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Dresvyannikova AE, Watanabe N, Muterko AF, Krasnikov AA, Goncharov NP, Dobrovolskaya OB. Characterization of a dominant mutation for the liguleless trait: Aegilops tauschii liguleless (Lg t). BMC PLANT BIOLOGY 2019; 19:55. [PMID: 30813900 PMCID: PMC6393956 DOI: 10.1186/s12870-019-1635-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND Leaves of Poaceae have a unique morphological feature: they consist of a proximal sheath and a distal blade separated by a ligular region. The sheath provides structural support and protects young developing leaves, whereas the main function of the blade is photosynthesis. The auricles allow the blade to tilt back for optimal photosynthesis and determine the angle of a leaf, whereas the ligule protects the stem from the entry of water, microorganisms, and pests. Liguleless variants have an upright leaf blade that wraps around the culm. Research on liguleless mutants of maize and other cereals has led to identification of genes that are involved in leaf patterning and differentiation. RESULTS We characterized an induced liguleless mutant (LM) of Aegilops tauschii Coss., a donor of genome D of bread wheat Triticum aestivum L.. The liguleless phenotype of LM is under dominant monogenic control (Lgt). To determine precise position of Lgt on the Ae. tauschii genetic map, highly saturated genetic maps were constructed containing 887 single-nucleotide polymorphism (SNP) markers derived via diversity arrays technology (DArT)seq. The Lgt gene was mapped to chromosome 5DS. Taking into account coordinates of the SNP markers, flanking Lgt, on the pseudomolecule 5D, a chromosomal region that contains this gene was determined, and a list of candidate genes was identified. Morphological features of the LM phenotype suggest that Lgt participates in the control of leaf development, mainly, in leaf proximal-distal patterning, and its dominant mutation causes abnormal ligular region but does not affect reproductive development. CONCLUSIONS Here we report characterization of a liguleless Ae. tauschii mutant, whose phenotype is under control of a dominant mutation of Lgt. The dominant mode of inheritance of the liguleless trait in a Triticeae species is reported for the first time. The position of the Lgt locus on chromosome 5DS allowed us to identify a list of candidate genes. This list does not contain Ae. tauschii orthologs of any well-characterized cereal genes whose mutations cause liguleless phenotypes. Thus, the characterized Lgt mutant represents a new model for further investigation of plant leaf patterning and differentiation.
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Affiliation(s)
- Alina E. Dresvyannikova
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, Pirogova, 2, Novosibirsk, 630090 Russia
| | | | - Alexander F. Muterko
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
| | - Alexander A. Krasnikov
- Central Siberian Botanical Garden SB RAS, Zolotodolinskaya Str., 101, Novosibirsk, 630090 Russia
| | - Nikolay P. Goncharov
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
| | - Oxana B. Dobrovolskaya
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, Pirogova, 2, Novosibirsk, 630090 Russia
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Bao A, Burritt DJ, Chen H, Zhou X, Cao D, Tran LSP. The CRISPR/Cas9 system and its applications in crop genome editing. Crit Rev Biotechnol 2019; 39:321-336. [PMID: 30646772 DOI: 10.1080/07388551.2018.1554621] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated protein9) system is an RNA-guided genome editing tool that consists of a Cas9 nuclease and a single-guide RNA (sgRNA). By base-pairing with a DNA target sequence, the sgRNA enables Cas9 to recognize and cut a specific target DNA sequence, generating double strand breaks (DSBs) that trigger cell repair mechanisms and mutations at or near the DSBs sites. Since its discovery, the CRISPR/Cas9 system has revolutionized genome editing and is now becoming widely utilized to edit the genomes of a diverse range of crop plants. In this review, we present an overview of the CRISPR/Cas9 system itself, including its mechanism of action, system construction strategies, and the screening methods used to identify mutants containing edited genes. We evaluate recent examples of the use of CRISPR/Cas9 for crop plant improvement, and research into the function(s) of genes involved in determining crop yields, quality, environmental stress tolerance/resistance, regulation of gene transcription and translation, and the construction of mutant libraries and production of transgene-free genome-edited crops. In addition, challenges and future opportunities for the use of the CRISPR/Cas9 system in crop breeding are discussed.
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Affiliation(s)
- Aili Bao
- a Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture , Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences , Wuhan , China
| | - David J Burritt
- b Department of Botany , University of Otago , Dunedin , New Zealand
| | - Haifeng Chen
- a Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture , Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences , Wuhan , China
| | - Xinan Zhou
- a Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture , Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences , Wuhan , China
| | - Dong Cao
- a Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture , Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences , Wuhan , China
| | - Lam-Son Phan Tran
- c Institute of Research and Development, Duy Tan University , Da Nang, Vietnam.,d Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science , Yokohama , Japan
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Conklin PA, Strable J, Li S, Scanlon MJ. On the mechanisms of development in monocot and eudicot leaves. THE NEW PHYTOLOGIST 2019; 221:706-724. [PMID: 30106472 DOI: 10.1111/nph.15371] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 05/22/2023]
Abstract
Contents Summary 706 I. Introduction 707 II. Leaf zones in monocot and eudicot leaves 707 III. Monocot and eudicot leaf initiation: differences in degree and timing, but not kind 710 IV. Reticulate and parallel venation: extending the model? 711 V. Flat laminar growth: patterning and coordination of adaxial-abaxial and mediolateral axes 713 VI. Stipules and ligules: ontogeny of primordial elaborations 715 VII. Leaf architecture 716 VIII. Stomatal development: shared and diverged mechanisms for making epidermal pores 717 IX. Conclusion 719 Acknowledgements 720 References 720 SUMMARY: Comparisons of concepts in monocot and eudicot leaf development are presented, with attention to the morphologies and mechanisms separating these angiosperm lineages. Monocot and eudicot leaves are distinguished by the differential elaborations of upper and lower leaf zones, the formation of sheathing/nonsheathing leaf bases and vasculature patterning. We propose that monocot and eudicot leaves undergo expansion of mediolateral domains at different times in ontogeny, directly impacting features such as venation and leaf bases. Furthermore, lineage-specific mechanisms in compound leaf development are discussed. Although models for the homologies of enigmatic tissues, such as ligules and stipules, are proposed, tests of these hypotheses are rare. Likewise, comparisons of stomatal development are limited to Arabidopsis and a few grasses. Future studies may investigate correlations in the ontogenies of parallel venation and linear stomatal files in monocots, and the reticulate patterning of veins and dispersed stoma in eudicots. Although many fundamental mechanisms of leaf development are shared in eudicots and monocots, variations in the timing, degree and duration of these ontogenetic events may contribute to key differences in morphology. We anticipate that the incorporation of an ever-expanding number of sequenced genomes will enrich our understanding of the developmental mechanisms generating eudicot and monocot leaves.
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Affiliation(s)
- Phillip A Conklin
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Josh Strable
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Shujie Li
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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Richardson AE, Hake S. Drawing a Line: Grasses and Boundaries. PLANTS 2018; 8:plants8010004. [PMID: 30585196 PMCID: PMC6359313 DOI: 10.3390/plants8010004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/12/2018] [Accepted: 12/18/2018] [Indexed: 11/26/2022]
Abstract
Delineation between distinct populations of cells is essential for organ development. Boundary formation is necessary for the maintenance of pluripotent meristematic cells in the shoot apical meristem (SAM) and differentiation of developing organs. Boundaries form between the meristem and organs, as well as between organs and within organs. Much of the research into the boundary gene regulatory network (GRN) has been carried out in the eudicot model Arabidopsis thaliana. This work has identified a dynamic network of hormone and gene interactions. Comparisons with other eudicot models, like tomato and pea, have shown key conserved nodes in the GRN and species-specific alterations, including the recruitment of the boundary GRN in leaf margin development. How boundaries are defined in monocots, and in particular the grass family which contains many of the world’s staple food crops, is not clear. In this study, we review knowledge of the grass boundary GRN during vegetative development. We particularly focus on the development of a grass-specific within-organ boundary, the ligule, which directly impacts leaf architecture. We also consider how genome engineering and the use of natural diversity could be leveraged to influence key agronomic traits relative to leaf and plant architecture in the future, which is guided by knowledge of boundary GRNs.
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Affiliation(s)
- Annis E Richardson
- Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
| | - Sarah Hake
- Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- USDA Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710, USA.
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Maugarny-Calès A, Laufs P. Getting leaves into shape: a molecular, cellular, environmental and evolutionary view. Development 2018; 145:145/13/dev161646. [PMID: 29991476 DOI: 10.1242/dev.161646] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Leaves arise from groups of undifferentiated cells as small primordia that go through overlapping phases of morphogenesis, growth and differentiation. These phases are genetically controlled and modulated by environmental cues to generate a stereotyped, yet plastic, mature organ. Over the past couple of decades, studies have revealed that hormonal signals, transcription factors and miRNAs play major roles during leaf development, and more recent findings have highlighted the contribution of mechanical signals to leaf growth. In this Review, we discuss how modulating the activity of some of these regulators can generate diverse leaf shapes during development, in response to a varying environment, or between species during evolution.
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Affiliation(s)
- Aude Maugarny-Calès
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.,Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Patrick Laufs
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
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García-Cano E, Hak H, Magori S, Lazarowitz SG, Citovsky V. The Agrobacterium F-Box Protein Effector VirF Destabilizes the Arabidopsis GLABROUS1 Enhancer/Binding Protein-Like Transcription Factor VFP4, a Transcriptional Activator of Defense Response Genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:576-586. [PMID: 29264953 PMCID: PMC5953515 DOI: 10.1094/mpmi-07-17-0188-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Agrobacterium-mediated genetic transformation not only represents a technology of choice to genetically manipulate plants, but it also serves as a model system to study mechanisms employed by invading pathogens to counter the myriad defenses mounted against them by the host cell. Here, we uncover a new layer of plant defenses that is targeted by A. tumefaciens to facilitate infection. We show that the Agrobacterium F-box effector VirF, which is exported into the host cell, recognizes an Arabidopsis transcription factor VFP4 and targets it for proteasomal degradation. We hypothesize that VFP4 resists Agrobacterium infection and that the bacterium utilizes its VirF effector to degrade VFP4 and thereby mitigate the VFP4-based defense. Indeed, loss-of-function mutations in VFP4 resulted in differential expression of numerous biotic stress-response genes, suggesting that one of the functions of VFP4 is to control a spectrum of plant defenses, including those against Agrobacterium tumefaciens. We identified one such gene, ATL31, known to mediate resistance to bacterial pathogens. ATL31 was transcriptionally repressed in VFP4 loss-of-function plants and activated in VFP4 gain-of-function plants. Gain-of-function lines of VFP4 and ATL31 exhibited recalcitrance to Agrobacterium tumorigenicity, suggesting that A. tumefaciens may utilize the host ubiquitin/proteasome system to destabilize transcriptional regulators of the host disease response machinery.
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Affiliation(s)
- Elena García-Cano
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
| | - Hagit Hak
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
- Corresponding author: Hagit Hak;
| | - Shimpei Magori
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
| | - Sondra G. Lazarowitz
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215, USA
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Okagaki RJ, Haaning A, Bilgic H, Heinen S, Druka A, Bayer M, Waugh R, Muehlbauer GJ. ELIGULUM-A Regulates Lateral Branch and Leaf Development in Barley. PLANT PHYSIOLOGY 2018; 176:2750-2760. [PMID: 29440592 PMCID: PMC5884586 DOI: 10.1104/pp.17.01459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/28/2018] [Indexed: 05/02/2023]
Abstract
The shoot apical and axillary meristems control shoot development, effectively influencing lateral branch and leaf formation. The barley (Hordeum vulgare) uniculm2 (cul2) mutation blocks axillary meristem development, and mutant plants lack lateral branches (tillers) that normally develop from the crown. A genetic screen for cul2 suppressors recovered two recessive alleles of ELIGULUM-A (ELI-A) that partially rescued the cul2 tillering phenotype. Mutations in ELI-A produce shorter plants with fewer tillers and disrupt the leaf blade-sheath boundary, producing liguleless leaves and reduced secondary cell wall development in stems and leaves. ELI-A is predicted to encode an unannotated protein containing an RNaseH-like domain that is conserved in land plants. ELI-A transcripts accumulate at the preligule boundary, the developing ligule, leaf margins, cells destined to develop secondary cell walls, and cells surrounding leaf vascular bundles. Recent studies have identified regulatory similarities between boundary development in leaves and lateral organs. Interestingly, we observed ELI-A transcripts at the preligule boundary, suggesting that ELI-A contributes to boundary formation between the blade and sheath. However, we did not observe ELI-A transcripts at the axillary meristem boundary in leaf axils, suggesting that ELI-A is not involved in boundary development for axillary meristem development. Our results show that ELI-A contributes to leaf and lateral branch development by acting as a boundary gene during ligule development but not during lateral branch development.
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Affiliation(s)
- Ron J Okagaki
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Allison Haaning
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Hatice Bilgic
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Shane Heinen
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Arnis Druka
- James Hutton Institute, Dundee, United Kingdom
| | - Micha Bayer
- James Hutton Institute, Dundee, United Kingdom
| | | | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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Jia H, Sun W, Li M, Zhang Z. Integrated Analysis of Protein Abundance, Transcript Level, and Tissue Diversity To Reveal Developmental Regulation of Maize. J Proteome Res 2018; 17:822-833. [DOI: 10.1021/acs.jproteome.7b00586] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Haitao Jia
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Wei Sun
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Manfei Li
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Zuxin Zhang
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
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59
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Li C, Liu C, Qi X, Wu Y, Fei X, Mao L, Cheng B, Li X, Xie C. RNA-guided Cas9 as an in vivo desired-target mutator in maize. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1566-1576. [PMID: 28379609 PMCID: PMC5698053 DOI: 10.1111/pbi.12739] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 05/20/2023]
Abstract
The RNA-guided Cas9 system is a versatile tool for genome editing. Here, we established a RNA-guided endonuclease (RGEN) system as an in vivo desired-target mutator (DTM) in maize to reduce the linkage drag during breeding procedure, using the LIGULELESS1 (LG1) locus as a proof-of-concept. Our system showed 51.5%-91.2% mutation frequency in T0 transgenic plants. We then crossed the T1 plants stably expressing DTM with six diverse recipient maize lines and found that 11.79%-28.71% of the plants tested were mutants induced by the DTM effect. Analysis of successive F2 plants indicated that the mutations induced by the DTM effect were largely heritable. Moreover, DTM-generated hybrids had significantly smaller leaf angles that were reduced more than 50% when compared with that of the wild type. Planting experiments showed that DTM-generated maize plants can be grown with significantly higher density and hence greater yield potential. Our work demonstrate that stably expressed RGEN could be implemented as an in vivoDTM to rapidly generate and spread desired mutations in maize through hybridization and subsequent backcrossing, and hence bypassing the linkage drag effect in convention introgression methodology. This proof-of-concept experiment can be a potentially much more efficient breeding strategy in crops employing the RNA-guided Cas9 genome editing.
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Affiliation(s)
- Chuxi Li
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
| | - Changlin Liu
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
| | - Xiantao Qi
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
- Anhui Agricultural UniversityHefeiAnhui ProvinceChina
| | - Yongchun Wu
- AgGene Bio‐tech Seed Industry GroupShenzhenChina
| | - Xiaohong Fei
- AgGene Bio‐tech Seed Industry GroupShenzhenChina
| | - Long Mao
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
| | - Beijiu Cheng
- Anhui Agricultural UniversityHefeiAnhui ProvinceChina
| | - Xinhai Li
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
| | - Chuanxiao Xie
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Gene Resources and Genetic ImprovementBeijingChina
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Rebocho AB, Kennaway JR, Bangham JA, Coen E. Formation and Shaping of the Antirrhinum Flower through Modulation of the CUP Boundary Gene. Curr Biol 2017; 27:2610-2622.e3. [PMID: 28867204 DOI: 10.1016/j.cub.2017.07.064] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/15/2017] [Accepted: 07/27/2017] [Indexed: 10/18/2022]
Abstract
Boundary domain genes, expressed within or around organ primordia, play a key role in the formation, shaping, and subdivision of planar plant organs, such as leaves. However, the role of boundary genes in formation of more elaborate 3D structures, which also derive from organ primordia, remains unclear. Here we analyze the role of the boundary domain gene CUPULIFORMIS (CUP) in formation of the ornate Antirrhinum flower shape. We show that CUP expression becomes cleared from boundary subdomains between petal primordia, most likely contributing to formation of congenitally fused petals (sympetally) and modulation of growth at sinuses. At later stages, CUP is activated by dorsoventral genes in an intermediary region of the corolla. In contrast to its role at organ boundaries, intermediary CUP activity leads to growth promotion rather than repression and formation of the palate, lip, and characteristic folds of the closed Antirrhinum flower. Intermediary expression of CUP homologs is also observed in related sympetalous species, Linaria and Mimulus, suggesting that changes in boundary gene activity have played a key role in the development and evolution of diverse 3D plant shapes.
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Affiliation(s)
- Alexandra B Rebocho
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - J Richard Kennaway
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - J Andrew Bangham
- School of Computational Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Enrico Coen
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
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Ma S, Ding Z, Li P. Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. BMC PLANT BIOLOGY 2017; 17:131. [PMID: 28764653 PMCID: PMC5540570 DOI: 10.1186/s12870-017-1077-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The advent of big data in biology offers opportunities while poses challenges to derive biological insights. For maize, a large amount of publicly available transcriptome datasets have been generated but a comprehensive analysis is lacking. RESULTS We constructed a maize gene co-expression network based on the graphical Gaussian model, using massive RNA-seq data. The network, containing 20,269 genes, assembles into 964 gene modules that function in a variety of plant processes, such as cell organization, the development of inflorescences, ligules and kernels, the uptake and utilization of nutrients (e.g. nitrogen and phosphate), the metabolism of benzoxazionids, oxylipins, flavonoids, and wax, and the response to stresses. Among them, the inflorescences development module is enriched with domestication genes (like ra1, ba1, gt1, tb1, tga1) that control plant architecture and kernel structure, while multiple other modules relate to diverse agronomic traits. Contained within these modules are transcription factors acting as known or potential expression regulators for the genes within the same modules, suggesting them as candidate regulators for related biological processes. A comparison with an established Arabidopsis network revealed conserved gene association patterns for specific modules involved in cell organization, nutrients uptake & utilization, and metabolism. The analysis also identified significant divergences between the two species for modules that orchestrate developmental pathways. CONCLUSIONS This network sheds light on how gene modules are organized between different species in the context of evolutionary divergence and highlights modules whose structure and gene content can provide important resources for maize gene functional studies with application potential.
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Affiliation(s)
- Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui China
| | - Zehong Ding
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan China
| | - Pinghua Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong China
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Strable J, Wallace JG, Unger-Wallace E, Briggs S, Bradbury PJ, Buckler ES, Vollbrecht E. Maize YABBY Genes drooping leaf1 and drooping leaf2 Regulate Plant Architecture. THE PLANT CELL 2017; 29:1622-1641. [PMID: 28698237 PMCID: PMC5559738 DOI: 10.1105/tpc.16.00477] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 06/12/2017] [Accepted: 07/07/2017] [Indexed: 05/19/2023]
Abstract
Leaf architecture directly influences canopy structure, consequentially affecting yield. We discovered a maize (Zea mays) mutant with aberrant leaf architecture, which we named drooping leaf1 (drl1). Pleiotropic mutations in drl1 affect leaf length and width, leaf angle, and internode length and diameter. These phenotypes are enhanced by natural variation at the drl2 enhancer locus, including reduced expression of the drl2-Mo17 allele in the Mo17 inbred. A second drl2 allele, produced by transposon mutagenesis, interacted synergistically with drl1 mutants and reduced drl2 transcript levels. The drl genes are required for proper leaf patterning, development and cell proliferation of leaf support tissues, and for restricting auricle expansion at the midrib. The paralogous loci encode maize CRABS CLAW co-orthologs in the YABBY family of transcriptional regulators. The drl genes are coexpressed in incipient and emergent leaf primordia at the shoot apex, but not in the vegetative meristem or stem. Genome-wide association studies using maize NAM-RIL (nested association mapping-recombinant inbred line) populations indicated that the drl loci reside within quantitative trait locus regions for leaf angle, leaf width, and internode length and identified rare single nucleotide polymorphisms with large phenotypic effects for the latter two traits. This study demonstrates that drl genes control the development of key agronomic traits in maize.
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Affiliation(s)
- Josh Strable
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
- Interdepartmental Plant Biology, Iowa State University, Ames, Iowa 50011
| | - Jason G Wallace
- Department of Crop and Soil Sciences, The University of Georgia, Athens, Georgia 30602
| | - Erica Unger-Wallace
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Sarah Briggs
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Peter J Bradbury
- U.S. Department of Agriculture-Agriculture Research Service, Ithaca, New York 14853
| | - Edward S Buckler
- U.S. Department of Agriculture-Agriculture Research Service, Ithaca, New York 14853
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
| | - Erik Vollbrecht
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
- Interdepartmental Plant Biology, Iowa State University, Ames, Iowa 50011
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Lockhart J. Exploring Maize Leaf Architecture from Different Angles. THE PLANT CELL 2017; 29:1550-1551. [PMID: 28698236 PMCID: PMC5559748 DOI: 10.1105/tpc.17.00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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64
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Tsuda K, Abraham-Juarez MJ, Maeno A, Dong Z, Aromdee D, Meeley R, Shiroishi T, Nonomura KI, Hake S. KNOTTED1 Cofactors, BLH12 and BLH14, Regulate Internode Patterning and Vein Anastomosis in Maize. THE PLANT CELL 2017; 29:1105-1118. [PMID: 28381444 PMCID: PMC5466031 DOI: 10.1105/tpc.16.00967] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/03/2017] [Accepted: 03/28/2017] [Indexed: 05/20/2023]
Abstract
Monocot stems lack the vascular cambium and instead have characteristic structures in which intercalary meristems generate internodes and veins remain separate and scattered. However, developmental processes of these unique structures have been poorly described. BELL1-like homeobox (BLH) transcription factors (TFs) are known to heterodimerize with KNOTTED1-like homeobox TFs to play crucial roles in shoot meristem maintenance, but their functions are elusive in monocots. We found that maize (Zea mays) BLH12 and BLH14 have redundant but important roles in stem development. BLH12/14 interact with KNOTTED1 (KN1) in vivo and accumulate in overlapping domains in shoot meristems, young stems, and provascular bundles. Similar to kn1 loss-of-function mutants, blh12 blh14 (blh12/14) double mutants fail to maintain axillary meristems. Unique to blh12/14 is an abnormal tassel branching and precocious internode differentiation that results in dwarfism and reduced veins in stems. Micro-computed tomography observation of vascular networks revealed that blh12/14 double mutants had reduced vein number due to fewer intermediate veins in leaves and precocious anastomosis in young stems. Based on these results, we propose two functions of BLH12/14 during stem development: (1) maintaining intercalary meristems that accumulate KN1 and prevent precocious internode differentiation and (2) preventing precocious anastomosis of provascular bundles in young stems to ensure the production of sufficient independent veins.
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Affiliation(s)
- Katsutoshi Tsuda
- Experimental Farm, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Maria-Jazmin Abraham-Juarez
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, University of California at Berkeley, Albany, California 94710
| | - Akiteru Maeno
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Zhaobin Dong
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, University of California at Berkeley, Albany, California 94710
| | - Dale Aromdee
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, University of California at Berkeley, Albany, California 94710
| | | | - Toshihiko Shiroishi
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ken-Ichi Nonomura
- Experimental Farm, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Sarah Hake
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Plant and Microbial Biology Department, University of California at Berkeley, Albany, California 94710
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Espinosa-Ruiz A, Martínez C, de Lucas M, Fàbregas N, Bosch N, Caño-Delgado AI, Prat S. TOPLESS mediates brassinosteroid control of shoot boundaries and root meristem development in Arabidopsis thaliana. Development 2017; 144:1619-1628. [PMID: 28320734 DOI: 10.1242/dev.143214] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/27/2017] [Indexed: 01/07/2023]
Abstract
The transcription factor BRI1-EMS-SUPRESSOR 1 (BES1) is a master regulator of brassinosteroid (BR)-regulated gene expression. BES1 together with BRASSINAZOLE-RESISTANT 1 (BZR1) drive activated or repressed expression of several genes, and have a prominent role in negative regulation of BR synthesis. Here, we report that BES1 interaction with TOPLESS (TPL), via its ERF-associated amphiphilic repression (EAR) motif, is essential for BES1-mediated control of organ boundary formation in the shoot apical meristem and the regulation of quiescent center (QC) cell division in roots. We show that TPL binds via BES1 to the promoters of the CUC3 and BRAVO targets and suppresses their expression. Ectopic expression of TPL leads to similar organ boundary defects and alterations in QC cell division rate to the bes1-d mutation, while bes1-d defects are suppressed by the dominant interfering protein encoded by tpl-1, with these effects respectively correlating with changes in CUC3 and BRAVO expression. Together, our data unveil a pivotal role of the co-repressor TPL in the shoot and root meristems, which relies on its interaction with BES1 and regulation of BES1 target gene expression.
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Affiliation(s)
- Ana Espinosa-Ruiz
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, Madrid E-28049, Spain
| | - Cristina Martínez
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, Madrid E-28049, Spain
| | - Miguel de Lucas
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, Madrid E-28049, Spain
| | - Norma Fàbregas
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona E-08193, Spain
| | - Nadja Bosch
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona E-08193, Spain
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona E-08193, Spain
| | - Salomé Prat
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, Madrid E-28049, Spain
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66
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Rosa M, Abraham-Juárez MJ, Lewis MW, Fonseca JP, Tian W, Ramirez V, Luan S, Pauly M, Hake S. The Maize MID-COMPLEMENTING ACTIVITY Homolog CELL NUMBER REGULATOR13/NARROW ODD DWARF Coordinates Organ Growth and Tissue Patterning. THE PLANT CELL 2017; 29:474-490. [PMID: 28254777 PMCID: PMC5385958 DOI: 10.1105/tpc.16.00878] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/13/2017] [Accepted: 02/27/2017] [Indexed: 05/07/2023]
Abstract
Organogenesis occurs through cell division, expansion, and differentiation. How these cellular processes are coordinated remains elusive. The maize (Zea mays) leaf provides a robust system to study cellular differentiation due to its distinct tissues and cell types. The narrow odd dwarf (nod) mutant displays defects at both the cellular and tissue level that increase in severity throughout growth. nod mutant leaves have reduced size due to fewer and smaller cells compared with the wild type. The juvenile-to-adult transition is delayed, and proximal distal-patterning is abnormal in this mutant. Differentiation of specialized cells such as those forming stomata and trichomes is incomplete. Analysis of nod-1 sectors suggests that NOD plays a cell-autonomous function in the leaf. We cloned nod positionally and found that it encodes CELL NUMBER REGULATOR13 (CNR13), the maize MID-COMPLEMENTING ACTIVITY homolog. CNR13/NOD is localized to the membrane and is enriched in dividing tissues. Transcriptome analysis of nod mutants revealed overrepresentation of cell wall, hormone metabolism, and defense gene categories. We propose that NOD coordinates cell activity in response to intrinsic and extrinsic cues.
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Affiliation(s)
- Marisa Rosa
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720
| | | | - Michael W Lewis
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720
| | - João Pedro Fonseca
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94143
| | - Wang Tian
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720
| | - Vicente Ramirez
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720
| | - Markus Pauly
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720
| | - Sarah Hake
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720
- Plant Gene Expression Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
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67
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Liang Z, Schnable JC. RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73. PLoS One 2016; 11:e0157942. [PMID: 27348435 PMCID: PMC4922647 DOI: 10.1371/journal.pone.0157942] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/07/2016] [Indexed: 12/23/2022] Open
Abstract
Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized genetic variation as a result of cross contamination of stocks, unintentional crossing, residual heterozygosity within original stocks, or de novo mutation. 27 public, large scale, RNA-seq datasets from 20 independent research groups around the world were used to assess variation within the maize (Zea mays ssp. mays) inbred B73, a four decade old variety which served as the reference genotype for the original maize genome sequencing project and is widely used in genetic, genomic, and phenotypic research. Several clearly distinct clades were identified among putatively B73 samples. A number of these clades were defined by the presence of clearly defined genomic blocks containing a haplotype which did not match the published B73 reference genome. The overall proportion of the maize genotype where multiple distinct haplotypes were observed across different research groups was approximately 2.3%. In some cases the relationship among B73 samples generated by different research groups recapitulated mentor/mentee relationships within the maize genetics community.
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Affiliation(s)
- Zhikai Liang
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - James C. Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States of America
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68
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Huang P, Brutnell TP. A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:91-9. [PMID: 27078208 DOI: 10.1016/j.pbi.2016.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/17/2016] [Accepted: 03/22/2016] [Indexed: 05/23/2023]
Abstract
C4 photosynthesis is used by only three percent of all flowering plants, but explains a quarter of global primary production, including some of the worlds' most important cereals and bioenergy grasses. Recent advances in our understanding of C4 development can be attributed to the application of comparative transcriptomics approaches that has been fueled by high throughput sequencing. Global surveys of gene expression conducted between different developmental stages or on phylogenetically closely related C3 and C4 species are providing new insights into C4 function, development and evolution. Importantly, through co-expression analysis and comparative genomics, these studies help define novel candidate genes that transcend traditional genetic screens. In this review, we briefly summarize the major findings from recent transcriptomic studies, compare and contrast these studies to summarize emerging consensus, and suggest new approaches to exploit the data. Finally, we suggest using Setaria viridis as a model system to relieve a major bottleneck in genetic studies of C4 photosynthesis, and discuss the challenges and new opportunities for future comparative transcriptomic studies.
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Affiliation(s)
- Pu Huang
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St Louis, MO 63132, USA
| | - Thomas P Brutnell
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St Louis, MO 63132, USA.
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69
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Freeling M, Scanlon MJ, Fowler JE. Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences. Curr Opin Genet Dev 2015; 35:110-8. [PMID: 26657818 DOI: 10.1016/j.gde.2015.11.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 12/11/2022]
Abstract
A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes. Subfunctionalization--the founding term of the Xfunctionalization lexicon--while not the general cause of differences in duplicate gene retention, becomes primary as the number of a gene's cis-regulatory sites increases. Balanced gene drive explains retention for the average gene. Both maintenance-of-balance and subfunctionalization drive gene content nonrandomly, and currently fall outside of our accepted Theory of Evolution. The 'typical' mutation encountered by a gene duplicate is not a neutral loss-of-function; dominant mutations (Muller's lexicon; these are not neutral) abound, and confound X functionalization terms like 'neofunctionalization'. Confusion of words may cause confusion of thought. As with many plants, fish tetraploidies provide a higher throughput surrogate-genetic method to infer function from human and other vertebrate ENCODE-like regulatory sites.
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Affiliation(s)
- Michael Freeling
- Department of Plant and Microbial Biology, Univ. California, Berkeley, CA 94720, United States.
| | - Michael J Scanlon
- Section of Plant Biology, Cornell University, Ithaca, NY 14853, United States
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
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70
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García-Cano E, Magori S, Sun Q, Ding Z, Lazarowitz SG, Citovsky V. Interaction of Arabidopsis Trihelix-Domain Transcription Factors VFP3 and VFP5 with Agrobacterium Virulence Protein VirF. PLoS One 2015; 10:e0142128. [PMID: 26571494 PMCID: PMC4646629 DOI: 10.1371/journal.pone.0142128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/16/2015] [Indexed: 02/01/2023] Open
Abstract
Agrobacterium is a natural genetic engineer of plants that exports several virulence proteins into host cells in order to take advantage of the cell machinery to facilitate transformation and support bacterial growth. One of these effectors is the F-box protein VirF, which presumably uses the host ubiquitin/proteasome system (UPS) to uncoat the packaging proteins from the invading bacterial T-DNA. By analogy to several other bacterial effectors, VirF most likely has several functions in the host cell and, therefore, several interacting partners among host proteins. Here we identify one such interactor, an Arabidopsis trihelix-domain transcription factor VFP3, and further show that its very close homolog VFP5 also interacted with VirF. Interestingly, interactions of VirF with either VFP3 or VFP5 did not activate the host UPS, suggesting that VirF might play other UPS-independent roles in bacterial infection. To better understand the potential scope of VFP3 function, we used RNAi to reduce expression of the VFP3 gene. Transcriptome profiling of these VFP3-silenced plants using high-throughput cDNA sequencing (RNA-seq) revealed that VFP3 substantially affected plant gene expression; specifically, 1,118 genes representing approximately 5% of all expressed genes were significantly either up- or down-regulated in the VFP3 RNAi line compared to wild-type Col-0 plants. Among the 507 up-regulated genes were genes implicated in the regulation of transcription, protein degradation, calcium signaling, and hormone metabolism, whereas the 611 down-regulated genes included those involved in redox regulation, light reactions of photosynthesis, and metabolism of lipids, amino acids, and cell wall. Overall, this pattern of changes in gene expression is characteristic of plants under stress. Thus, VFP3 likely plays an important role in controlling plant homeostasis.
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Affiliation(s)
- Elena García-Cano
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, New York, United States of America
| | - Shimpei Magori
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, New York, United States of America
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York, United States of America
| | - Zehong Ding
- Computational Biology Service Unit, Cornell University, Ithaca, New York, United States of America
| | - Sondra G. Lazarowitz
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, New York, United States of America
- * E-mail:
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71
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Abstract
The detailed analysis of leaf growth dynamics, when coupled with transcriptomic research, can facilitate the discovery of genes required for leaf elongation. Please see related Research article: http://www.genomebiology.com/2015/16/1/168
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Affiliation(s)
- Michael J Scanlon
- School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA.
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72
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Yu P, Eggert K, von Wirén N, Li C, Hochholdinger F. Cell Type-Specific Gene Expression Analyses by RNA Sequencing Reveal Local High Nitrate-Triggered Lateral Root Initiation in Shoot-Borne Roots of Maize by Modulating Auxin-Related Cell Cycle Regulation. PLANT PHYSIOLOGY 2015; 169:690-704. [PMID: 26198256 PMCID: PMC4577424 DOI: 10.1104/pp.15.00888] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 05/18/2023]
Abstract
Plants have evolved a unique plasticity of their root system architecture to flexibly exploit heterogeneously distributed mineral elements from soil. Local high concentrations of nitrate trigger lateral root initiation in adult shoot-borne roots of maize (Zea mays) by increasing the frequency of early divisions of phloem pole pericycle cells. Gene expression profiling revealed that, within 12 h of local high nitrate induction, cell cycle activators (cyclin-dependent kinases and cyclin B) were up-regulated, whereas repressors (Kip-related proteins) were down-regulated in the pericycle of shoot-borne roots. In parallel, a ubiquitin protein ligase S-Phase Kinase-Associated Protein1-cullin-F-box protein(S-Phase Kinase-Associated Protein 2B)-related proteasome pathway participated in cell cycle control. The division of pericycle cells was preceded by increased levels of free indole-3-acetic acid in the stele, resulting in DR5-red fluorescent protein-marked auxin response maxima at the phloem poles. Moreover, laser-capture microdissection-based gene expression analyses indicated that, at the same time, a significant local high nitrate induction of the monocot-specific PIN-FORMED9 gene in phloem pole cells modulated auxin efflux to pericycle cells. Time-dependent gene expression analysis further indicated that local high nitrate availability resulted in PIN-FORMED9-mediated auxin efflux and subsequent cell cycle activation, which culminated in the initiation of lateral root primordia. This study provides unique insights into how adult maize roots translate information on heterogeneous nutrient availability into targeted root developmental responses.
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Affiliation(s)
- Peng Yu
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
| | - Kai Eggert
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
| | - Nicolaus von Wirén
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
| | - Chunjian Li
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
| | - Frank Hochholdinger
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China (P.Y., C.L.);Division of Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany (P.Y., F.H.); andMolecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany (K.E., N.v.W.)
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73
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Differences in properties and proteomes of the midribs contribute to the size of the leaf angle in two near-isogenic maize lines. J Proteomics 2015; 128:113-22. [PMID: 26244907 DOI: 10.1016/j.jprot.2015.07.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/16/2015] [Accepted: 07/23/2015] [Indexed: 12/23/2022]
Abstract
The midrib of maize leaves provides the primary support for the blade and is largely associated with leaf angle size. To elucidate the role of the midrib in leaf angle formation, the maize line Shen137 (larger leaf angle) and a near isogenic line (NIL, smaller leaf angle) were used in the present study. The results of the analysis showed that both the puncture forces and proximal collenchyma number of the midribs of the first and second leaves above the ear were higher in NIL than in Shen137. Comparative proteomic analysis was performed to reveal protein profile differences in the midribs of the 5th, 10th and 19th newly expanded leaves between Shen137 and NIL. Quantitative analysis of 24 identified midrib proteins indicated that the maximum changes in abundance of 22 proteins between Shen137 and NIL appeared at the 10th leaf stage, of which phosphoglycerate kinase, adenosine kinase, fructose-bisphosphate aldolase and adenylate kinase were implicated in glycometabolism. Thus, glycometabolism might be associated with leaf angle formation and the physical and mechanical properties of the midribs. These results provide insight into the mechanism underlying maize leaf angle formation.
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74
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Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proc Natl Acad Sci U S A 2015; 112:8529-36. [PMID: 26124102 DOI: 10.1073/pnas.1424031112] [Citation(s) in RCA: 510] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The world's crop productivity is stagnating whereas population growth, rising affluence, and mandates for biofuels put increasing demands on agriculture. Meanwhile, demand for increasing cropland competes with equally crucial global sustainability and environmental protection needs. Addressing this looming agricultural crisis will be one of our greatest scientific challenges in the coming decades, and success will require substantial improvements at many levels. We assert that increasing the efficiency and productivity of photosynthesis in crop plants will be essential if this grand challenge is to be met. Here, we explore an array of prospective redesigns of plant systems at various scales, all aimed at increasing crop yields through improved photosynthetic efficiency and performance. Prospects range from straightforward alterations, already supported by preliminary evidence of feasibility, to substantial redesigns that are currently only conceptual, but that may be enabled by new developments in synthetic biology. Although some proposed redesigns are certain to face obstacles that will require alternate routes, the efforts should lead to new discoveries and technical advances with important impacts on the global problem of crop productivity and bioenergy production.
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75
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Sluis A, Hake S. Organogenesis in plants: initiation and elaboration of leaves. Trends Genet 2015; 31:300-6. [PMID: 26003219 DOI: 10.1016/j.tig.2015.04.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 11/24/2022]
Abstract
Plant organs initiate from meristems and grow into diverse forms. After initiation, organs enter a morphological phase where they develop their shape, followed by differentiation into mature tissue. Investigations into these processes have revealed numerous factors necessary for proper development, including transcription factors such as the KNOTTED-LIKE HOMEOBOX (KNOX) genes, the hormone auxin, and miRNAs. Importantly, these factors have been shown to play a role in organogenesis in various diverse model species, revealing both deep conservation of regulatory strategies and evolutionary novelties that led to new plant forms. We review here recent work in understanding the regulation of organogenesis and in particular leaf formation, highlighting how regulatory modules are often redeployed in different organ types and stages of development to achieve diverse forms through the balance of growth and differentiation.
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Affiliation(s)
- Aaron Sluis
- Plant Gene Expression Center, UC Berkeley and USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
| | - Sarah Hake
- Plant Gene Expression Center, UC Berkeley and USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
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76
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Hepworth SR, Pautot VA. Beyond the Divide: Boundaries for Patterning and Stem Cell Regulation in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1052. [PMID: 26697027 PMCID: PMC4673312 DOI: 10.3389/fpls.2015.01052] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/12/2015] [Indexed: 05/04/2023]
Abstract
The initiation of plant lateral organs from the shoot apical meristem (SAM) is closely associated with the formation of specialized domains of restricted growth known as the boundaries. These zones are required in separating the meristem from the growing primordia or adjacent organs but play a much broader role in regulating stem cell activity and shoot patterning. Studies have revealed a network of genes and hormone pathways that establish and maintain boundaries between the SAM and leaves. Recruitment of these pathways is shown to underlie a variety of processes during the reproductive phase including axillary meristems production, flower patterning, fruit development, and organ abscission. This review summarizes the role of conserved gene modules in patterning boundaries throughout the life cycle.
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Affiliation(s)
- Shelley R. Hepworth
- Department of Biology, Institute of Biochemistry, Carleton University, OttawaON, Canada
- *Correspondence: Shelley R. Hepworth, ; Véronique A. Pautot,
| | - Véronique A. Pautot
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
- *Correspondence: Shelley R. Hepworth, ; Véronique A. Pautot,
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