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Pang H, Dai X, Yan X, Liu Y, Li Q. C2H2 zinc finger protein PagIDD15A regulates secondary wall thickening and lignin biosynthesis in poplar. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112159. [PMID: 38901779 DOI: 10.1016/j.plantsci.2024.112159] [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: 02/29/2024] [Revised: 05/14/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Wood production is largely determined by the activity of cambial cell proliferation, and the secondary cell wall (SCW) thickening of xylem cells determines the wood property. In this study, we identified an INDETERMINATE DOMAIN (IDD) type C2H2 zinc finger transcription factor PagIDD15A as a regulator of wood formation in Populus alba × Populus glandulosa. Downregulation of PagIDD15A expression by RNA interference (RNAi) inhibited xylem development and xylem cell secondary wall thickening. RNA-seq analysis showed that PagPAL1, PagCCR2 and PagCCoAOMT1 were downregulated in the differentiating xylem of the PagIDD15A-RNAi transgenic plants, showing that PagIDD15A may regulate SCW biosynthesis through inhibiting lignin biosynthesis. The downregulation of PagVND6-B2, PagMYB10 and PagMYC4 and upregulation of PagWRKY12 in the differentiating xylem of RNAi transgenic plants suggest that PagIDD15A may also regulate these transcription factor (TF) genes to affect SCW thickening. RT-qPCR analysis in the phloem-cambium of RNAi transgenic demonstrates that PagIDD15A may regulate the expression of the genes associated with cell proliferation, including, PagSHR (SHORTROOT), PagSCR (SCARECROW), PagCYCD3;1 (CYCLIN D3;1) and PagSMR4 (SIAMESE-RELATED4), to affect the cambial activity. This study provides the knowledge of the IDD-type C2H2 zinc finger protein in regulating wood formation.
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Affiliation(s)
- Hongying Pang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Yingli Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.
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2
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Liu W, Yang Z, Cai G, Li B, Liu S, Willemsen V, Xu L. MpANT regulates meristem development in Marchantia polymorpha. Cell Rep 2024; 43:114466. [PMID: 38985681 DOI: 10.1016/j.celrep.2024.114466] [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: 05/19/2023] [Revised: 03/05/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024] Open
Abstract
Meristems are crucial for organ formation, but our knowledge of their molecular evolution is limited. Here, we show that AINTEGUMENTA (MpANT) in the euANT branch of the APETALA2-like transcription factor family is essential for meristem development in the nonvascular plant Marchantia polymorpha. MpANT is expressed in the thallus meristem. Mpant mutants show defects to maintain meristem identity and undergo meristem duplication, while MpANT overexpressers show ectopic thallus growth. MpANT directly upregulates MpGRAS9 in the SHORT-ROOT (SHR) branch of the GRAS family. In the vascular plant Arabidopsis thaliana, the euANT-branch genes PLETHORAs (AtPLTs) and AtANT are involved in the formation and maintenance of root/shoot apical meristems and lateral organ primordia, and AtPLTs directly target SHR-branch genes. In addition, euANTs bind through a similar DNA-binding motif to many conserved homologous genes in M. polymorpha and A. thaliana. Overall, the euANT pathway has an evolutionarily conserved role in meristem development.
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Affiliation(s)
- Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Zhengfei Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Bingyu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Shujing Liu
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Viola Willemsen
- Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China.
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3
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Fu G, Yu S, Wu K, Yang M, Altaf MA, Wu Z, Deng Q, Lu X, Fu H, Wang Z, Cheng S. Genome-wide association study and candidate gene identification for agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum. Sci Rep 2024; 14:14691. [PMID: 38926509 PMCID: PMC11208541 DOI: 10.1038/s41598-024-65332-6] [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: 02/20/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
Pepper agronomic traits serve as pivotal indicators for characterizing germplasm attributes and correlations. It is important to study differential genotypic variation through phenotypic differences of target traits. Whole genome resequencing was used to sequence the whole genome among different individuals of species with known reference genomes and annotations, and based on this, differential analyses of individuals or populations were carried out to identify SNPs for agronomic traits related to pepper. This study conducted a genome-wide association study encompassing 26 key agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum. The population structure (phylogenetics, population structure, population principal component analysis, genetic relationship) and linkage disequilibrium analysis were realized to ensure the accuracy and reliability of GWAS results, and the optimal statistical model was determined. A total of 929 SNPs significantly associated with 26 agronomic traits, were identified, alongside the detection of 519 candidate genes within 100 kb region adjacent to these SNPs. Additionally, through gene annotation and expression pattern scrutiny, genes such as GAUT1, COP10, and DDB1 correlated with fruit traits in Capsicum frutescens and Capsicum annuum were validated via qRT-PCR. In the CH20 (Capsicum annuum) and YB-4 (Capsicum frutescens) cultivars, GAUT1 and COP10 were cloned with cDNA lengths of 1065 bp and 561 bp, respectively, exhibiting only a small number of single nucleotide variations and nucleotide deletions. This validation provides a robust reference for molecular marker-assisted breeding of pepper agronomic traits, offering both genetic resources and theoretical foundations for future endeavors in molecular marker-assisted breeding for pepper.
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Affiliation(s)
- Genying Fu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Shuang Yu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Kun Wu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Mengxian Yang
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Muhammad Ahsan Altaf
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Zhuo Wu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Qin Deng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Xu Lu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Huizhen Fu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China.
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
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Pérez-Sancho J, Van den Broeck L, García-Caparros P, Sozzani R. Insights into multilevel spatial regulation within the root stem cell niche. Curr Opin Genet Dev 2024; 86:102200. [PMID: 38704928 DOI: 10.1016/j.gde.2024.102200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024]
Abstract
All differentiated root cells derive from stem cells spatially organized within the stem cell niche (SCN), a microenvironment located within the root tip. Here, we compiled recent advances in the understanding of how the SCN drives the establishment and maintenance of cell types. The quiescent center (QC) is widely recognized as the primary driver of cell fate determination, but it is recently considered a convergence center of multiple signals. Cell identity of the cortex endodermis initials is mainly driven by the regulatory feedback loops between transcription factors (TFs), acting as mobile signals between neighboring cells, including the QC. As exemplified in the vascular initials, the precise spatial expression of these regulatory TFs is connected with a dynamic hormonal interplay. Thus, stem cell maintenance and cell differentiation are regulated by a plethora of signals forming a complex, multilevel regulatory network. Integrating the transcriptional and post-translational regulations, protein-protein interactions, and mobile signals into models will be fundamental for the comprehensive understanding of SCN maintenance and differentiation.
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Affiliation(s)
| | - Lisa Van den Broeck
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695, USA. https://twitter.com/@LisaVandenBroec
| | | | - Rosangela Sozzani
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695, USA.
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5
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Cao S, Zhao X, Li Z, Yu R, Li Y, Zhou X, Yan W, Chen D, He C. Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification. PLANT DIVERSITY 2024; 46:372-385. [PMID: 38798726 PMCID: PMC11119547 DOI: 10.1016/j.pld.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/29/2024]
Abstract
Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks in a cell-type specific manner. Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings. This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets, addressing batch effects and conserving biological variance. This integration spans a broad spectrum of tissues, including both below- and above-ground parts. Utilizing a rigorous approach for cell type annotation, we identified 47 distinct cell types or states, largely expanding our current view of plant cell compositions. We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression. Taken together, our study not only offers extensive plant cell atlas exploration that serves as a valuable resource, but also provides molecular insights into gene-regulatory programs that varies from different cell types.
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Affiliation(s)
- Shanni Cao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhuojin Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yuqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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6
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Mohanta TK, Mohanta YK, Kaushik P, Kumar J. Physiology, genomics, and evolutionary aspects of desert plants. J Adv Res 2024; 58:63-78. [PMID: 37160225 PMCID: PMC10982872 DOI: 10.1016/j.jare.2023.04.019] [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: 11/17/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Despite the exposure to arid environmental conditions across the globe ultimately hampering the sustainability of the living organism, few plant species are equipped with several unique genotypic, biochemical, and physiological features to counter such harsh conditions. Physiologically, they have evolved with reduced leaf size, spines, waxy cuticles, thick leaves, succulent hydrenchyma, sclerophyll, chloroembryo, and photosynthesis in nonfoliar and other parts. At the biochemical level, they are evolved to perform efficient photosynthesis through Crassulacean acid metabolism (CAM) and C4 pathways with the formation of oxaloacetic acid (Hatch-Slack pathway) instead of the C3 pathway. Additionally, comparative genomics with existing data provides ample evidence of the xerophytic plants' positive selection to adapt to the arid environment. However, adding more high-throughput sequencing of xerophyte plant species is further required for a comparative genomic study toward trait discovery related to survival. Learning from the mechanism to survive in harsh conditions could pave the way to engineer crops for future sustainable agriculture. AIM OF THE REVIEW The distinct physiology of desert plants allows them to survive in harsh environments. However, the genomic composition also contributes significantly to this and requires great attention. This review emphasizes the physiological and genomic adaptation of desert plants. Other important parameters, such as desert biodiversity and photosynthetic strategy, are also discussed with recent progress in the field. Overall, this review discusses the different features of desert plants, which prepares them for harsh conditions intending to translate knowledge to engineer plant species for sustainable agriculture. KEY SCIENTIFIC CONCEPTS OF REVIEW This review comprehensively presents the physiology, molecular mechanism, and genomics of desert plants aimed towards engineering a sustainable crop.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 611, Oman.
| | - Yugal Kishore Mohanta
- Dept. of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya 793101, India
| | - Prashant Kaushik
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, United States
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Schreiber JM, Limpens E, de Keijzer J. Distributing Plant Developmental Regulatory Proteins via Plasmodesmata. PLANTS (BASEL, SWITZERLAND) 2024; 13:684. [PMID: 38475529 DOI: 10.3390/plants13050684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
During plant development, mobile proteins, including transcription factors, abundantly serve as messengers between cells to activate transcriptional signaling cascades in distal tissues. These proteins travel from cell to cell via nanoscopic tunnels in the cell wall known as plasmodesmata. Cellular control over this intercellular movement can occur at two likely interdependent levels. It involves regulation at the level of plasmodesmata density and structure as well as at the level of the cargo proteins that traverse these tunnels. In this review, we cover the dynamics of plasmodesmata formation and structure in a developmental context together with recent insights into the mechanisms that may control these aspects. Furthermore, we explore the processes involved in cargo-specific mechanisms that control the transport of proteins via plasmodesmata. Instead of a one-fits-all mechanism, a pluriform repertoire of mechanisms is encountered that controls the intercellular transport of proteins via plasmodesmata to control plant development.
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Affiliation(s)
- Joyce M Schreiber
- Laboratory of Cell and Developmental Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Erik Limpens
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jeroen de Keijzer
- Laboratory of Cell and Developmental Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Lindsay P, Swentowsky KW, Jackson D. Cultivating potential: Harnessing plant stem cells for agricultural crop improvement. MOLECULAR PLANT 2024; 17:50-74. [PMID: 38130059 DOI: 10.1016/j.molp.2023.12.014] [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: 10/14/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.
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Affiliation(s)
- Penelope Lindsay
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Perez-Garcia P, Pucciariello O, Sanchez-Corrionero A, Cabrera J, Del Barrio C, Del Pozo JC, Perales M, Wabnik K, Moreno-Risueno MA. The cold-induced factor CBF3 mediates root stem cell activity, regeneration, and developmental responses to cold. PLANT COMMUNICATIONS 2023; 4:100737. [PMID: 37865820 PMCID: PMC10721530 DOI: 10.1016/j.xplc.2023.100737] [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: 01/13/2023] [Revised: 09/01/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Plant growth and development involve the specification and regeneration of stem cell niches (SCNs). Although plants are exposed to disparate environmental conditions, how environmental cues affect developmental programs and stem cells is not well understood. Root stem cells are accommodated in meristems in SCNs around the quiescent center (QC), which maintains their activity. Using a combination of genetics and confocal microscopy to trace morphological defects and correlate them with changes in gene expression and protein levels, we show that the cold-induced transcription factor (TF) C-REPEAT BINDING FACTOR 3 (CBF3), which has previously been associated with cold acclimation, regulates root development, stem cell activity, and regeneration. CBF3 is integrated into the SHORT-ROOT (SHR) regulatory network, forming a feedback loop that maintains SHR expression. CBF3 is primarily expressed in the root endodermis, whereas the CBF3 protein is localized to other meristematic tissues, including root SCNs. Complementation of cbf3-1 using a wild-type CBF3 gene and a CBF3 fusion with reduced mobility show that CBF3 movement capacity is required for SCN patterning and regulates root growth. Notably, cold induces CBF3, affecting QC activity. Furthermore, exposure to moderate cold around 10°C-12°C promotes root regeneration and QC respecification in a CBF3-dependent manner during the recuperation period. By contrast, CBF3 does not appear to regulate stem cell survival, which has been associated with recuperation from more acute cold (∼4°C). We propose a role for CBF3 in mediating the molecular interrelationships among the cold response, stem cell activity, and development.
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Affiliation(s)
- Pablo Perez-Garcia
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain.
| | - Ornella Pucciariello
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Alvaro Sanchez-Corrionero
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Cristina Del Barrio
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Juan Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain.
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Bahafid E, Bradtmöller I, Thies AM, Nguyen TTON, Gutierrez C, Desvoyes B, Stahl Y, Blilou I, Simon RGW. The Arabidopsis SHORTROOT network coordinates shoot apical meristem development with auxin-dependent lateral organ initiation. eLife 2023; 12:e83334. [PMID: 37862096 PMCID: PMC10642969 DOI: 10.7554/elife.83334] [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: 09/08/2022] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Plants produce new organs post-embryonically throughout their entire life cycle. This is due to stem cells present in the shoot and root apical meristems, the SAM and RAM, respectively. In the SAM, stem cells are located in the central zone where they divide slowly. Stem cell daughters are displaced laterally and enter the peripheral zone, where their mitotic activity increases and lateral organ primordia are formed. How the spatial arrangement of these different domains is initiated and controlled during SAM growth and development, and how sites of lateral organ primordia are determined in the peripheral zone is not yet completely understood. We found that the SHORTROOT (SHR) transcription factor together with its target transcription factors SCARECROW (SCR), SCARECROW-LIKE23 (SCL23) and JACKDAW (JKD), promotes formation of lateral organs and controls shoot meristem size. SHR, SCR, SCL23, and JKD are expressed in distinct, but partially overlapping patterns in the SAM. They can physically interact and activate expression of key cell cycle regulators such as CYCLIND6;1 (CYCD6;1) to promote the formation of new cell layers. In the peripheral zone, auxin accumulates at sites of lateral organ primordia initiation and activates SHR expression via the auxin response factor MONOPTEROS (MP) and auxin response elements in the SHR promoter. In the central zone, the SHR-target SCL23 physically interacts with the key stem cell regulator WUSCHEL (WUS) to promote stem cell fate. Both SCL23 and WUS expression are subject to negative feedback regulation from stem cells through the CLAVATA signaling pathway. Together, our findings illustrate how SHR-dependent transcription factor complexes act in different domains of the shoot meristem to mediate cell division and auxin dependent organ initiation in the peripheral zone, and coordinate this activity with stem cell maintenance in the central zone of the SAM.
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Affiliation(s)
- Elmehdi Bahafid
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Imke Bradtmöller
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Ann M Thies
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Thi TON Nguyen
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, CantoblancoMadridSpain
| | - Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, CantoblancoMadridSpain
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology, Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Rüdiger GW Simon
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
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11
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Liu Q, Teng S, Deng C, Wu S, Li H, Wang Y, Wu J, Cui X, Zhang Z, Quick WP, Brutnell TP, Sun X, Lu T. SHORT ROOT and INDETERMINATE DOMAIN family members govern PIN-FORMED expression to regulate minor vein differentiation in rice. THE PLANT CELL 2023; 35:2848-2870. [PMID: 37154077 PMCID: PMC10396363 DOI: 10.1093/plcell/koad125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/08/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023]
Abstract
C3 and C4 grasses directly and indirectly provide the vast majority of calories to the human diet, yet our understanding of the molecular mechanisms driving photosynthetic productivity in grasses is largely unexplored. Ground meristem cells divide to form mesophyll or vascular initial cells early in leaf development in C3 and C4 grasses. Here we define a genetic circuit composed of SHORT ROOT (SHR), INDETERMINATE DOMAIN (IDD), and PIN-FORMED (PIN) family members that specifies vascular identify and ground cell proliferation in leaves of both C3 and C4 grasses. Ectopic expression and loss-of-function mutant studies of SHR paralogs in the C3 plant Oryza sativa (rice) and the C4 plant Setaria viridis (green millet) revealed the roles of these genes in both minor vein formation and ground cell differentiation. Genetic and in vitro studies further suggested that SHR regulates this process through its interactions with IDD12 and 13. We also revealed direct interactions of these IDD proteins with a putative regulatory element within the auxin transporter gene PIN5c. Collectively, these findings indicate that a SHR-IDD regulatory circuit mediates auxin transport by negatively regulating PIN expression to modulate minor vein patterning in the grasses.
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Affiliation(s)
- Qiming Liu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Shouzhen Teng
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Chen Deng
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Suting Wu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Haoshu Li
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Yanwei Wang
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Jinxia Wu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Xuean Cui
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Zhiguo Zhang
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - William Paul Quick
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
- C4 Rice Centre, International Rice Research Institute, Los Banos, Laguna 4030, Philippines
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Thomas P Brutnell
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Xuehui Sun
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
| | - Tiegang Lu
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China
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12
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Lee Y, Hoang NV, Do VG, Foster TM, McGhie TK, Kim S, Yang SJ, Park JH, Park J, Lee JY. Identification of genes associated with the regulation of cold tolerance and the RNA movement in the grafted apple. Sci Rep 2023; 13:11583. [PMID: 37463950 DOI: 10.1038/s41598-023-38571-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
In grafted apple, rootstock-derived signals influence scion cold tolerance by initiating physiological changes to survive over the winter. To understand the underlying molecular interactions between scion and rootstock responsive to cold, we developed transcriptomics and metabolomics data in the stems of two scion/rootstock combinations, 'Gala'/'G202' (cold resistant rootstock) and 'Gala'/'M9' (cold susceptible rootstock). Outer layers of scion and rootstock stem, including vascular tissues, were collected from the field-grown grafted apple during the winter. The clustering of differentially expressed genes (DEGs) and gene ontology enrichment indicated distinct expression dynamics in the two graft combinations, which supports the dependency of scion cold tolerance on the rootstock genotypes. We identified 544 potentially mobile mRNAs of DEGs showing highly-correlated seasonal dynamics between scion and rootstock. The mobility of a subset of 544 mRNAs was validated by translocated genome-wide variants and the measurements of selected RNA mobility in tobacco and Arabidopsis. We detected orthologous genes of potentially mobile mRNAs in Arabidopsis thaliana, which belong to cold regulatory networks with RNA mobility. Together, our study provides a comprehensive insight into gene interactions and signal exchange between scion and rootstock responsive to cold. This will serve for future research to enhance cold tolerance of grafted tree crops.
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Affiliation(s)
- Youngsuk Lee
- School of Biological Sciences, College of National Science, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, South Korea.
- Apple Research Institute, National Institute of Horticultural and Herbal Science, Rural Development Administration, 107, Soboangye-Ro, Gunwi, 39000, South Korea.
| | - Nam V Hoang
- School of Biological Sciences, College of National Science, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, South Korea
- Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Van Giap Do
- Apple Research Institute, National Institute of Horticultural and Herbal Science, Rural Development Administration, 107, Soboangye-Ro, Gunwi, 39000, South Korea
| | - Toshi M Foster
- The New Zealand Institute for Plant and Food Research Limited, 55 Old Mill Road, Motueka, New Zealand
| | - Tony K McGhie
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, New Zealand
| | - Seonae Kim
- Apple Research Institute, National Institute of Horticultural and Herbal Science, Rural Development Administration, 107, Soboangye-Ro, Gunwi, 39000, South Korea
| | - Sang Jin Yang
- Apple Research Institute, National Institute of Horticultural and Herbal Science, Rural Development Administration, 107, Soboangye-Ro, Gunwi, 39000, South Korea
| | - Ju-Hyeon Park
- Apple Research Institute, National Institute of Horticultural and Herbal Science, Rural Development Administration, 107, Soboangye-Ro, Gunwi, 39000, South Korea
| | - Jongsung Park
- School of Biological Sciences, College of National Science, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, South Korea
| | - Ji-Young Lee
- School of Biological Sciences, College of National Science, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, South Korea.
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13
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Khan SI, Yamada R, Shiroma R, Abe T, Kozaki A. Properties of INDETERMINATE DOMAIN Proteins from Physcomitrium patens: DNA-Binding, Interaction with GRAS Proteins, and Transcriptional Activity. Genes (Basel) 2023; 14:1249. [PMID: 37372429 DOI: 10.3390/genes14061249] [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: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
INDETERMINATE DOMAIN (IDD) proteins are plant-specific transcription factors that interact with GRAS proteins, such as DELLA and SHORT ROOT (SHR), to regulate target genes. The combination of IDD and DELLA proteins regulates genes involved in gibberellic acid (GA) synthesis and GA signaling, whereas the combination of IDD with the complex of SHR and SCARECROW, another GRAS protein, regulates genes involved in root tissue formation. Previous bioinformatic research identified seven IDDs, two DELLA, and two SHR genes in Physcomitrium patens, a model organism for non-vascular plants (bryophytes), which lack a GA signaling pathway and roots. In this study, DNA-binding properties and protein-protein interaction of IDDs from P. patens (PpIDD) were analyzed. Our results showed that the DNA-binding properties of PpIDDs were largely conserved between moss and seed plants. Four PpIDDs showed interaction with Arabidopsis DELLA (AtDELLA) proteins but not with PpDELLAs, and one PpIDD showed interaction with PpSHR but not with AtSHR. Moreover, AtIDD10 (JACKDAW) interacted with PpSHR but not with PpDELLAs. Our results indicate that DELLA proteins have modified their structure to interact with IDD proteins during evolution from moss lineage to seed plants, whereas the interaction of IDD and SHR was already present in moss lineage.
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Affiliation(s)
- Saiful Islam Khan
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Ren Yamada
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Ryoichi Shiroma
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tatsuki Abe
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Akiko Kozaki
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
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14
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Wang B, Shi X, Gao J, Liao R, Fu J, Bai J, Cui H. SCARECROW maintains the stem cell niche in Arabidopsis roots by ensuring telomere integrity. PLANT PHYSIOLOGY 2023; 192:1115-1131. [PMID: 36943300 PMCID: PMC10231454 DOI: 10.1093/plphys/kiad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 06/01/2023]
Abstract
Stem cells are the ultimate source of cells for various tissues and organs and thus are essential for postembryonic plant growth and development. SCARECROW (SCR) is a plant-specific transcription regulator well known for its role in stem cell renewal in plant roots, but the mechanism by which SCR exerts this function remains unclear. To address this question, we carried out a genetic screen for mutants that no longer express SCR in the stem cell niche of Arabidopsis (Arabidopsis thaliana) roots and characterized 1 of these mutants. Molecular genetics methods allowed us to pinpoint the causal mutation in this mutant in TELOMERIC PATHWAYS IN ASSOCIATION WITH STN 1 (TEN1), encoding a factor that protects telomere ends. Interestingly, TEN1 expression was dramatically reduced in the scr mutant. Telomerase and STN1 and CONSERVED TELOMERE MAINTENANCE COMPONENT 1 (CTC1), components of the same protein complex as TEN1, were also dramatically downregulated in scr. Loss of STN1, CTC1, and telomerase caused defects in root stem cells. These results together suggest that SCR maintains root stem cells by promoting expression of genes that ensure genome integrity. Supporting this conclusion, we demonstrated that the scr mutant accumulates more DNA damage than wild-type Arabidopsis and that this problem is aggravated after exposure to zeocin, a DNA damage reagent. Finally, we identified 2 previously uncharacterized motifs in TEN1 and provide evidence that a conserved amino acid residue in 1 of the motifs is indispensable for TEN1 function. SCR thus provides a connection between genome integrity and stem cell maintenance in Arabidopsis roots.
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Affiliation(s)
- Bingxin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaowen Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jingbo Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rui Liao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Juan Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongchang Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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15
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Cui H. NAC1 goes TOPLESS to manage cortex proliferation. MOLECULAR PLANT 2023; 16:804-805. [PMID: 37016581 DOI: 10.1016/j.molp.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 05/04/2023]
Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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16
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Hughes TE, Sedelnikova O, Thomas M, Langdale JA. Mutations in NAKED-ENDOSPERM IDD genes reveal functional interactions with SCARECROW during leaf patterning in C4 grasses. PLoS Genet 2023; 19:e1010715. [PMID: 37068119 PMCID: PMC10138192 DOI: 10.1371/journal.pgen.1010715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/27/2023] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
Leaves comprise a number of different cell-types that are patterned in the context of either the epidermal or inner cell layers. In grass leaves, two distinct anatomies develop in the inner leaf tissues depending on whether the leaf carries out C3 or C4 photosynthesis. In both cases a series of parallel veins develops that extends from the leaf base to the tip but in ancestral C3 species veins are separated by a greater number of intervening mesophyll cells than in derived C4 species. We have previously demonstrated that the GRAS transcription factor SCARECROW (SCR) regulates the number of photosynthetic mesophyll cells that form between veins in the leaves of the C4 species maize, whereas it regulates the formation of stomata in the epidermal leaf layer in the C3 species rice. Here we show that SCR is required for inner leaf patterning in the C4 species Setaria viridis but in this species the presumed ancestral stomatal patterning role is also retained. Through a comparative mutant analysis between maize, setaria and rice we further demonstrate that loss of NAKED-ENDOSPERM (NKD) INDETERMINATE DOMAIN (IDD) protein function exacerbates loss of function scr phenotypes in the inner leaf tissues of maize and setaria but not rice. Specifically, in both setaria and maize, scr;nkd mutants exhibit an increased proportion of fused veins with no intervening mesophyll cells. Thus, combined action of SCR and NKD may control how many mesophyll cells are specified between veins in the leaves of C4 but not C3 grasses. Together our results provide insight into the evolution of cell patterning in grass leaves and demonstrate a novel patterning role for IDD genes in C4 leaves.
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Affiliation(s)
- Thomas E Hughes
- Department of Biology, University of Oxford, Oxford, England
| | | | - Mimi Thomas
- Department of Biology, University of Oxford, Oxford, England
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, England
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17
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Marsh JI, Nestor BJ, Petereit J, Tay Fernandez CG, Bayer PE, Batley J, Edwards D. Legume-wide comparative analysis of pod shatter locus PDH1 reveals phaseoloid specificity, high cowpea expression, and stress responsive genomic context. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36970933 DOI: 10.1111/tpj.16209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Pod dehiscence is a major source of yield loss in legumes, which is exacerbated by aridity. Disruptive mutations in "Pod indehiscent 1" (PDH1), a pod sclerenchyma-specific lignin biosynthesis gene, has been linked to significant reductions in dehiscence in several legume species. We compared syntenic PDH1 regions across 12 legumes and two outgroups to uncover key historical evolutionary trends at this important locus. Our results clarified the extent to which PDH1 orthologs are present in legumes, showing the typical genomic context surrounding PDH1 has only arisen relatively recently in certain phaseoloid species (Vigna, Phaseolus, Glycine). The notable absence of PDH1 in Cajanus cajan may be a major contributor to its indehiscent phenotype compared with other phaseoloids. In addition, we identified a novel PDH1 ortholog in Vigna angularis and detected remarkable increases in PDH1 transcript abundance during Vigna unguiculata pod development. Investigation of the shared genomic context of PDH1 revealed it lies in a hotspot of transcription factors and signaling gene families that respond to abscisic acid and drought stress, which we hypothesize may be an additional factor influencing expression of PDH1 under specific environmental conditions. Our findings provide key insights into the evolutionary history of PDH1 and lay the foundation for optimizing the pod dehiscence role of PDH1 in major and understudied legume species.
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Affiliation(s)
- Jacob I Marsh
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, Australia
| | - Benjamin J Nestor
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, Australia
| | - Jakob Petereit
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, Australia
| | - Cassandria G Tay Fernandez
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, Australia
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18
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Zentella R, Wang Y, Zahn E, Hu J, Jiang L, Shabanowitz J, Hunt DF, Sun TP. SPINDLY O-fucosylates nuclear and cytoplasmic proteins involved in diverse cellular processes in plants. PLANT PHYSIOLOGY 2023; 191:1546-1560. [PMID: 36740243 PMCID: PMC10022643 DOI: 10.1093/plphys/kiad011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/12/2022] [Indexed: 05/28/2023]
Abstract
SPINDLY (SPY) is a novel nucleocytoplasmic protein O-fucosyltransferase that regulates target protein activity or stability via O-fucosylation of specific Ser/Thr residues. Previous genetic studies indicate that AtSPY regulates plant development during vegetative and reproductive growth by modulating gibberellin and cytokinin responses. AtSPY also regulates the circadian clock and plant responses to biotic and abiotic stresses. The pleiotropic phenotypes of spy mutants point to the likely role of AtSPY in regulating key proteins functioning in diverse cellular pathways. However, very few AtSPY targets are known. Here, we identified 88 SPY targets from Arabidopsis (Arabidopsis thaliana) and Nicotiana benthamiana via the purification of O-fucosylated peptides using Aleuria aurantia lectin followed by electron transfer dissociation-MS/MS analysis. Most AtSPY targets were nuclear proteins that function in DNA repair, transcription, RNA splicing, and nucleocytoplasmic transport. Cytoplasmic AtSPY targets were involved in microtubule-mediated cell division/growth and protein folding. A comparison with the published O-linked-N-acetylglucosamine (O-GlcNAc) proteome revealed that 30% of AtSPY targets were also O-GlcNAcylated, indicating that these distinct glycosylations could co-regulate many protein functions. This study unveiled the roles of O-fucosylation in modulating many key nuclear and cytoplasmic proteins and provided a valuable resource for elucidating the regulatory mechanisms involved.
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Affiliation(s)
- Rodolfo Zentella
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Yan Wang
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Emily Zahn
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Jianhong Hu
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Liang Jiang
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia 22903, USA
| | - Tai-ping Sun
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
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19
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Zhai N, Pan X, Zeng M, Xu L. Developmental trajectory of pluripotent stem cell establishment in Arabidopsis callus guided by a quiescent center-related gene network. Development 2023; 150:286991. [PMID: 36762604 DOI: 10.1242/dev.200879] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
In plant tissue culture, callus formation is induced by a high auxin concentration. Among the three cell layers (the outer, middle and inner cell layers) of the callus, pluripotency acquisition in the middle cell layer is required for the potential ability of the callus to regenerate organs. Here, we reveal the developmental trajectory of middle cell layer initiation and maintenance in callus tissue originating from Arabidopsis thaliana hypocotyls. The S phase of the cell cycle is essential for the expression of quiescent center-related SCARECROW (SCR), PLETHORA1 (PLT1) and WUSCHEL-RELATED HOMEOBOX5 (WOX5) genes during the division of callus founder cells to initiate the callus primordium. After callus initiation, SHOOT-ROOT (SHR) proteins move from the inner to the middle cell layer and act together with SCR to promote the expression of PLT1 and WOX5. WOX5 represses the expression of VASCULAR-RELATED NAC-DOMAIN (VND) genes, thereby preventing callus tissue from differentiating into xylem cells. PLT1 and PLT2 directly activate JACKDAW (JKD), which is necessary for pluripotency acquisition in the middle cell layer. We hypothesize that the middle cell layer could have pluripotent stem cell activity and its establishment requires the quiescent center-related SCR-SHR-WOX5-PLT1/2-JKD gene network.
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Affiliation(s)
- Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xuan Pan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Minhuan Zeng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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20
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Zhang Y, Xu T, Dong J. Asymmetric cell division in plant development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:343-370. [PMID: 36610013 PMCID: PMC9975081 DOI: 10.1111/jipb.13446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/05/2023] [Indexed: 05/03/2023]
Abstract
Asymmetric cell division (ACD) is a fundamental process that generates new cell types during development in eukaryotic species. In plant development, post-embryonic organogenesis driven by ACD is universal and more important than in animals, in which organ pattern is preset during embryogenesis. Thus, plant development provides a powerful system to study molecular mechanisms underlying ACD. During the past decade, tremendous progress has been made in our understanding of the key components and mechanisms involved in this important process in plants. Here, we present an overview of how ACD is determined and regulated in multiple biological processes in plant development and compare their conservation and specificity among different model cell systems. We also summarize the molecular roles and mechanisms of the phytohormones in the regulation of plant ACD. Finally, we conclude with the overarching paradigms and principles that govern plant ACD and consider how new technologies can be exploited to fill the knowledge gaps and make new advances in the field.
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Affiliation(s)
- Yi Zhang
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Correspondences: Yi Zhang (); Juan Dong (). Yi Zhang and Juan Dong are fully responsible for the distribution of all materials associated with this article
| | - Tongda Xu
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08891, USA
- Correspondences: Yi Zhang (); Juan Dong (). Yi Zhang and Juan Dong are fully responsible for the distribution of all materials associated with this article
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Bais P, Alidrissi L, Blilou I. Detecting Protein-Protein Interactions Using Bimolecular Fluorescence Complementation (BiFC) and Luciferase Complementation Assays (LCA). Methods Mol Biol 2023; 2690:121-131. [PMID: 37450143 DOI: 10.1007/978-1-0716-3327-4_12] [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] [Indexed: 07/18/2023]
Abstract
In multicellular organisms, establishing the full body plane involves cell-cell signaling where protein associations are important for the diverse cellular functions within the cells. For the study of protein-protein interactions (PPI), bimolecular fluorescence complementation (BiFC) and luciferase complementation assays (LCA) have proven to be reliable tools that can be used to confirm the physical association of two proteins in a semi-in vivo environment. This chapter provides a detailed description of these two techniques using Nicotiana benthamiana as a semi-in vivo transient expression system. As an example, we will use the interaction of the two well-described transcription factors SHORT-ROOT (SHR) and SCARECROW (SCR), which are known as regulators of asymmetric cell division and stem cell specification in the root meristem of the model plant Arabidopsis thaliana. While the BiFC assay provides subcellular information by displaying a fluorescence signal, nuclear in this case, resulting from the reconstituted fluorophore, the LCA generates a quantitative readout of the SCR-SHR interaction. The combination of both assays provides information on the localization and strength of the PPI.
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Affiliation(s)
- Pepijn Bais
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Louai Alidrissi
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ikram Blilou
- BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
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22
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Identification and functional validation of super-enhancers in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2022; 119:e2215328119. [PMID: 36409894 PMCID: PMC9860255 DOI: 10.1073/pnas.2215328119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Super-enhancers (SEs) are exceptionally large enhancers and are recognized to play prominent roles in cell identity in mammalian species. We surveyed the genomic regions containing large clusters of accessible chromatin regions (ACRs) marked by deoxyribonuclease (DNase) I hypersensitivity in Arabidopsis thaliana. We identified a set of 749 putative SEs, which have a minimum length of 1.5 kilobases and represent the top 2.5% of the largest ACR clusters. We demonstrate that the genomic regions associating with these SEs were more sensitive to DNase I than other nonpromoter ACRs. The SEs were preferentially associated with topologically associating domains. Furthermore, the SEs and their predicted cognate genes were frequently associated with organ development and tissue identity in A. thaliana. Therefore, the A. thaliana SEs and their cognate genes mirror the functional characteristics of those reported in mammalian species. We developed CRISPR/Cas-mediated deletion lines of a 3,578-bp SE associated with the thalianol biosynthetic gene cluster (BGC). Small deletions (131-157 bp) within the SE resulted in distinct phenotypic changes and transcriptional repression of all five thalianol genes. In addition, T-DNA insertions in the SE region resulted in transcriptional alteration of all five thalianol genes. Thus, this SE appears to play a central role in coordinating the operon-like expression pattern of the thalianol BGC.
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23
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Yoon EK, Oh J, Lim J. (Don't) Look Up!: Is short-root just a short-root plant? FRONTIERS IN PLANT SCIENCE 2022; 13:1069996. [PMID: 36466291 PMCID: PMC9712719 DOI: 10.3389/fpls.2022.1069996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
SHORT-ROOT (SHR) is a mobile transcription factor that plays important roles in ground tissue patterning, stem cell niche specification and maintenance, and vascular development in Arabidopsis roots. Although mRNA and protein of SHR are also found in hypocotyls, inflorescence stems, and leaves, its role in the above-ground organs has been less explored. In most developmental cases, SHR, together with its partner SCARECROW (SCR), regulates the expression of downstream target genes in controlling formative and proliferative cell divisions. Accumulating evidence on the regulatory role of SHR in shoots suggests that SHR may also play key roles in the above-ground organs. Interestingly, recent work has provided new evidence that SHR is also required for cell elongation in the hypocotyl of the etiolated seedling. This suggests that the novel roles of SHR and SHR-mediated regulatory networks can be found in shoots. Furthermore, comparative research on SHR function in roots and shoots will broaden and deepen our understanding of plant growth and development.
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Guo X, Zhou M, Chen J, Shao M, Zou L, Ying Y, Liu S. Genome-Wide Identification of the Highly Conserved INDETERMINATE DOMAIN ( IDD) Zinc Finger Gene Family in Moso Bamboo ( Phyllostachys edulis). Int J Mol Sci 2022; 23:ijms232213952. [PMID: 36430436 PMCID: PMC9695771 DOI: 10.3390/ijms232213952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/05/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
INDETERMINATE DOMAIN (IDD) proteins, a family of transcription factors unique to plants, function in multiple developmental processes. Although the IDD gene family has been identified in many plants, little is known about it in moso bamboo. In this present study, we identified 32 PheIDD family genes in moso bamboo and randomly sequenced the full-length open reading frames (ORFs) of ten PheIDDs. All PheIDDs shared a highly conserved IDD domain that contained two canonical C2H2-ZFs, two C2HC-ZFs, and a nuclear localization signal. Collinearity analysis showed that segmental duplication events played an important role in expansion of the PheIDD gene family. Synteny analysis indicated that 30 PheIDD genes were orthologous to those of rice (Oryza sativa). Thirty PheIDDs were expressed at low levels, and most PheIDDs exhibited characteristic organ-specific expression patterns. Despite their diverse expression patterns in response to exogenous plant hormones, 8 and 22 PheIDDs responded rapidly to IAA and 6-BA treatments, respectively. The expression levels of 23 PheIDDs were closely related to the outgrowth of aboveground branches and 20 PheIDDs were closely related to the awakening of underground dormant buds. In addition, we found that the PheIDD21 gene generated two products by alternative splicing. Both isoforms interacted with PheDELLA and PheSCL3. Furthermore, both isoforms could bind to the cis-elements of three genes (PH02Gene17121, PH02Gene35441, PH02Gene11386). Taken together, our work provides valuable information for studying the molecular breeding mechanism of lateral organ development in moso bamboo.
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25
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Liu J, Shu D, Tan Z, Ma M, Guo N, Gao S, Duan G, Kuai B, Hu Y, Li S, Cui D. The Arabidopsis IDD14 transcription factor interacts with bZIP-type ABFs/AREBs and cooperatively regulates ABA-mediated drought tolerance. THE NEW PHYTOLOGIST 2022; 236:929-942. [PMID: 35842794 DOI: 10.1111/nph.18381] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The INDETERMINATE DOMAIN (IDD) transcription factors mediate various aspects of plant growth and development. We previously reported that an Arabidopsis IDD subfamily regulates spatial auxin accumulation, and thus organ morphogenesis and gravitropic responses. However, its functions in stress responses are not well defined. Here, we use a combination of physiological, biochemical, molecular, and genetic approaches to provide evidence that the IDD14 cooperates with basic leucine zipper-type binding factors/ABA-responsive element (ABRE)-binding proteins (ABRE-binding factors (ABFs)/AREBs) in ABA-mediated drought tolerance. idd14-1D, a gain-of-function mutant of IDD14, exhibits decreased leaf water loss and improved drought tolerance, whereas inactivation of IDD14 in idd14-1 results in increased transpiration and reduced drought tolerance. Altered IDD14 expression affects ABA sensitivity and ABA-mediated stomatal closure. IDD14 can physically interact with ABF1-4 and subsequently promote their transcriptional activities. Moreover, ectopic expression and mutation of ABFs could, respectively, suppress and enhance plant sensitivity to drought stress in the idd14-1 mutant. Our results demonstrate that IDD14 forms a functional complex with ABFs and positively regulates drought-stress responses, thus revealing a previously unidentified role of IDD14 in ABA signaling and drought responses.
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Affiliation(s)
- Jing Liu
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Defeng Shu
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Zilong Tan
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Mei Ma
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Ning Guo
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
- School of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Shan Gao
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Guangyou Duan
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Benke Kuai
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shipeng Li
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
| | - Dayong Cui
- School of Life Sciences, Qilu Normal University, Jinan, 250200, China
- School of Life Sciences, Shandong Normal University, Jinan, 250014, China
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26
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Xie C, Ding Z. NAC1 Maintains Root Meristem Activity by Repressing the Transcription of E2Fa in Arabidopsis. Int J Mol Sci 2022; 23:ijms232012258. [PMID: 36293114 PMCID: PMC9603599 DOI: 10.3390/ijms232012258] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Root meristem is a reserve of undifferentiated cells which guide root development. To maintain root meristem identity and therefore continuous root growth, the rate of cell differentiation must coordinate with the rate of generation of new cells. The E2 promoter-binding factor a (E2Fa) has been shown to regulate root growth through controlling G1/S cell cycle transitions in Arabidopsis thaliana. Here, we found that NAC1, a member of the NAM/ATAF/CUC family of transcription factors, regulated root growth by directly repressing the transcription of E2Fa. Loss of NAC1 triggers an up-regulation of the E2Fa expression and causes a reduced meristem size and short-root phenotype, which are largely rescued by mutation of E2Fa. Further analysis showed that NAC1 was shown to regulate root meristem by controlling endopolyploidy levels in an E2Fa-dependent manner. This study provides evidence to show that NAC1 maintains root meristem size and root growth by directly repressing the transcription of E2Fa in Arabidopsis.
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Lardon R, Trinh HK, Xu X, Vu LD, Van De Cotte B, Pernisová M, Vanneste S, De Smet I, Geelen D. Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants. FRONTIERS IN PLANT SCIENCE 2022; 13:894208. [PMID: 36684719 PMCID: PMC9847488 DOI: 10.3389/fpls.2022.894208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/27/2022] [Indexed: 06/17/2023]
Abstract
Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.
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Affiliation(s)
- Robin Lardon
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Hoang Khai Trinh
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Biotechnology Research and Development Institute, Can Tho University, Can Tho, Vietnam
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Brigitte Van De Cotte
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Markéta Pernisová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Steffen Vanneste
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon, South Korea
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Jaiswal V, Kakkar M, Kumari P, Zinta G, Gahlaut V, Kumar S. Multifaceted Roles of GRAS Transcription Factors in Growth and Stress Responses in Plants. iScience 2022; 25:105026. [PMID: 36117995 PMCID: PMC9474926 DOI: 10.1016/j.isci.2022.105026] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Vandana Jaiswal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mrinalini Kakkar
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Priya Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Corresponding author
| | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
- Corresponding author
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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Waseem M, Nkurikiyimfura O, Niyitanga S, Jakada BH, Shaheen I, Aslam MM. GRAS transcription factors emerging regulator in plants growth, development, and multiple stresses. Mol Biol Rep 2022; 49:9673-9685. [PMID: 35713799 DOI: 10.1007/s11033-022-07425-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/23/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
GRAS transcription factors play multifunctional roles in plant growth, development, and resistance to various biotic and abiotic stresses. The structural and functional features of GRAS TFs have been unveiled in the last two decades. A typical GRAS protein contained a C-terminal GRAS domain with a highly variable N-terminal region. Studies on these TFs increase in numbers and are reported to be involved in various important developmental processes such as flowering, root formation, and stress responses. The GRAS TFs and hormone signaling crosstalk can be implicated in plant development and to stress responses. There are relatively few reports about GRAS TFs roles in plants, and no related reviews have been published. In this review, we summarized the features of GRAS TFs, their targets, and the roles these GRAS TFs playing in plant development and multiple stresses.
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Affiliation(s)
- Muhammad Waseem
- Department of Botany, University of Narowal, Narowal, Punjab, Pakistan. .,College of Life Science, Hainan University, Hainan, P.R. China.
| | - Oswald Nkurikiyimfura
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Sylvain Niyitanga
- Department of Plant Pathology, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Bello Hassan Jakada
- College of Life Science, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Iffat Shaheen
- Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
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30
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Chen Y, Yu H, Wang Y, Li F, Xing Y, Ge X. Uniconazole Augments Abscisic Acid in Promoting Somatic Embryogenesis in Cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:865778. [PMID: 35444669 PMCID: PMC9014122 DOI: 10.3389/fpls.2022.865778] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/23/2022] [Indexed: 06/01/2023]
Abstract
During somatic embryogenesis (SE), somatic cells initiate embryogenic development under appropriate conditions. Uniconazole, a plant growth regulator, was found to inhibit the proliferation of callus but promoted the conversion of callus into an embryogenic callus (EC) in cotton. The supplementation of uniconazole in the culture medium significantly suppressed the endogenous auxin [indole acetic acid (IAA)] level in callus tissues in both the callus initiation and proliferation stage but enhanced the abscisic acid (ABA) level only in the callus proliferation stage. Exogenous ABA and uniconazole showed cooperative effects on promoting the differentiation rate of callus into EC. These findings were verified by RNA-seq analysis, which elucidated that the genes involved in the IAA biosynthesis, metabolism, and signaling, and ABA metabolism pathways were regulated by uniconazole during the callus development and SE. Overall, the results suggest that uniconazole could modulate callus proliferation and callus differentiation rate by regulating the endogenous levels of IAA and ABA.
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Affiliation(s)
- Yanli Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hongxia Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- College of Plant Science and Technology of Huazhong Agricultural University, Wuhan, China
| | - Ye Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yadi Xing
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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31
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Lube V, Noyan MA, Przybysz A, Salama K, Blilou I. MultipleXLab: A high-throughput portable live-imaging root phenotyping platform using deep learning and computer vision. PLANT METHODS 2022; 18:38. [PMID: 35346267 PMCID: PMC8958799 DOI: 10.1186/s13007-022-00864-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Profiling the plant root architecture is vital for selecting resilient crops that can efficiently take up water and nutrients. The high-performance imaging tools available to study root-growth dynamics with the optimal resolution are costly and stationary. In addition, performing nondestructive high-throughput phenotyping to extract the structural and morphological features of roots remains challenging. RESULTS We developed the MultipleXLab: a modular, mobile, and cost-effective setup to tackle these limitations. The system can continuously monitor thousands of seeds from germination to root development based on a conventional camera attached to a motorized multiaxis-rotational stage and custom-built 3D-printed plate holder with integrated light-emitting diode lighting. We also developed an image segmentation model based on deep learning that allows the users to analyze the data automatically. We tested the MultipleXLab to monitor seed germination and root growth of Arabidopsis developmental, cell cycle, and auxin transport mutants non-invasively at high-throughput and showed that the system provides robust data and allows precise evaluation of germination index and hourly growth rate between mutants. CONCLUSION MultipleXLab provides a flexible and user-friendly root phenotyping platform that is an attractive mobile alternative to high-end imaging platforms and stationary growth chambers. It can be used in numerous applications by plant biologists, the seed industry, crop scientists, and breeding companies.
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Affiliation(s)
- Vinicius Lube
- Laboratory of Plant Cell and Developmental Biology (LPCDB), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | | | - Alexander Przybysz
- Sensors Lab, Advanced Membranes and Porous Materials Center (AMPMC), Computer, Electrical and Mathematical Science and Engineering (CEMSE), KAUST, Thuwal, Saudi Arabia
| | - Khaled Salama
- Sensors Lab, Advanced Membranes and Porous Materials Center (AMPMC), Computer, Electrical and Mathematical Science and Engineering (CEMSE), KAUST, Thuwal, Saudi Arabia
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology (LPCDB), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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32
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Liu S, Cheng H, Ashraf J, Zhang Y, Wang Q, Lv L, He M, Song G, Zuo D. Interpretation of convolutional neural networks reveals crucial sequence features involving in transcription during fiber development. BMC Bioinformatics 2022; 23:91. [PMID: 35291940 PMCID: PMC8922751 DOI: 10.1186/s12859-022-04619-9] [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: 03/16/2021] [Accepted: 02/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upland cotton provides the most natural fiber in the world. During fiber development, the quality and yield of fiber were influenced by gene transcription. Revealing sequence features related to transcription has a profound impact on cotton molecular breeding. We applied convolutional neural networks to predict gene expression status based on the sequences of gene transcription start regions. After that, a gradient-based interpretation and an N-adjusted kernel transformation were implemented to extract sequence features contributing to transcription. RESULTS Our models had approximate 80% accuracies, and the area under the receiver operating characteristic curve reached over 0.85. Gradient-based interpretation revealed 5' untranslated region contributed to gene transcription. Furthermore, 6 DOF binding motifs and 4 transcription activator binding motifs were obtained by N-adjusted kernel-motif transformation from models in three developmental stages. Apart from 10 general motifs, 3 DOF5.1 genes were also detected. In silico analysis about these motifs' binding proteins implied their potential functions in fiber formation. Besides, we also found some novel motifs in plants as important sequence features for transcription. CONCLUSIONS In conclusion, the N-adjusted kernel transformation method could interpret convolutional neural networks and reveal important sequence features related to transcription during fiber development. Potential functions of motifs interpreted from convolutional neural networks could be validated by further wet-lab experiments and applied in cotton molecular breeding.
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Affiliation(s)
- Shang Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hailiang Cheng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Javaria Ashraf
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Punjab, 63100, Pakistan
| | - Youping Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Qiaolian Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Limin Lv
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Man He
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Guoli Song
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Dongyun Zuo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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Genome-wide identification and expression analysis of the GRAS gene family in response to drought stress in chickpea ( Cicer arietinum L.). 3 Biotech 2022; 12:64. [PMID: 35186661 PMCID: PMC8828820 DOI: 10.1007/s13205-021-03104-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 12/28/2021] [Indexed: 11/01/2022] Open
Abstract
The GRAS (gibberellic acid insensitive, repressor of GAI and scarecrow) transcription factors (TFs) regulate diverse biological processes involved in plant growth and development. These TFs are also known to regulate gene expression in response to various abiotic stress factors like cold, drought, etc. In chickpea one of the most devastating abiotic stress factors is terminal drought. The GRAS TF family has not been characterized in chickpea (Cicer arietinum L.) until now. In this study, we report 46 GRAS TF genes (CaGRAS genes) in the chickpea genome. The CaGRAS proteins were categorized into nine subfamilies based on their phylogenetic relationship with known GRAS members of Arabidopsis and soybean. The PAT subfamily was the largest consisting of ten CaGRAS members whereas the LAS subfamily was the smallest with only one member. Gene duplication analysis revealed that segmental duplication was the primary reason for the expansion of this gene family within the chickpea genome. The gene expression levels of CaGRAS genes were analysed using two different chickpea varieties contrasting for drought tolerance trait, i.e., ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive). On exposure to drought stress, the two chickpea genotypes, exhibited differential drought response, which was quantified and estimated in terms of differences in leaf relative water content (RWC). The well-watered or control plants of the drought tolerant variety were able to maintain a higher leaf RWC by the end of the drought stress period, whereas the control plants of the drought sensitive variety continued to show a decline in leaf RWC. The two genotypes also differed in their root morphologies, under well-watered and drought stress conditions. The gene expression analysis revealed a potential role of PAT, SCR, SCL3 and SHR GRAS members in the regulation of differential response to drought, in the root tissues, for both the genotypes. CaGRAS 12 (SCR) was identified as a drought-responsive GRAS TF gene, which could serve as a potential candidate gene for utilization in developing chickpea varieties with improved drought tolerance. This study demonstrates the drought-responsive expression of CaGRAS genes in chickpea and also describes the morpho-physiological response of chickpea plants to drought stress conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03104-z.
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Dal Santo S, De Paoli E, Pagliarani C, Amato A, Celii M, Boccacci P, Zenoni S, Gambino G, Perrone I. Stress responses and epigenomic instability mark the loss of somatic embryogenesis competence in grapevine. PLANT PHYSIOLOGY 2022; 188:490-508. [PMID: 34726761 PMCID: PMC8774814 DOI: 10.1093/plphys/kiab477] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Somatic embryogenesis (SE) represents the most appropriate tool for next-generation breeding methods in woody plants such as grapevine (Vitis vinifera L.). However, in this species, the SE competence is strongly genotype-dependent and the molecular basis of this phenomenon is poorly understood. We explored the genetic and epigenetic basis of SE in grapevine by profiling the transcriptome, epigenome, and small RNAome of undifferentiated, embryogenic, and non-embryogenic callus tissues derived from two genotypes differing in competence for SE, Sangiovese and Cabernet Sauvignon. During the successful formation of embryonic callus, we observed the upregulation of epigenetic-related transcripts and short interfering RNAs in association with DNA hypermethylation at transposable elements in both varieties. Nevertheless, the switch to nonembryonic development matched the incomplete reinforcement of transposon silencing, and the evidence of such effect was more apparent in the recalcitrant Cabernet Sauvignon. Transcriptomic differences between the two genotypes were maximized already at early stage of culture where the recalcitrant variety expressed a broad panel of genes related to stress responses and secondary metabolism. Our data provide a different angle on the SE molecular dynamics that can be exploited to leverage SE as a biotechnological tool for fruit crop breeding.
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Affiliation(s)
- Silvia Dal Santo
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Emanuele De Paoli
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Mirko Celii
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
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Tian Y, Zhao N, Wang M, Zhou W, Guo J, Han C, Zhou C, Wang W, Wu S, Tang W, Fan M, Bai MY. Integrated regulation of periclinal cell division by transcriptional module of BZR1-SHR in Arabidopsis roots. THE NEW PHYTOLOGIST 2022; 233:795-808. [PMID: 34693527 DOI: 10.1111/nph.17824] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The timing and extent of cell division are crucial for the correct patterning of multicellular organism. In Arabidopsis, root ground tissue maturation involves the periclinal cell division of the endodermis to generate two cell layers: endodermis and middle cortex. However, the molecular mechanism underlying this pattern formation remains unclear. Here, we report that phytohormone brassinosteroid (BR) and redox signal hydrogen peroxide (H2 O2 ) interdependently promote periclinal division during root ground tissue maturation by regulating the activity of SHORT-ROOT (SHR), a master regulator of root growth and development. BR-activated transcription factor BRASSINAZOLE RESISTANT1 (BZR1) directly binds to the promoter of SHR to induce its expression, and physically interacts with SHR to increase the transcripts of RESPIRATORY BURST OXIDASE HOMOLOGs (RBOHs) and elevate the levels of H2 O2 , which feedback enhances the interaction between BZR1 and SHR. Additionally, genetic analysis shows that SHR is required for BZR1-promoted periclinal division, and BZR1 enhances the promoting effects of SHR on periclinal division. Together, our finding reveals that the transcriptional module of BZR1-SHR fine-tunes periclinal division during root ground tissue maturation in response to hormone and redox signals.
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Affiliation(s)
- Yanchen Tian
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Na Zhao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Minmin Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Wenying Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Jieqiong Guo
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Chao Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Wenfei Wang
- College of Horticulture, College of Life Sciences, Hai xia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuang Wu
- College of Horticulture, College of Life Sciences, Hai xia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenqiang Tang
- The Key Laboratory of Molecular and Cellular Biology, Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Min Fan
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
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Wu LY, Shang GD, Wang FX, Gao J, Wan MC, Xu ZG, Wang JW. Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration. Dev Cell 2022; 57:526-542.e7. [DOI: 10.1016/j.devcel.2021.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/31/2021] [Accepted: 12/19/2021] [Indexed: 02/06/2023]
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Zhai N, Xu L. Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration. NATURE PLANTS 2021; 7:1453-1460. [PMID: 34782770 DOI: 10.1038/s41477-021-01015-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/05/2021] [Indexed: 05/12/2023]
Abstract
In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
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Affiliation(s)
- Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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Pardal R, Heidstra R. Root stem cell niche networks: it's complexed! Insights from Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6727-6738. [PMID: 34173817 PMCID: PMC8513229 DOI: 10.1093/jxb/erab272] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/05/2021] [Indexed: 05/02/2023]
Abstract
The presence of two meristematic cell populations in the root and shoot apex allows plants to grow indefinitely. Due to its simple and predictable tissue organization, the Arabidopsis root apical meristem remains an ideal model to study mechanisms such as stem cell specification, asymmetric cell division, and differentiation in plants. The root stem cell niche consists of a quiescent organizing centre surrounded by mitotically active stem cells, which originate all root tissues. The transcription factors PLETHORA, SCARECROW, and WOX5 form signalling hubs that integrate multiple inputs from an increasing number of proteins implicated in the regulation of stem cell niche function. Recently, locally produced auxin was added to the list of important mobile factors in the stem cell niche. In addition, protein-protein interaction data elegantly demonstrate how parallel pathways can meet in a common objective. Here we discuss how multiple networks converge to specify and maintain the root stem cell niche.
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Affiliation(s)
- Renan Pardal
- Wageningen University & Research, Plant Sciences department, Plant Developmental Biology group, Droevendaalsesteeg 1, 6708PB Wageningen, Netherlands
| | - Renze Heidstra
- Wageningen University & Research, Plant Sciences department, Plant Developmental Biology group, Droevendaalsesteeg 1, 6708PB Wageningen, Netherlands
- Correspondence:
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39
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Matosevich R, Efroni I. The quiescent center and root regeneration. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6739-6745. [PMID: 34324634 PMCID: PMC8513162 DOI: 10.1093/jxb/erab319] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/03/2021] [Indexed: 05/26/2023]
Abstract
Since its discovery by F.A.L Clowes, extensive research has been dedicated to identifying the functions of the quiescent center (QC). One of the earliest hypotheses was that it serves a key role in regeneration of the root meristem. Recent works provided support for this hypothesis and began to elucidate the molecular mechanisms underlying this phenomenon. There are two scenarios to consider when assessing the role of the QC in regeneration: one, when the damage leaves the QC intact; and the other, when the QC itself is destroyed. In the first scenario, multiple factors are recruited to activate QC cell division in order to replace damaged cells, but whether the QC has a role in the second scenario is less clear. Both using gene expression studies and following the cell division pattern have shown that the QC is assembled gradually, only to appear as a coherent identity late in regeneration. Similar late emergence of the QC was observed during the de novo formation of the lateral root meristem. These observations can lead to the conclusion that the QC has no role in regeneration. However, activities normally occurring in QC cells, such as local auxin biosynthesis, are still found during regeneration but occur in different cells in the regenerating meristem. Thus, we explore an alternative hypothesis, that following destruction of the QC, QC-related gene activity is temporarily distributed to other cells in the regenerating meristem, and only coalesce into a distinct cell identity when regeneration is complete.
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Affiliation(s)
- Rotem Matosevich
- The Institute of Plant Sciences, Faculty of Agriculture, The Hebrew University, Rehovot, Israel
| | - Idan Efroni
- The Institute of Plant Sciences, Faculty of Agriculture, The Hebrew University, Rehovot, Israel
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40
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Hernández-Coronado M, Ortiz-Ramírez C. Root Patterning: Tuning SHORT ROOT Function Creates Diversity in Form. FRONTIERS IN PLANT SCIENCE 2021; 12:745861. [PMID: 34659316 PMCID: PMC8514818 DOI: 10.3389/fpls.2021.745861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Roots have a fundamental role in plant growth and adaptation to different environments. Diversity in root morphology and architecture enables plants to acquire water and nutrients in contrasting substrate conditions, resist biotic and abiotic stress, and develop symbiotic associations. At its most fundamental level, morphology is determined by discrete changes in tissue patterning. Differences in the number and arrangement of the cell layers in the root can change tissue structure, as well as root length and girth, affecting important productivity traits. Therefore, understanding the molecular mechanisms controlling variation in developmental patterning is an important goal in biology. The ground tissue (GT) system is an ideal model to study the genetic basis of morphological diversity because it displays great interspecific variability in cell layer number. In addition, the genetic circuit controlling GT patterning in Arabidopsis thaliana has been well described, although little is known about species with more complex root anatomies. In this review, we will describe the Arabidopsis model for root radial patterning and present recent progress in elucidating the genetic circuitry controlling GT patterning in monocots and the legume Medicago truncatula (Mt), species that develop roots with more complex anatomies and multilayered cortex.
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Affiliation(s)
| | - Carlos Ortiz-Ramírez
- UGA Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Guanajuato, Mexico
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41
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Sahoo DP, Van Winkle LJ, Díaz de la Garza RI, Dubrovsky JG. Interkingdom Comparison of Threonine Metabolism for Stem Cell Maintenance in Plants and Animals. Front Cell Dev Biol 2021; 9:672545. [PMID: 34557481 PMCID: PMC8454773 DOI: 10.3389/fcell.2021.672545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/11/2021] [Indexed: 01/12/2023] Open
Abstract
In multicellular organisms, tissue generation, maintenance, and homeostasis depend on stem cells. Cellular metabolic status is an essential component of different differentiated states, from stem to fully differentiated cells. Threonine (Thr) metabolism has emerged as a critical factor required to maintain pluripotent/multipotent stem cells in both plants and animals. Thus, both kingdoms conserved or converged upon this fundamental feature of stem cell function. Here, we examine similarities and differences in Thr metabolism-dependent mechanisms supporting stem cell maintenance in these two kingdoms. We then consider common features of Thr metabolism in stem cell maintenance and predict and speculate that some knowledge about Thr metabolism and its role in stem cell function in one kingdom may apply to the other. Finally, we outline future research directions to explore these hypotheses.
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Affiliation(s)
- Debee Prasad Sahoo
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lon J. Van Winkle
- Department of Biochemistry, Midwestern University, Downers Grove, IL, United States
- Department of Medical Humanities, Rocky Vista University, Parker, CO, United States
| | | | - Joseph G. Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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42
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Polko JK, Potter KC, Burr CA, Schaller GE, Kieber JJ. Meta-analysis of transcriptomic studies of cytokinin-treated rice roots defines a core set of cytokinin response genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1387-1402. [PMID: 34165836 DOI: 10.1111/tpj.15386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/06/2021] [Accepted: 06/19/2021] [Indexed: 05/25/2023]
Abstract
Cytokinins regulate diverse aspects of plant growth and development, primarily through modulation of gene expression. The cytokinin-responsive transcriptome has been thoroughly described in dicots, especially Arabidopsis, but much less so in monocots. Here, we present a meta-analysis of five different transcriptomic analyses of rice (Oryza sativa) roots treated with cytokinin, including three previously unpublished experiments. We developed a treatment method in which hormone is added to the media of rice seedlings grown in sterile hydroponic culture under a continuous airflow, which resulted in minimal perturbation of the seedlings, thus greatly reducing changes in gene expression in the absence of exogenous hormone. We defined a core set of 205 upregulated and 86 downregulated genes that were differentially expressed in at least three of the transcriptomic datasets. This core set includes genes encoding the type-A response regulators (RRs) and cytokinin oxidases/dehydrogenases, which have been shown to be primary cytokinin response genes. GO analysis revealed that the upregulated genes were enriched for terms related to cytokinin/hormone signaling and metabolism, while the downregulated genes were significantly enriched for genes encoding transporters. Variations of type-B RR binding motifs were significantly enriched in the promoters of the upregulated genes, as were binding sites for other potential partner transcription factors. The promoters of the downregulated genes were generally enriched for distinct cis-acting motifs and did not include the type-B RR binding motif. This analysis provides insight into the molecular mechanisms underlying cytokinin action in a monocot and provides a useful foundation for future studies of this hormone in rice and other cereals.
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Affiliation(s)
- Joanna K Polko
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kevin C Potter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christian A Burr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification. Methods Mol Biol 2021. [PMID: 34251619 DOI: 10.1007/978-1-0716-1534-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Gene expression data analysis and the prediction of causal relationships within gene regulatory networks (GRNs) have guided the identification of key regulatory factors and unraveled the dynamic properties of biological systems. However, drawing accurate and unbiased conclusions requires a comprehensive understanding of relevant tools, computational methods, and their workflows. The topics covered in this chapter encompass the entire workflow for GRN inference including: (1) experimental design; (2) RNA sequencing data processing; (3) differentially expressed gene (DEG) selection; (4) clustering prior to inference; (5) network inference techniques; and (6) network visualization and analysis. Moreover, this chapter aims to present a workflow feasible and accessible for plant biologists without a bioinformatics or computer science background. To address this need, TuxNet, a user-friendly graphical user interface that integrates RNA sequencing data analysis with GRN inference, is chosen for the purpose of providing a detailed tutorial.
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Kao P, Schon MA, Mosiolek M, Enugutti B, Nodine MD. Gene expression variation in Arabidopsis embryos at single-nucleus resolution. Development 2021; 148:dev199589. [PMID: 34142712 PMCID: PMC8276985 DOI: 10.1242/dev.199589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022]
Abstract
Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA-sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Ping Kao
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael A. Schon
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Balaji Enugutti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael D. Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, The Netherlands
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45
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Kirschner GK, Xiao TT, Blilou I. Rooting in the Desert: A Developmental Overview on Desert Plants. Genes (Basel) 2021; 12:genes12050709. [PMID: 34068546 PMCID: PMC8151154 DOI: 10.3390/genes12050709] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 01/17/2023] Open
Abstract
Plants, as sessile organisms, have evolved a remarkable developmental plasticity to cope with their changing environment. When growing in hostile desert conditions, plants have to grow and thrive in heat and drought. This review discusses how desert plants have adapted their root system architecture (RSA) to cope with scarce water availability and poor nutrient availability in the desert soil. First, we describe how some species can survive by developing deep tap roots to access the groundwater while others produce shallow roots to exploit the short rain seasons and unpredictable rainfalls. Then, we discuss how desert plants have evolved unique developmental programs like having determinate meristems in the case of cacti while forming a branched and compact root system that allows efficient water uptake during wet periods. The remote germination mechanism in date palms is another example of developmental adaptation to survive in the dry and hot desert surface. Date palms have also designed non-gravitropic secondary roots, termed pneumatophores, to maximize water and nutrient uptake. Next, we highlight the distinct anatomical features developed by desert species in response to drought like narrow vessels, high tissue suberization, and air spaces within the root cortex tissue. Finally, we discuss the beneficial impact of the microbiome in promoting root growth in desert conditions and how these characteristics can be exploited to engineer resilient crops with a greater ability to deal with salinity induced by irrigation and with the increasing drought caused by global warming.
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Sultana S, Fujiwara D, Aoki K. Epidermal cell-patterning genes of the stem parasitic plant Cuscuta campestris are involved in the development of holdfasts. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:47-56. [PMID: 34177324 PMCID: PMC8215460 DOI: 10.5511/plantbiotechnology.20.1116a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 11/16/2020] [Indexed: 06/13/2023]
Abstract
Cuscuta campestris, a stem parasitic plant, commences its parasitic behavior by forming a specialized disk-like adhesive structure called a holdfast, which facilitates tight adhesion to the stem surface of the host plant. The morphology of epidermal cells in the holdfast is similar to that of the leaf trichome and root hairs of dicotyledonous plants. However, the regulatory network underlying the development of the holdfast has not been elucidated to date. In this study, we assessed the roles of epidermal cell-patterning genes in the development of a holdfast. Epidermal cell-patterning genes of C. campestris, including CcWER, CcGL3, CcTTG1, CcGL2, and CcJKD, were expressed slightly before the initiation of the outgrowth of stem epidermal cells. CcJKD-silencing repressed CcJKD, CcWER, CcGL3, CcTTG1, CcGL2; therefore, CcJKD is an upstream regulator of other epidermal cell-patterning genes. Unlike other genes, CcCPC was not upregulated after attachment to the host, and was not repressed by CcJKD-silencing. Protein interaction assays demonstrated that CcJKD interacted with CcTTG1 and CcCPC. Furthermore, CcJKD-silencing repressed the outgrowth of holdfast epidermal cells. Therefore, C. campestris invokes epidermal cell-patterning genes for the outgrowth of holdfast epidermal cells, and their regulatory mechanism is different from those for leaf trichome or root hairs.
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Affiliation(s)
- Sabrina Sultana
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka 599-8531, Japan
- Industrial Microbiology Division, Bangladesh Council of Scientific and Industrial Research (BCSIR) Laboratories, Chittagong, Chittagong Cantonment, Chittagong 4220, Bangladesh
| | - Daiki Fujiwara
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka 599-8531, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka 599-8531, Japan
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Cruz JO, San Martin JAB, Lubini G, Strini EJ, Sobral R, Pinoti VF, Ferreira PB, Thomé V, Quiapim AC, Dornelas MC, Pranchevicius MCS, Madueño F, Costa MMR, Goldman MHS. SCI1 Is a Direct Target of AGAMOUS and WUSCHEL and Is Specifically Expressed in the Floral Meristematic Cells. FRONTIERS IN PLANT SCIENCE 2021; 12:642879. [PMID: 33815449 PMCID: PMC8012853 DOI: 10.3389/fpls.2021.642879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The specified floral meristem will develop a pre-established number of floral organs and, thus, terminate the floral meristematic cells. The floral meristematic pool of cells is controlled, among some others, by WUSCHEL (WUS) and AGAMOUS (AG) transcription factors (TFs). Here, we demonstrate that the SCI1 (Stigma/style cell-cycle inhibitor 1) gene, a cell proliferation regulator, starts to be expressed since the floral meristem specification of Nicotiana tabacum and is expressed in all floral meristematic cells. Its expression is higher in the floral meristem and the organs being specified, and then it decreases from outside to inside whorls when the organs are differentiating. SCI1 is co-expressed with N. tabacum WUSCHEL (NtWUS) in the floral meristem and the whorl primordia at very early developmental stages. Later in development, SCI1 is co-expressed with NAG1 (N. tabacum AG) in the floral meristem and specialized tissues of the pistil. In silico analyses identified cis-regulatory elements for these TFs in the SCI1 genomic sequence. Yeast one-hybrid and electrophoresis mobility shift assay demonstrated that both TFs interact with the SCI1 promoter sequence. Additionally, the luciferase activity assay showed that NAG1 clearly activates SCI1 expression, while NtWUS could not do so. Taken together, our results suggest that during floral development, the spatiotemporal regulation of SCI1 by NtWUS and NAG1 may result in the maintenance or termination of proliferative cells in the floral meristem, respectively.
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Affiliation(s)
- Joelma O. Cruz
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Juca A. B. San Martin
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Greice Lubini
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Edward J. Strini
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Rómulo Sobral
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Center, University of Minho, Braga, Portugal
| | - Vitor F. Pinoti
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Pedro B. Ferreira
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanessa Thomé
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Andréa C. Quiapim
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Marcelo C. Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade de Campinas, Campinas, Brazil
| | | | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
| | - M. Manuela R. Costa
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Center, University of Minho, Braga, Portugal
| | - Maria Helena S. Goldman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- PPG-Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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Ito T, Fukazawa J. SCARECROW-LIKE3 regulates the transcription of gibberellin-related genes by acting as a transcriptional co-repressor of GAI-ASSOCIATED FACTOR1. PLANT MOLECULAR BIOLOGY 2021; 105:463-482. [PMID: 33474657 DOI: 10.1007/s11103-020-01101-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
SCL3 inhibits transcriptional activity of IDD-DELLA complex by acting as a co-repressor and repression activity is enhanced in the presence of GAF1 in a TOPLESS-independent manner. GRAS [GIBBERELLIN-INSENSITIVE (GAI), REPRESSOR OF ga1-3 (RGA) and SCARECROW (SCR)] proteins are a family of plant-specific transcriptional regulators that play diverse roles in development and signaling. GRAS family DELLA proteins act as growth repressors by inhibiting gibberellin (GA) signaling in response to developmental and environmental cues. DELLAs also act as co-activators of transcription factor GAI-ASSOCIATED FACTOR1 (GAF1)/INDETERMINATE DOMAIN2 (IDD2), the GAF1-DELLA complex activating transcription of GAF1 target genes. GAF1 also interacts with TOPLESS (TPL), a transcriptional co-repressor, in the absence of DELLA, the GAF1-TPL complex repressing transcription of the target genes. SCARECROW-LIKE3 (SCL3), another member of the GRAS family, is thought to inhibit transcriptional activity of the IDD-DELLA complex through competitive interaction with IDD. Here, we also revealed that SCL3 inhibits transcriptional activation by the GAF1-DELLA complex via repression activity rather than via competitive inhibition of the GAF1-DELLA interaction. Moreover, the repression activity of SCL3 was enhanced by GAF1 in a TPL-independent manner. While the GRAS domain of DELLA has transcriptional activation activity, that of SCL3 has repression activity. SCL3 also inhibited transcriptional activity of GAF1-RGA fusion proteins. Results from the co-immunoprecipitation assays and the yeast three-hybrid assay suggested the possibility that SCL3 forms a ternary complex with GAF1 and DELLA. These findings provide important information on DELLA-regulated GA signaling and new insight into the transcriptional repression mechanism.
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Affiliation(s)
- Takeshi Ito
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Jutarou Fukazawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
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Yang X, Zhang Y, Shan J, Sun J, Li D, Zhang X, Li W, Zhao L. GmIDD Is Induced by Short Days in Soybean and May Accelerate Flowering When Overexpressed in Arabidopsis via Inhibiting AGAMOUS-LIKE 18. FRONTIERS IN PLANT SCIENCE 2021; 12:629069. [PMID: 33841461 PMCID: PMC8029582 DOI: 10.3389/fpls.2021.629069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/22/2021] [Indexed: 05/31/2023]
Abstract
Photoperiod is one of the main climatic factors that determine flowering time and yield. Some members of the INDETERMINATE DOMAIN (IDD) transcription factor family have been reported to be involved in regulation of flowering time in Arabidopsis, maize, and rice. In this study, the domain analysis showed that GmIDD had a typical ID domain and was a member of the soybean IDD transcription factor family. Quantitative real-time PCR analysis showed that GmIDD was induced by short day conditions in leaves and regulated by circadian clock. Under long day conditions, transgenic Arabidopsis overexpressing GmIDD flowered earlier than wild-type, and idd mutants flowered later, while the overexpression of GmIDD rescued the late-flowering phenotype of idd mutants. Chromatin immunoprecipitation sequencing assays of GmIDD binding sites in GmIDD-overexpression (GmIDD-ox) Arabidopsis further identified potential direct targets, including a transcription factor, AGAMOUS-like 18 (AGL18). GmIDD might inhibit the transcriptional activity of flower repressor AGL18 by binding to the TTTTGGTCC motif of AGL18 promoter. Furthermore, the results also showed that GmIDD overexpression increased the transcription levels of flowering time-related genes FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), LEAFY (LFY) and APETALA1 (AP1) in Arabidopsis. Taken together, GmIDD appeared to inhibit the transcriptional activity of AGL18 and induced the expression of FT gene to promote Arabidopsis flowering.
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Raya-González J, Ojeda-Rivera JO, Mora-Macias J, Oropeza-Aburto A, Ruiz-Herrera LF, López-Bucio J, Herrera-Estrella L. MEDIATOR16 orchestrates local and systemic responses to phosphate scarcity in Arabidopsis roots. THE NEW PHYTOLOGIST 2021; 229:1278-1288. [PMID: 33034045 DOI: 10.1111/nph.16989] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 09/30/2020] [Indexed: 05/21/2023]
Abstract
Phosphate (Pi ) is a critical macronutrient for the biochemical and molecular functions of cells. Under phosphate limitation, plants manifest adaptative strategies to increase phosphate scavenging. However, how low phosphate sensing links to the transcriptional machinery remains unknown. The role of the MEDIATOR (MED) transcriptional co-activator, through its MED16 subunit in Arabidopsis root system architecture remodeling in response to phosphate limitation was assessed. Its critical function acting over the SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1)-ALUMINUM-ACTIVATED MALATE TRANSPORT1 (ALMT1) signaling module was tested through a combination of genetic, biochemical, and genome-wide transcriptomic approaches. Root system configuration in response to phosphate scarcity involved MED16 functioning, which modulates the expression of a large set of low-phosphate-induced genes that respond to local and systemic signals in the Arabidopsis root tip, including those directly activated by STOP1. Biomolecular fluorescence complementation analysis suggests that MED16 is required for the transcriptional activation of STOP1 targets, including the membrane permease ALMT1, to increase malate exudation in response to low phosphate. Our results unveil the function of a critical transcriptional component, MED16, in the root adaptive responses to a scarce plant macronutrient, which helps understanding how plant cells orchestrate root morphogenesis to gene expression with the STOP1-ALMT1 module.
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Affiliation(s)
- Javier Raya-González
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, 36821 Campus Irapuato, Guanajuato, Mexico
- Facultad de Químico Farmacobiología, Avenida Tzintzuntzan 173, Col. Matamoros, Morelia, Michoacán, Mexico
| | - Jonathan Odilón Ojeda-Rivera
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, 36821 Campus Irapuato, Guanajuato, Mexico
| | - Javier Mora-Macias
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, 36821 Campus Irapuato, Guanajuato, Mexico
| | - Araceli Oropeza-Aburto
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, 36821 Campus Irapuato, Guanajuato, Mexico
| | - León Francisco Ruiz-Herrera
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio B3, Ciudad Universitaria, Morelia, Michoacán, 58030, Mexico
| | - José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo. Edificio B3, Ciudad Universitaria, Morelia, Michoacán, 58030, Mexico
| | - Luis Herrera-Estrella
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, 36821 Campus Irapuato, Guanajuato, Mexico
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Box 42122, Lubbock, TX, 79409, USA
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