidopsis causes defects in the suppression of pluripotency in cells normally programmed for differentiation, giving rise to unique hypertrophic phenotypes during embryogenesis as well as in the shoot apical meristem. A role of AMP1 in the miRNA-dependent control of translation has recently been established, however, how this activity is connected to its developmental functions is not resolved. Here we identify members of the cytochrome P450 clade CYP78A to act in parallel with AMP1 to control cell fate in Arabidopsis. Mutation of CYP78A5 and its close homolog CYP78A7 in a cyp78a5,7 double mutant caused suspensor-to-embryo conversion and ectopic stem cell pool formation in the shoot meristem, phenotypes characteristic for amp1. The tissues affected in the mutants showed pronounced expression levels of AMP1 and CYP78A5 in wild type. A comparison of mutant transcriptomic responses revealed an intriguing degree of overlap and highlighted alterations in protein lipidation processes. Moreover, we also found elevated protein levels of selected miRNA targets in cyp78a5,7. Based on comprehensive genetic interaction studies we propose a model in which both enzyme classes act on a common downstream process to sustain cell fate decisions in the early embryo and the shoot apical meristem.
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Affiliation(s)
- Olena Poretska
- Research Unit Plant Growth Regulation, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Department for Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Saiqi Yang
- Research Unit Plant Growth Regulation, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Delphine Pitorre
- Department for Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Tobias Sieberer
- Research Unit Plant Growth Regulation, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Department for Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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Establishment of the Embryonic Shoot Meristem Involves Activation of Two Classes of Genes with Opposing Functions for Meristem Activities. Int J Mol Sci 2020; 21:ijms21165864. [PMID: 32824181 PMCID: PMC7461597 DOI: 10.3390/ijms21165864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022] Open
Abstract
The shoot meristem, a stem-cell-containing tissue initiated during plant embryogenesis, is responsible for continuous shoot organ production in postembryonic development. Although key regulatory factors including KNOX genes are responsible for stem cell maintenance in the shoot meristem, how the onset of such factors is regulated during embryogenesis is elusive. Here, we present evidence that the two KNOX genes STM and KNAT6 together with the two other regulatory genes BLR and LAS are functionally important downstream genes of CUC1 and CUC2, which are a redundant pair of genes that specify the embryonic shoot organ boundary. Combined expression of STM with any of KNAT6, BLR, and LAS can efficiently rescue the defects of shoot meristem formation and/or separation of cotyledons in cuc1cuc2 double mutants. In addition, CUC1 and CUC2 are also required for the activation of KLU, a cytochrome P450-encoding gene known to restrict organ production, and KLU counteracts STM in the promotion of meristem activity, providing a possible balancing mechanism for shoot meristem maintenance. Together, these results establish the roles for CUC1 and CUC2 in coordinating the activation of two classes of genes with opposite effects on shoot meristem activity.
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Ding L, Song A, Zhang X, Li S, Su J, Xia W, Zhao K, Zhao W, Guan Y, Fang W, Chen S, Jiang J, Chen F. The core regulatory networks and hub genes regulating flower development in Chrysanthemum morifolium. PLANT MOLECULAR BIOLOGY 2020; 103:669-688. [PMID: 32472481 DOI: 10.1007/s11103-020-01017-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/24/2020] [Indexed: 05/17/2023]
Abstract
The study has facilitated important insights into the regulatory networks involved in flower development in chrysanthemum (Asteraceae), and is informative with respect to the mechanism of flower shape determination. Chrysanthemum morifolium, valued as an ornamental species given the diversity of its inflorescence form, is viewed as a model for understanding flower development in the Asteraceae. Yet, the underlying regulatory networks remain largely unexplored. Here, a transcriptomic survey of the Chrysanthemum morifolium variety 'Jinba' was undertaken to uncover the global gene expression profiles and identify the modules of co-transcribed genes associated with flower development. The weighted gene coexpression network analysis revealed important networks and hub genes including ray floret petals-specific coexpression network, disc floret petals-specific network, B and E class genes involved network and CYC2 genes network. Three ray floret petal-specific hub genes were also strongly transcribed in the ray florets of a selection of six diverse varieties and especially so in those which form ligulate ray floret petals. CmCYC2c was strongly transcribed in the distal and lateral regions of the ray floret petals, and also, along with CmCYC2d, in the tubular ray florets. Furthermore, CmOFP, belonging to the family of ovate proteins, was identified in the CYC2 genes network. CmOFP can interact with CmCYC2d that physically interact with CmCYC2c. This work provides important insights into the regulatory networks involved in flower development in chrysanthemum, and is informative with respect to the mechanistic basis of the regulation of flower shape.
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Affiliation(s)
- Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Song Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiangshuo Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weikang Xia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kunkun Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenqian Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunxiao Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, 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, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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40
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Cao X, Jiao Y. Control of cell fate during axillary meristem initiation. Cell Mol Life Sci 2020; 77:2343-2354. [PMID: 31807816 PMCID: PMC11105066 DOI: 10.1007/s00018-019-03407-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 01/17/2023]
Abstract
Axillary meristems (AMs) are located in the leaf axil and can establish new growth axes. Whereas their neighboring cells are differentiated, the undifferentiated cells in the AM endow the AM with the same developmental potential as the shoot apical meristem. The AM is, therefore, an excellent system to study stem cell fate maintenance in plants. In this review, we summarize the current knowledge of AM initiation. Recent findings have shown that AMs derive from a stem cell lineage that is maintained in the leaf axil. This review covers AM progenitor cell fate maintenance, reactivation, and meristem establishment. We also highlight recent work that links transcription factors, phytohormones, and epigenetic regulation to AM initiation.
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Affiliation(s)
- Xiuwei Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Li Y, Xia T, Gao F, Li Y. Control of Plant Branching by the CUC2/CUC3-DA1-UBP15 Regulatory Module. THE PLANT CELL 2020; 32:1919-1932. [PMID: 32245753 PMCID: PMC7268791 DOI: 10.1105/tpc.20.00012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/18/2020] [Accepted: 03/26/2020] [Indexed: 05/22/2023]
Abstract
Lateral branches are important for plant architecture and production, but how plants determine their lateral branches remains to be further understood. Here, we report that the CUP-SHAPED COTYLEDON2 (CUC2)/CUC3-DA1-UBIQUITIN-SPECIFIC PROTEASE15 (UBP15) regulatory module controls the initiation of axillary meristems, thereby determining the number of lateral branches in Arabidopsis (Arabidopsis thaliana). Mutation in the ubiquitin-dependent peptidase DA1 causes fewer lateral branches due to defects in the initiation of axillary meristems. The transcription factors CUC2 and CUC3, which regulate the axillary meristem initiation, directly bind to the DA1 promoter and activate its expression. Further results show that UBP15, which is a direct substrate of DA1 peptidase, represses the initiation of axillary meristems. Genetic analyses support that CUC2/CUC3, DA1, and UBP15 function, at least in part, in a common pathway to regulate the initiation of axillary meristems. Therefore, our findings establish a genetic and molecular framework by which the CUC2/CUC3-DA1-UBP15 regulatory module controls the initiation of axillary meristems, thereby determining plant architecture.
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Affiliation(s)
- Yu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Science, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Tian Xia
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Science, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Fan Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Science, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences Centre for Excellence in Molecular Plant Science, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100039, China
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Regulation of Shoot Apical Meristem and Axillary Meristem Development in Plants. Int J Mol Sci 2020; 21:ijms21082917. [PMID: 32326368 PMCID: PMC7216077 DOI: 10.3390/ijms21082917] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/18/2020] [Accepted: 04/19/2020] [Indexed: 01/13/2023] Open
Abstract
Plants retain the ability to produce new organs throughout their life cycles. Continuous aboveground organogenesis is achieved by meristems, which are mainly organized, established, and maintained in the shoot apex and leaf axils. This paper will focus on reviewing the recent progress in understanding the regulation of shoot apical meristem and axillary meristem development. We discuss the genetics of plant meristems, the role of plant hormones and environmental factors in meristem development, and the impact of epigenetic factors on meristem organization and function.
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Zhang QQ, Wang JG, Wang LY, Wang JF, Wang Q, Yu P, Bai MY, Fan M. Gibberellin repression of axillary bud formation in Arabidopsis by modulation of DELLA-SPL9 complex activity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:421-432. [PMID: 31001922 DOI: 10.1111/jipb.12818] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/16/2019] [Indexed: 05/25/2023]
Abstract
The formation of lateral branches has an important and fundamental contribution to the remarkable developmental plasticity of plants, which allows plants to alter their architecture to adapt to the challenging environment conditions. The Gibberellin (GA) phytohormones have been known to regulate the outgrowth of axillary meristems (AMs), but the specific molecular mechanisms remain unclear. Here we show that DELLA proteins regulate axillary bud formation by interacting and regulating the DNA-binding ability of SQUAMOSA-PROMOTER BINDING PROTEIN LIKE 9 (SPL9), a microRNA156-targeted squamosa promoter binding protein-like transcription factor. SPL9 participates in the initial regulation of axillary buds by repressing the expression of LATERAL SUPPRESSOR (LAS), a key regulator in the initiation of AMs, and LAS contributes to the specific expression pattern of the GA deactivation enzyme GA2ox4, which is specifically expressed in the axils of leaves to form a low-GA cell niche in this anatomical region. Nevertheless, increasing GA levels in leaf axils by ectopically expressing the GA-biosynthesis enzyme GA20ox2 significantly impaired axillary meristem initiation. Our study demonstrates that DELLA-SPL9-LAS-GA2ox4 defines a core feedback regulatory module that spatially pattern GA content in the leaf axil and precisely control the axillary bud formation in different spatial and temporal.
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Affiliation(s)
- Qi-Qi Zhang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Jia-Gang Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Ling-Yan Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Jun-Fang Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Qun Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Ping Yu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Ming-Yi Bai
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Min Fan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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44
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45
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Zhu Y, Wagner D. Plant Inflorescence Architecture: The Formation, Activity, and Fate of Axillary Meristems. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a034652. [PMID: 31308142 DOI: 10.1101/cshperspect.a034652] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The above-ground plant body in different plant species can have very distinct forms or architectures that arise by recurrent redeployment of a finite set of building blocks-leaves with axillary meristems, stems or branches, and flowers. The unique architectures of plant inflorescences in different plant families and species, on which this review focuses, determine the reproductive success and yield of wild and cultivated plants. Major contributors to the inflorescence architecture are the activity and developmental trajectories adopted by axillary meristems, which determine the degree of branching and the number of flowers formed. Recent advances in genetic and molecular analyses in diverse flowering plants have uncovered both common regulatory principles and unique players and/or regulatory interactions that underlie inflorescence architecture. Modulating activity of these regulators has already led to yield increases in the field. Additional insight into the underlying regulatory interactions and principles will not only uncover how their rewiring resulted in altered plant form, but will also enhance efforts at optimizing plant architecture in desirable ways in crop species.
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Affiliation(s)
- Yang Zhu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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46
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Hallmark HT, Rashotte AM. Review - Cytokinin Response Factors: Responding to more than cytokinin. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110251. [PMID: 31623789 DOI: 10.1016/j.plantsci.2019.110251] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 05/12/2023]
Abstract
Cytokinin Response Factors (CRFs) are a family of transcription factors which make up a side branch of the classical cytokinin two-component signaling pathway. CRFs were originally identified and have been primarily studied in Arabidopsis thaliana, although orthologs have be found throughout all land plants. Research into the evolution of CRFs as sub-group members of the larger APETALA2/Ethylene Response Factor (AP2/ERF) family has yielded interesting and useful insights related to the functional roles of CRFs in plants. Recent studies of CRFs suggest that these transcription factors are a lot more than just a group of cytokinin related genes and play important roles in both plant development and environmental stress response. This review focuses on recent advances in understanding the roles of CRFs beyond cytokinin, in reproductive development and abiotic stress response, as well as to other environmental cues.
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Affiliation(s)
- H Tucker Hallmark
- 101 Rouse Life Sciences, Department of Biological Sciences, Auburn University, USA
| | - Aaron M Rashotte
- 101 Rouse Life Sciences, Department of Biological Sciences, Auburn University, USA.
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47
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Liu C, Xu H, Han R, Wang S, Liu G, Chen S, Chen J, Bian X, Jiang J. Overexpression of BpCUC2 Influences Leaf Shape and Internode Development in Betula pendula. Int J Mol Sci 2019; 20:E4722. [PMID: 31548512 PMCID: PMC6801603 DOI: 10.3390/ijms20194722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022] Open
Abstract
The CUP-SHAPED COTYLEDON 2 (CUC2) gene, which is negatively regulated by microRNA164 (miR164), has been specifically linked to the regulation of leaf margin serration and the maintenance of phyllotaxy in model plants. However, few studies have investigated these effects in woody plants. In this study, we integrated genomic, transcriptomic, and physiology approaches to explore the function of BpCUC2 gene in Betula pendula growth and development. Our results showed that Betula pendula plants overexpressing BpCUC2, which is targeted by BpmiR164, exhibit shortened internodes and abnormal leaf shapes. Subsequent analysis indicated that the short internodes of BpCUC2 overexpressed transgenic lines and were due to decreased epidermal cell size. Moreover, transcriptome analysis, yeast one-hybrid assays, and ChIP-PCR suggested that BpCUC2 directly binds to the LTRECOREATCOR15 (CCGAC), CAREOSREP1 (CAACTC), and BIHD1OS (TGTCA) motifs of a series of IAA-related and cyclin-related genes to regulate expression. These results may be useful to our understanding of the functional role and genetic regulation of BpCUC2.
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Affiliation(s)
- Chaoyi Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Huanwen Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Rui Han
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Shuo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Jiying Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Xiuyan Bian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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48
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Kulkarni SR, Vaneechoutte D, Van de Velde J, Vandepoele K. TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. Nucleic Acids Res 2019; 46:e31. [PMID: 29272447 PMCID: PMC5888541 DOI: 10.1093/nar/gkx1279] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/18/2017] [Indexed: 12/16/2022] Open
Abstract
A gene regulatory network (GRN) is a collection of regulatory interactions between transcription factors (TFs) and their target genes. GRNs control different biological processes and have been instrumental to understand the organization and complexity of gene regulation. Although various experimental methods have been used to map GRNs in Arabidopsis thaliana, their limited throughput combined with the large number of TFs makes that for many genes our knowledge about regulating TFs is incomplete. We introduce TF2Network, a tool that exploits the vast amount of TF binding site information and enables the delineation of GRNs by detecting potential regulators for a set of co-expressed or functionally related genes. Validation using two experimental benchmarks reveals that TF2Network predicts the correct regulator in 75–92% of the test sets. Furthermore, our tool is robust to noise in the input gene sets, has a low false discovery rate, and shows a better performance to recover correct regulators compared to other plant tools. TF2Network is accessible through a web interface where GRNs are interactively visualized and annotated with various types of experimental functional information. TF2Network was used to perform systematic functional and regulatory gene annotations, identifying new TFs involved in circadian rhythm and stress response.
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Affiliation(s)
- Shubhada R Kulkarni
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Dries Vaneechoutte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Jan Van de Velde
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- To whom correspondence should be addressed. Tel: +32 9 3313822; Fax: +32 9 3313809;
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49
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Yao H, Skirpan A, Wardell B, Matthes MS, Best NB, McCubbin T, Durbak A, Smith T, Malcomber S, McSteen P. The barren stalk2 Gene Is Required for Axillary Meristem Development in Maize. MOLECULAR PLANT 2019; 12:374-389. [PMID: 30690173 DOI: 10.1016/j.molp.2018.12.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/08/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
The diversity of plant architecture is determined by axillary meristems (AMs). AMs are produced from small groups of stem cells in the axils of leaf primordia and generate vegetative branches and reproductive inflorescences. Previous studies identified genes critical for AM development that function in auxin biosynthesis, transport, and signaling. barren stalk1 (ba1), a basic helix-loop-helix transcription factor, acts downstream of auxin to control AM formation. Here, we report the cloning and characterization of barren stalk2 (ba2), a mutant that fails to produce ears and has fewer branches and spikelets in the tassel, indicating that ba2 functions in reproductive AM development. Furthermore, the ba2 mutation suppresses tiller growth in the teosinte branched1 mutant, indicating that ba2 also plays an essential role in vegetative AM development. The ba2 gene encodes a protein that co-localizes and heterodimerizes with BA1 in the nucleus. Characterization of the genetic interaction between ba2 and ba1 demonstrates that ba1 shows a gene dosage effect in ba2 mutants, providing further evidence that BA1 and BA2 act together in the same pathway. Characterization of the molecular and genetic interaction between ba2 and additional genes required for the regulation of ba1 further supports this finding. The ba1 and ba2 genes are orthologs of rice genes, LAX PANICLE1 (LAX1) and LAX2, respectively, hence providing insights into pathways controlling AMs development in grasses.
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Affiliation(s)
- Hong Yao
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Andrea Skirpan
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Brian Wardell
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Michaela S Matthes
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Norman B Best
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Tyler McCubbin
- Division of Biological Sciences, Interdisciplinary Plant Group, Columbia, MO 65211, USA
| | - Amanda Durbak
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Taylor Smith
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Simon Malcomber
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Paula McSteen
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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50
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A gene expression map of shoot domains reveals regulatory mechanisms. Nat Commun 2019; 10:141. [PMID: 30635575 PMCID: PMC6329838 DOI: 10.1038/s41467-018-08083-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/18/2018] [Indexed: 02/05/2023] Open
Abstract
Gene regulatory networks control development via domain-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from the SAM peripheral zone. After initiation, leaves develop polarity patterns to form a planar shape. Here we compare translating RNAs among SAM and leaf domains. Using translating ribosome affinity purification and RNA sequencing to quantify gene expression in target domains, we generate a domain-specific translatome map covering representative vegetative stage SAM and leaf domains. We discuss the predicted cellular functions of these domains and provide evidence that dome seemingly unrelated domains, utilize common regulatory modules. Experimental follow up shows that the RABBIT EARS and HANABA TARANU transcription factors have roles in axillary meristem initiation. This dataset provides a community resource for further study of shoot development and response to internal and environmental signals. The shoot apical meristem (SAM) maintains stem cells and generates new leaves and flowers from its periphery. Here via spatially resolved translatome profiling, Tian et al. define distinct molecular signatures of different SAM and leaf domains and identify regulators of axillary meristem initiation.
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