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Machado R, Muchut SE, Dezar C, Reutemann AG, Alesso CA, Günthardt MM, Vegetti AC, Vogel J, Uberti Manassero NG. BdRCN4, a Brachypodium distachyon TFL1 homologue, is involved in regulation of apical meristem fate. PLANT MOLECULAR BIOLOGY 2024; 114:81. [PMID: 38940986 DOI: 10.1007/s11103-024-01467-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 05/13/2024] [Indexed: 06/29/2024]
Abstract
In higher plants, the shift from vegetative to reproductive development is governed by complex interplay of internal and external signals. TERMINALFLOWER1 (TFL1) plays a crucial role in the regulation of flowering time and inflorescence architecture in Arabidopsis thaliana. This study aimed to explore the function of BdRCN4, a homolog of TFL1 in Brachypodium distachyon, through functional analyses in mutant and transgenic plants. The results revealed that overexpression of BdRCN4 in B. distachyon leads to an extended vegetative phase and reduced production of spikelets. Similar results were found in A. thaliana, where constitutive expression of BdRCN4 promoted a delay in flowering time, followed by the development of hypervegetative shoots, with no flowers or siliques produced. Our results suggest that BdRCN4 acts as a flowering repressor analogous to TFL1, negatively regulating AP1, but no LFY expression. To further validate this hypothesis, a 35S::LFY-GR co-transformation approach on 35::BdRCN4 lines was performed. Remarkably, AP1 expression levels and flower formation were restored to normal in co-transformed plants when treated with dexamethasone. Although further molecular studies will be necessary, the evidence in B. distachyon support the idea that a balance between LFY and BdRCN4/TFL1 seems to be essential for activating AP1 expression and initiating floral organ identity gene expression. This study also demonstrates interesting conservation through the molecular pathways that regulate flowering meristem transition and identity across the evolution of monocot and dicot plants.
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Affiliation(s)
- Rodrigo Machado
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Concordia, Santa Fe, Argentina
| | - Sebastián Elias Muchut
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Santa Fe, 3080, Argentina
| | - Carlos Dezar
- ICiAgro Litoral, FCA, UNL-CONICET, Esperanza, Santa Fe, 3080, Argentina
| | | | | | - María Margarita Günthardt
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Santa Fe, 3080, Argentina
| | | | - John Vogel
- DOE Joint Genome Institute, Walnut Creek, CA, 94595, USA
| | - Nora G Uberti Manassero
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Santa Fe, 3080, Argentina.
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2
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Thieme M, Minadakis N, Himber C, Keller B, Xu W, Rutowicz K, Matteoli C, Böhrer M, Rymen B, Laudencia-Chingcuanco D, Vogel JP, Sibout R, Stritt C, Blevins T, Roulin AC. Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon. PLoS Genet 2024; 20:e1011200. [PMID: 38470914 PMCID: PMC10959353 DOI: 10.1371/journal.pgen.1011200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/22/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Long terminal repeat retrotransposons (LTR-RTs) are powerful mutagens regarded as a major source of genetic novelty and important drivers of evolution. Yet, the uncontrolled and potentially selfish proliferation of LTR-RTs can lead to deleterious mutations and genome instability, with large fitness costs for their host. While population genomics data suggest that an ongoing LTR-RT mobility is common in many species, the understanding of their dual role in evolution is limited. Here, we harness the genetic diversity of 320 sequenced natural accessions of the Mediterranean grass Brachypodium distachyon to characterize how genetic and environmental factors influence plant LTR-RT dynamics in the wild. When combining a coverage-based approach to estimate global LTR-RT copy number variations with mobilome-sequencing of nine accessions exposed to eight different stresses, we find little evidence for a major role of environmental factors in LTR-RT accumulations in B. distachyon natural accessions. Instead, we show that loss of RNA polymerase IV (Pol IV), which mediates RNA-directed DNA methylation in plants, results in high transcriptional and transpositional activities of RLC_BdisC024 (HOPPLA) LTR-RT family elements, and that these effects are not stress-specific. This work supports findings indicating an ongoing mobility in B. distachyon and reveals that host RNA-directed DNA methylation rather than environmental factors controls their mobility in this wild grass model.
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Affiliation(s)
- Michael Thieme
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Christophe Himber
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Bettina Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Wenbo Xu
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Kinga Rutowicz
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Calvin Matteoli
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Marcel Böhrer
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Bart Rymen
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Debbie Laudencia-Chingcuanco
- United States Department of Agriculture Agricultural Research Service Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Richard Sibout
- Institut National de la Recherche Agronomique Unité BIA- 1268 Biopolymères Interactions Assemblages Equipe Paroi Végétale et Polymères Pariétaux (PVPP), Nantes, France
| | - Christoph Stritt
- Swiss Tropical and Public Health Institute (Swiss TPH), Allschwil, Switzerland
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Anne C. Roulin
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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3
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Hsiao PY, Zeng CY, Shih MC. Group VII ethylene response factors forming distinct regulatory loops mediate submergence responses. PLANT PHYSIOLOGY 2024; 194:1745-1763. [PMID: 37837603 PMCID: PMC10904320 DOI: 10.1093/plphys/kiad547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/16/2023]
Abstract
Group VII ethylene response factors (ERFVIIs), whose stability is oxygen concentration-dependent, play key roles in regulating hypoxia response genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) during submergence. To understand the evolution of flooding tolerance in cereal crops, we evaluated whether Brachypodium distachyon ERFVII genes (BdERFVIIs) are related to submergence tolerance. We found that three BdERFVIIs, BdERF108, BdERF018, and BdERF961, form a feedback regulatory loop to mediate downstream responses. BdERF108 and BdERF018 activated the expression of BdERF961 and PHYTOGLOBIN 1 (PGB1), which promoted nitric oxide turnover and preserved ERFVII protein stability. The activation of PGB1 was subsequently counteracted by increased BdERF961 accumulation through negative feedback regulation. Interestingly, we found that OsERF67, the orthologue of BdERF961 in rice, activated PHYTOGLOBIN (OsHB2) expression and formed distinct regulatory loops during submergence. Overall, the divergent regulatory mechanisms exhibited by orthologs collectively offer perspectives for the development of submergence-tolerant crops.
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Affiliation(s)
- Pao-Yuan Hsiao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Cyong-Yu Zeng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
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Lehman TA, Rosas MA, Brew-Appiah RAT, Solanki S, York ZB, Dannay R, Wu Y, Roalson EH, Zheng P, Main D, Baskin TI, Sanguinet KA. BUZZ: an essential gene for postinitiation root hair growth and a mediator of root architecture in Brachypodium distachyon. THE NEW PHYTOLOGIST 2023. [PMID: 37421201 DOI: 10.1111/nph.19079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/10/2023] [Indexed: 07/10/2023]
Abstract
Here, we discover a player in root development. Recovered from a forward-genetic screen in Brachypodium distachyon, the buzz mutant initiates root hairs but they fail to elongate. In addition, buzz roots grow twice as fast as wild-type roots. Also, lateral roots show increased sensitivity to nitrate, whereas primary roots are less sensitive to nitrate. Using whole-genome resequencing, we identified the causal single nucleotide polymorphism as occurring in a conserved but previously uncharacterized cyclin-dependent kinase (CDK)-like gene. The buzz mutant phenotypes are rescued by the wild-type B. distachyon BUZZ coding sequence and by an apparent homolog in Arabidopsis thaliana. Moreover, T-DNA mutants in A. thaliana BUZZ have shorter root hairs. BUZZ mRNA localizes to epidermal cells and develops root hairs and, in the latter, partially colocalizes with the NRT1.1A nitrate transporter. Based on qPCR and RNA-Seq, buzz overexpresses ROOT HAIRLESS LIKE SIX-1 and -2 and misregulates genes related to hormone signaling, RNA processing, cytoskeletal, and cell wall organization, and to the assimilation of nitrate. Overall, these data demonstrate that BUZZ is required for tip growth after root hair initiation and root architectural responses to nitrate.
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Affiliation(s)
- Thiel A Lehman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Miguel A Rosas
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
| | - Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Zara B York
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Rachel Dannay
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Tobias I Baskin
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
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Medina-Chávez L, Camacho C, Martínez-Rodríguez JA, Barrera-Figueroa BE, Nagel DH, Juntawong P, Peña-Castro JM. Submergence Stress Alters the Expression of Clock Genes and Configures New Zeniths and Expression of Outputs in Brachypodium distachyon. Int J Mol Sci 2023; 24:ijms24108555. [PMID: 37239900 DOI: 10.3390/ijms24108555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/04/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Plant networks of oscillating genes coordinate internal processes with external cues, contributing to increased fitness. We hypothesized that the response to submergence stress may dynamically change during different times of the day. In this work, we determined the transcriptome (RNA sequencing) of the model monocotyledonous plant, Brachypodium distachyon, during a day of submergence stress, low light, and normal growth. Two ecotypes of differential tolerance, Bd21 (sensitive) and Bd21-3 (tolerant), were included. We submerged 15-day-old plants under a long-day diurnal cycle (16 h light/8 h dark) and collected samples after 8 h of submergence at ZT0 (dawn), ZT8 (midday), ZT16 (dusk), ZT20 (midnight), and ZT24 (dawn). Rhythmic processes were enriched both with up- and down-regulated genes, and clustering highlighted that the morning and daytime oscillator components (PRRs) show peak expression in the night, and a decrease in the amplitude of the clock genes (GI, LHY, RVE) was observed. Outputs included photosynthesis-related genes losing their known rhythmic expression. Up-regulated genes included oscillating suppressors of growth, hormone-related genes with new late zeniths (e.g., JAZ1, ZEP), and mitochondrial and carbohydrate signaling genes with shifted zeniths. The results highlighted genes up-regulated in the tolerant ecotype such as METALLOTHIONEIN3 and ATPase INHIBITOR FACTOR. Finally, we show by luciferase assays that Arabidopsis thaliana clock genes are also altered by submergence changing their amplitude and phase. This study can guide the research of chronocultural strategies and diurnal-associated tolerance mechanisms.
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Affiliation(s)
- Lucisabel Medina-Chávez
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
- Programa de Doctorado en Biotecnología, División de Estudios de Posgrado, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
| | - Christian Camacho
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Jorge Arturo Martínez-Rodríguez
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
| | - Blanca Estela Barrera-Figueroa
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
| | - Dawn H Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Piyada Juntawong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Julián Mario Peña-Castro
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico
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6
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Cell Wall Glycan Changes in Different Brachypodium Tissues Give Insights into Monocot Biomass. FERMENTATION 2023. [DOI: 10.3390/fermentation9010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The annual temperate grass Brachypodium distachyon has become a model system for monocot biomass crops and for understanding lignocellulosic recalcitrance to employ better saccharification and fermentation approaches. It is a monocot plant used to study the grass cell walls that differ from the cell walls of dicot plants such as the eudicot model Arabidopsis. The B. distachyon cell wall is predominantly composed of cellulose, arabinoxylans, and mixed-linkage glucans, and it resembles the cell walls of other field grasses. It has a vascular bundle anatomy similar to C3 grasses. These features make Brachypodium an ideal model to study cell walls. Cell walls are composed of polymers with complex structures that vary between cell types and at different developmental stages. Antibodies that recognize specific cell wall components are currently one of the most effective and specific molecular probes to determine the location and distribution of polymers in plant cell walls in situ. Here, we investigated the glycan distribution in the cell walls of the root and leaf tissues of Brachypodium by employing cell-wall-directed antibodies against diverse glycan epitopes. There are distinct differences in the presence of the epitopes between the root and leaf tissues as well as in the cell type level, which gives insights into monocot biomass.
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Watson-Lazowski A, Raven E, Feike D, Hill L, Barclay JE, Smith AM, Seung D. Loss of PROTEIN TARGETING TO STARCH 2 has variable effects on starch synthesis across organs and species. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6367-6379. [PMID: 35716106 PMCID: PMC9578351 DOI: 10.1093/jxb/erac268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/15/2022] [Indexed: 05/12/2023]
Abstract
Recent work has identified several proteins involved in starch granule initiation, the first step of starch synthesis. However, the degree of conservation in the granule initiation process remains poorly understood, especially among grass species differing in patterns of carbohydrate turnover in leaves, and granule morphology in the endosperm. We therefore compared mutant phenotypes of Hordeum vulgare (barley), Triticum turgidum (durum wheat), and Brachypodium distachyon defective in PROTEIN TARGETING TO STARCH 2 (PTST2), a key granule initiation protein. We report striking differences across species and organs. Loss of PTST2 from leaves resulted in fewer, larger starch granules per chloroplast and normal starch content in wheat, fewer granules per chloroplast and lower starch content in barley, and almost complete loss of starch in Brachypodium. The loss of starch in Brachypodium leaves was accompanied by high levels of ADP-glucose and detrimental effects on growth and physiology. Additionally, we found that loss of PTST2 increased granule initiation in Brachypodium amyloplasts, resulting in abnormal compound granule formation throughout the seed. These findings suggest that the importance of PTST2 varies greatly with the genetic and developmental background and inform the extent to which the gene can be targeted to improve starch in crops.
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Affiliation(s)
| | - Emma Raven
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Doreen Feike
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Lionel Hill
- John Innes Centre, Norwich Research Park, Norwich, UK
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Sharma M, Charron JB, Rani M, Jabaji S. Bacillus velezensis strain B26 modulates the inflorescence and root architecture of Brachypodium distachyon via hormone homeostasis. Sci Rep 2022; 12:7951. [PMID: 35562386 PMCID: PMC9106653 DOI: 10.1038/s41598-022-12026-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) influence plant health. However, the genotypic variations in host organisms affect their response to PGPR. To understand the genotypic effect, we screened four diverse B. distachyon genotypes at varying growth stages for their ability to be colonized by B. velezensis strain B26. We reasoned that B26 may have an impact on the phenological growth stages of B. distachyon genotypes. Phenotypic data suggested the role of B26 in increasing the number of awns and root weight in wild type genotypes and overexpressing transgenic lines. Thus, we characterized the expression patterns of flowering pathway genes in inoculated plants and found that strain B26 modulates the transcript abundance of flowering genes. An increased root volume of inoculated plants was estimated by CT-scanning which suggests the role of B26 in altering the root architecture. B26 also modulated plant hormone homeostasis. A differential response was observed in the transcript abundance of auxin and gibberellins biosynthesis genes in inoculated roots. Our results reveal that B. distachyon plant genotype is an essential determinant of whether a PGPR provides benefit or harm to the host and shed new insight into the involvement of B. velezensis in the expression of flowering genes.
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Affiliation(s)
- Meha Sharma
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada
| | - Jean-Benoit Charron
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada
| | - Mamta Rani
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada
| | - Suha Jabaji
- Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada.
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Raissig MT, Woods DP. The wild grass Brachypodium distachyon as a developmental model system. Curr Top Dev Biol 2022; 147:33-71. [PMID: 35337454 DOI: 10.1016/bs.ctdb.2021.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The arrival of cheap and high-throughput sequencing paired with efficient gene editing technologies allows us to use non-traditional model systems and mechanistically approach biological phenomena beyond what was conceivable just a decade ago. Venturing into different model systems enables us to explore for example clade-specific environmental responses to changing climates or the genetics and development of clade-specific organs, tissues and cell types. We-both early career researchers working with the wild grass model Brachypodium distachyon-want to use this review to (1) highlight why we think B. distachyon is a fantastic grass developmental model system, (2) summarize the tools and resources that have enabled discoveries made in B. distachyon, and (3) discuss a handful of developmental biology vignettes made possible by using B. distachyon as a model system. Finally, we want to conclude by (4) relating our personal stories with this emerging model system and (5) share what we think is important to consider before starting work with an emerging model system.
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Affiliation(s)
- Michael T Raissig
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany; Institute of Plant Sciences, University of Bern, Bern, Switzerland.
| | - Daniel P Woods
- Department of Plant Sciences, University of California, Davis, CA, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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10
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Zhang D, Spiegelhalder RP, Abrash EB, Nunes TDG, Hidalgo I, Anleu Gil MX, Jesenofsky B, Lindner H, Bergmann DC, Raissig MT. Opposite polarity programs regulate asymmetric subsidiary cell divisions in grasses. eLife 2022; 11:79913. [PMID: 36537077 PMCID: PMC9767456 DOI: 10.7554/elife.79913] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Grass stomata recruit lateral subsidiary cells (SCs), which are key to the unique stomatal morphology and the efficient plant-atmosphere gas exchange in grasses. Subsidiary mother cells (SMCs) strongly polarise before an asymmetric division forms a SC. Yet apart from a proximal polarity module that includes PANGLOSS1 (PAN1) and guides nuclear migration, little is known regarding the developmental processes that form SCs. Here, we used comparative transcriptomics of developing wild-type and SC-less bdmute leaves in the genetic model grass Brachypodium distachyon to identify novel factors involved in SC formation. This approach revealed BdPOLAR, which forms a novel, distal polarity domain in SMCs that is opposite to the proximal PAN1 domain. Both polarity domains are required for the formative SC division yet exhibit various roles in guiding pre-mitotic nuclear migration and SMC division plane orientation, respectively. Nonetheless, the domains are linked as the proximal domain controls polarisation of the distal domain. In summary, we identified two opposing polarity domains that coordinate the SC division, a process crucial for grass stomatal physiology.
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Affiliation(s)
- Dan Zhang
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | | | - Emily B Abrash
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Tiago DG Nunes
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Inés Hidalgo
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | | | - Barbara Jesenofsky
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Heike Lindner
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany,Institute of Plant Sciences, University of BernBernSwitzerland
| | - Dominique C Bergmann
- Department of Biology, Stanford UniversityStanfordUnited States,Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Michael T Raissig
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany,Institute of Plant Sciences, University of BernBernSwitzerland
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11
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Della Coletta R, Lavell AA, Garvin DF. A Homolog of the Arabidopsis TIME FOR COFFEE Gene Is Involved in Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1298-1306. [PMID: 34340534 DOI: 10.1094/mpmi-06-21-0137-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plants resist infection by pathogens using both preexisting barriers and inducible defense responses. Inducible responses are governed in a complex manner by various hormone signaling pathways. The relative contribution of hormone signaling pathways to nonhost resistance to pathogens is not well understood. In this study, we examined the molecular basis of disrupted nonhost resistance to the fungal species Puccinia graminis, which causes stem rust of wheat, in an induced mutant of the model grass Brachypodium distachyon. Through bioinformatic analysis, a 1-bp deletion in the mutant genotype was identified that introduces a premature stop codon in the gene Bradi1g24100, which is a homolog of the Arabidopsis thaliana gene TIME FOR COFFEE (TIC). In Arabidopsis, TIC is central to the regulation of the circadian clock and plays a crucial role in jasmonate signaling by attenuating levels of the transcription factor protein MYC2, and its mutational disruption results in enhanced susceptibility to the hemibiotroph Pseudomonas syringae. Our similar finding for an obligate biotroph suggests that the biochemical role of TIC in mediating disease resistance to biotrophs is conserved in grasses, and that the correct modulation of jasmonate signaling during infection by Puccinia graminis may be essential for nonhost resistance to wheat stem rust in B. distachyon.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, DF, Brazil
| | - Anastasiya A Lavell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - David F Garvin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN 55108, U.S.A
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12
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Comparative Hessian Fly Larval Transcriptomics Provides Novel Insight into Host and Nonhost Resistance. Int J Mol Sci 2021; 22:ijms222111498. [PMID: 34768928 PMCID: PMC8583952 DOI: 10.3390/ijms222111498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The Hessian fly is a destructive pest of wheat. Employing additional molecular strategies can complement wheat's native insect resistance. However, this requires functional characterization of Hessian-fly-responsive genes, which is challenging because of wheat genome complexity. The diploid Brachypodium distachyon (Bd) exhibits nonhost resistance to Hessian fly and displays phenotypic/molecular responses intermediate between resistant and susceptible host wheat, offering a surrogate genome for gene characterization. Here, we compared the transcriptomes of Biotype L larvae residing on resistant/susceptible wheat, and nonhost Bd plants. Larvae from susceptible wheat and nonhost Bd plants revealed similar molecular responses that were distinct from avirulent larval responses on resistant wheat. Secreted salivary gland proteins were strongly up-regulated in all larvae. Genes from various biological pathways and molecular processes were up-regulated in larvae from both susceptible wheat and nonhost Bd plants. However, Bd larval expression levels were intermediate between larvae from susceptible and resistant wheat. Most genes were down-regulated or unchanged in avirulent larvae, correlating with their inability to establish feeding sites and dying within 4-5 days after egg-hatch. Decreased gene expression in Bd larvae, compared to ones on susceptible wheat, potentially led to developmentally delayed 2nd-instars, followed by eventually succumbing to nonhost resistance defense mechanisms.
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13
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Yang X, Hill KA, Austin RS, Tian L. Differential Gene Expression of Brachypodium distachyon Roots Colonized by Gluconacetobacter diazotrophicus and the Role of BdCESA8 in the Colonization. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1143-1156. [PMID: 34709058 DOI: 10.1094/mpmi-06-20-0170-r] [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] [Indexed: 06/13/2023]
Abstract
Alternatives to synthetic nitrogen fertilizer are needed to reduce the costs of crop production and offset environmental damage. Nitrogen-fixing bacterium Gluconacetobacter diazotrophicus has been proposed as a possible biofertilizer for monocot crop production. However, the colonization of G. diazotrophicus in most monocot crops is limited and deep understanding of the response of host plants to G. diazotrophicus colonization is still lacking. In this study, the molecular response of the monocot plant model Brachypodium distachyon was studied during G. diazotrophicus root colonization. The gene expression profiles of B. distachyon root tissues colonized by G. diazotrophicus were generated via next-generation RNA sequencing, and investigated through gene ontology and metabolic pathway analysis. The RNA sequencing results indicated that Brachypodium is actively involved in G. diazotrophicus colonization via cell wall synthesis. Jasmonic acid, ethylene, gibberellin biosynthesis. nitrogen assimilation, and primary and secondary metabolite pathways are also modulated to accommodate and control the extent of G. diazotrophicus colonization. Cellulose synthesis is significantly downregulated during colonization. The loss of function mutant for Brachypodium cellulose synthase 8 (BdCESA8) showed decreased cellulose content in xylem and increased resistance to G. diazotrophicus colonization. This result suggested that the cellulose synthesis of the secondary cell wall is involved in G. diazotrophicus colonization. The results of this study provide insights for future research in regard to gene manipulation for efficient colonization of nitrogen-fixing bacteria in Brachypodium and monocot crops.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Xuan Yang
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Kathleen A Hill
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Ryan S Austin
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
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14
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Smith RA, Cass CL, Petrik DL, Padmakshan D, Ralph J, Sedbrook JC, Karlen SD. Stacking AsFMT overexpression with BdPMT loss of function enhances monolignol ferulate production in Brachypodium distachyon. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1878-1886. [PMID: 33949064 PMCID: PMC8428837 DOI: 10.1111/pbi.13606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
To what degree can the lignin subunits in a monocot be derived from monolignol ferulate (ML-FA) conjugates? This simple question comes with a complex set of variables. Three potential requirements for optimizing ML-FA production are as follows: (1) The presence of an active FERULOYL-CoA MONOLIGNOL TRANSFERASE (FMT) enzyme throughout monolignol production; (2) Suppression or elimination of enzymatic pathways competing for monolignols and intermediates during lignin biosynthesis; and (3) Exclusion of alternative phenolic compounds that participate in lignification. A 16-fold increase in lignin-bound ML-FA incorporation was observed by introducing an AsFMT gene into Brachypodium distachyon. On its own, knocking out the native p-COUMAROYL-CoA MONOLIGNOL TRANSFERASE (BdPMT) pathway that competes for monolignols and the p-coumaroyl-CoA intermediate did not change ML-FA incorporation, nor did partial loss of CINNAMOYL-CoA REDUCTASE1 (CCR1) function, which reduced metabolic flux to monolignols. However, stacking AsFMT into the Bdpmt-1 mutant resulted in a 32-fold increase in ML-FA incorporation into lignin over the wild-type level.
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Affiliation(s)
- Rebecca A. Smith
- U.S. Department of Energy Great Lakes Bioenergy Research Center and the Department of BiochemistryWisconsin Energy InstituteUniversity of WisconsinMadisonWIUSA
| | - Cynthia L. Cass
- School of Biological SciencesIllinois State UniversityNormalILUSA
- U.S. Department of Energy Great Lakes Bioenergy Research CenterMadisonWIUSA
| | - Deborah L. Petrik
- School of Biological SciencesIllinois State UniversityNormalILUSA
- U.S. Department of Energy Great Lakes Bioenergy Research CenterMadisonWIUSA
- Department of BiologyNortheastern State UniversityTahlequahOKUSA
| | - Dharshana Padmakshan
- U.S. Department of Energy Great Lakes Bioenergy Research Center and the Department of BiochemistryWisconsin Energy InstituteUniversity of WisconsinMadisonWIUSA
| | - John Ralph
- U.S. Department of Energy Great Lakes Bioenergy Research Center and the Department of BiochemistryWisconsin Energy InstituteUniversity of WisconsinMadisonWIUSA
| | - John C. Sedbrook
- School of Biological SciencesIllinois State UniversityNormalILUSA
- U.S. Department of Energy Great Lakes Bioenergy Research CenterMadisonWIUSA
| | - Steven D. Karlen
- U.S. Department of Energy Great Lakes Bioenergy Research Center and the Department of BiochemistryWisconsin Energy InstituteUniversity of WisconsinMadisonWIUSA
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15
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Henningsen EC, Omidvar V, Della Coletta R, Michno JM, Gilbert E, Li F, Miller ME, Myers CL, Gordon SP, Vogel JP, Steffenson BJ, Kianian SF, Hirsch CD, Figueroa M. Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:657796. [PMID: 33968112 PMCID: PMC8097158 DOI: 10.3389/fpls.2021.657796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 05/30/2023]
Abstract
Wheat stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is a global threat to wheat production. Fast evolving populations of Pgt limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with Pgt infection in susceptible and resistant Triticum aestivum genotypes as well as the non-host Brachypodium distachyon. We targeted our analysis to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and report several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes.
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Affiliation(s)
- Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Vahid Omidvar
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Jean-Michel Michno
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
| | - Erin Gilbert
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Chad L. Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | | | - John P. Vogel
- Joint Genome Institute, Walnut Creek, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, United States
| | - Cory D. Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
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16
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Bain M, van de Meene A, Costa R, Doblin MS. Characterisation of Cellulose Synthase Like F6 ( CslF6) Mutants Shows Altered Carbon Metabolism in β-D-(1,3;1,4)-Glucan Deficient Grain in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2021; 11:602850. [PMID: 33505412 PMCID: PMC7829222 DOI: 10.3389/fpls.2020.602850] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Brachypodium distachyon is a small, fast growing grass species in the Pooideae subfamily that has become established as a model for other temperate cereals of agricultural significance, such as barley (Hordeum vulgare) and wheat (Triticum aestivum). The unusually high content in whole grains of β-D-(1,3;1,4)-glucan or mixed linkage glucan (MLG), considered a valuable dietary fibre due to its increased solubility in water compared with cellulose, makes B. distachyon an attractive model for these polysaccharides. The carbohydrate composition of grain in B. distachyon is interesting not only in understanding the synthesis of MLG, but more broadly in the mechanism(s) of carbon partitioning in cereal grains. Several mutants in the major MLG synthase, cellulose synthase like (CSL) F6, were identified in a screen of a TILLING population that show a loss of function in vitro. Surprisingly, loss of cslf6 synthase capacity appears to have a severe impact on survival, growth, and development in B. distachyon in contrast to equivalent mutants in barley and rice. One mutant, A656T, which showed milder growth impacts in heterozygotes shows a 21% (w/w) reduction in average grain MLG and more than doubling of starch compared with wildtype. The endosperm architecture of grains with the A656T mutation is altered, with a reduction in wall thickness and increased deposition of starch in larger granules than typical of wildtype B. distachyon. Together these changes demonstrate an alteration in the carbon storage of cslf6 mutant grains in response to reduced MLG synthase capacity and a possible cross-regulation with starch synthesis which should be a focus in future work in composition of these grains. The consequences of these findings for the use of B. distachyon as a model species for understanding MLG synthesis, and more broadly the implications for improving the nutritional value of cereal grains through alteration of soluble dietary fibre content are discussed.
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Affiliation(s)
- Melissa Bain
- Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, The School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Allison van de Meene
- Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, The School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Rafael Costa
- Institute of Plant Sciences Paris-Saclay (IPS2), Centre National de la Recherche Scientifique (CNRS), L’Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), Univ Evry, Université Paris-Saclay, Orsay, France
- Centre National de la Recherche Scientifique (CNRS), L’Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE), Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, Orsay, France
| | - Monika S. Doblin
- Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, The School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Department of Animal Plant and Soil Sciences, La Trobe Institute for Agriculture and Food (LIAF), La Trobe University, Melbourne, VIC, Australia
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17
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Sharma M, Saleh D, Charron JB, Jabaji S. A Crosstalk Between Brachypodium Root Exudates, Organic Acids, and Bacillus velezensis B26, a Growth Promoting Bacterium. Front Microbiol 2020; 11:575578. [PMID: 33123106 PMCID: PMC7573104 DOI: 10.3389/fmicb.2020.575578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) are associated with plant roots and use organic compounds that are secreted from root exudates as food and energy source. Root exudates can chemoattract and help bacteria to colonize the surface of plant roots by inducing chemotactic responses of rhizospheric bacteria. In this study, we show that root colonization of Brachypodium distachyon by Bacillus velezensis strain B26 depends on several factors. These include root exudates, organic acids, and their biosynthetic genes, chemotaxis, biofilm formation and the induction of biofilm encoding genes. Analysis of root exudates by GC-MS identified five intermediates of the TCA cycle; malic, fumaric, citric, succinic, oxaloacetic acids, and were subsequently evaluated. The strongest chemotactic responses were induced by malic, succinic, citric, and fumaric acids. In comparison, the biofilm formation was induced by all organic acids with maximal induction by citric acid. Relative to the control, the individual organic acids, succinic and citric acids activated the epsD gene related to EPS biofilm, and also the genes encoding membrane protein (yqXM) and hydrophobin component (bslA) of the biofilm of strain B26. Whereas epsA and epsB genes were highly induced genes by succinic acid. Similarly, concentrated exudates released from inoculated roots after 48 h post-inoculation also induced all biofilm-associated genes. The addition of strain B26 to wild type and to icdh mutant line led to a slight induction but not biologically significant relative to their respective controls. Thus, B26 has no effect on the expression of the ICDH gene, both in the wild type and the mutant backgrounds. Our results indicate that root exudates and individual organic acids play an important role in selective recruitment and colonization of PGPR and inducing biofilm. The current study increases the understanding of molecular mechanisms behind biofilm induction by organic acids.
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Affiliation(s)
- Meha Sharma
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Dina Saleh
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Jean-Benoit Charron
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Suha Jabaji
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
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18
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Tripathi RK, Overbeek W, Singh J. Global analysis of SBP gene family in Brachypodium distachyon reveals its association with spike development. Sci Rep 2020; 10:15032. [PMID: 32929136 PMCID: PMC7490389 DOI: 10.1038/s41598-020-72005-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
SQUAMOSA-promoter binding like proteins (SBPs/SPLs) are plant specific transcription factors targeted by miR156 and involved in various biological pathways, playing multi-faceted developmental roles. This gene family is not well characterized in Brachypodium. We identified a total of 18 SBP genes in B. distachyon genome. Phylogenetic analysis revealed that SBP gene family in Brachypodium expanded through large scale duplication. A total of 10 BdSBP genes were identified as targets of miR156. Transcript cleavage analysis of selected BdSBPs by miR156 confirmed their antagonistic connection. Alternative splicing was observed playing an important role in BdSBPs and miR156 interaction. Characterization of T-DNA Bdsbp9 mutant showed reduced plant growth and spike length, reflecting its involvement in the spike development. Expression of a majority of BdSBPs elevated during spikelet initiation. Specifically, BdSBP1 and BdSBP3 differentially expressed in response to vernalization. Differential transcript abundance of BdSBP1, BdSBP3, BdSBP8, BdSBP9, BdSBP14, BdSBP18 and BdSBP23 genes was observed during the spike development under high temperature. Co-expression network, protein-protein interaction and biological pathway analysis indicate that BdSBP genes mainly regulate transcription, hormone, RNA and transport pathways. Our work reveals the multi-layered control of SBP genes and demonstrates their association with spike development and temperature sensitivity in Brachypodium.
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Affiliation(s)
- Rajiv K Tripathi
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Quebec, H9X 3V9, Canada.
| | - William Overbeek
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Quebec, H9X 3V9, Canada
| | - Jaswinder Singh
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Quebec, H9X 3V9, Canada.
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19
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Coomey JH, Sibout R, Hazen SP. Grass secondary cell walls, Brachypodium distachyon as a model for discovery. THE NEW PHYTOLOGIST 2020; 227:1649-1667. [PMID: 32285456 DOI: 10.1111/nph.16603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/05/2020] [Indexed: 05/20/2023]
Abstract
A key aspect of plant growth is the synthesis and deposition of cell walls. In specific tissues and cell types including xylem and fibre, a thick secondary wall comprised of cellulose, hemicellulose and lignin is deposited. Secondary cell walls provide a physical barrier that protects plants from pathogens, promotes tolerance to abiotic stresses and fortifies cells to withstand the forces associated with water transport and the physical weight of plant structures. Grasses have numerous cell wall features that are distinct from eudicots and other plants. Study of the model species Brachypodium distachyon as well as other grasses has revealed numerous features of the grass cell wall. These include the characterisation of xylosyl and arabinosyltransferases, a mixed-linkage glucan synthase and hydroxycinnamate acyltransferases. Perhaps the most fertile area for discovery has been the formation of lignins, including the identification of novel substrates and enzyme activities towards the synthesis of monolignols. Other enzymes function as polymerising agents or transferases that modify lignins and facilitate interactions with polysaccharides. The regulatory aspects of cell wall biosynthesis are largely overlapping with those of eudicots, but salient differences among species have been resolved that begin to identify the determinants that define grass cell walls.
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Affiliation(s)
- Joshua H Coomey
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | - Richard Sibout
- Biopolymères Interactions Assemblages, INRAE, UR BIA, F-44316, Nantes, France
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
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20
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Zaidi MA, O'Leary SJB, Gagnon C, Chabot D, Wu S, Hubbard K, Tran F, Sprott D, Hassan D, Vucurevich T, Sheedy C, Laroche A, Gleddie S, Robert LS. A triticale tapetal non-specific lipid transfer protein (nsLTP) is translocated to the pollen cell wall. PLANT CELL REPORTS 2020; 39:1185-1197. [PMID: 32638075 DOI: 10.1007/s00299-020-02556-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/05/2020] [Indexed: 05/28/2023]
Abstract
A Triticeae type III non-specific lipid transfer protein (nsLTP) was shown for the first time to be translocated from the anther tapetum to the pollen cell wall. Two anther-expressed non-specific lipid transfer proteins (nsLTPs) were identified in triticale (× Triticosecale Wittmack). LTPc3a and LTPc3b contain a putative signal peptide sequence and eight cysteine residues in a C-Xn-C-Xn-CC-Xn-CXC-Xn-C-Xn-C pattern. These proteins belong to the type III class of nsLTPs which are expressed exclusively in the inflorescence of angiosperms. The level of LTPc3 transcript in the anther was highest at the tetrad and uninucleate microspore stages, and absent in mature pollen. In situ hybridization showed that LTPc3 was expressed in the tapetal layer of the developing triticale anther. The expression of the LTPc3 protein peaked at the uninucleate microspore stage, but was also found to be associated with the mature pollen. Accordingly, an LTPc3a::GFP translational fusion expressed in transgenic Brachypodium distachyon first showed activity in the tapetum, then in the anther locule, and later on the mature pollen grain. Altogether, these results represent the first detailed characterization of a Triticeae anther-expressed type III nsLTP with possible roles in pollen cell wall formation.
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Affiliation(s)
- Mohsin Abbas Zaidi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, PE, C1A 4N6, Canada
| | - Stephen J B O'Leary
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
- Aquatic and Crop Resource Development Research Centre, National Research Council, of Canada, 1411 Oxford Street, Halifax, NS, B3H 3Z1, Canada
| | - Christine Gagnon
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Denise Chabot
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Shaobo Wu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, 26 Huacai Road, Chengdu, 610052, Sichuan, China
| | - Keith Hubbard
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Frances Tran
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C and E Trail, Lacombe, AB, T4L 1W1, Canada
| | - Dave Sprott
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Dhuha Hassan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Tara Vucurevich
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, PO Box 3000, Lethbridge, AB, T1J 4B1, Canada
| | - Claudia Sheedy
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, PO Box 3000, Lethbridge, AB, T1J 4B1, Canada
| | - André Laroche
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, PO Box 3000, Lethbridge, AB, T1J 4B1, Canada
| | - Steve Gleddie
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Laurian S Robert
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
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21
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Hus K, Betekhtin A, Pinski A, Rojek-Jelonek M, Grzebelus E, Nibau C, Gao M, Jaeger KE, Jenkins G, Doonan JH, Hasterok R. A CRISPR/Cas9-Based Mutagenesis Protocol for Brachypodium distachyon and Its Allopolyploid Relative, Brachypodium hybridum. FRONTIERS IN PLANT SCIENCE 2020; 11:614. [PMID: 32508865 PMCID: PMC7251944 DOI: 10.3389/fpls.2020.00614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
The CRISPR/Cas9 system enables precise genome editing and is a useful tool for functional genomic studies. Here we report a detailed protocol for targeted genome editing in the model grass Brachypodium distachyon and its allotetraploid relative B. hybridum, describing gRNA design, a transient protoplast assay to test gRNA efficiency, Agrobacterium-mediated transformation and the selection and analysis of regenerated plants. In B. distachyon, we targeted the gene encoding phytoene desaturase (PDS), which is a crucial enzyme in the chlorophyll biosynthesis pathway. The albino phenotype of mutants obtained confirmed the effectiveness of the protocol for functional gene analysis. Additionally, we targeted two genes related to cell wall maintenance, encoding a fasciclin-like arabinogalactan protein (FLA) and a pectin methylesterase (PME), also in B. distachyon. Two genes encoding cyclin-dependent kinases (CDKG1 and CDKG2), which may be involved in DNA recombination were targeted in both B. distachyon and B. hybridum. Cas9 activity induces mainly insertions or deletions, resulting in frameshift mutations that, may lead to premature stop codons. Because of the close phylogenetic relationship between Brachypodium species and key temperate cereals and forage grasses, this protocol should be easily adapted to target genes underpinning agronomically important traits.
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Affiliation(s)
- Karolina Hus
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Alexander Betekhtin
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Artur Pinski
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Magdalena Rojek-Jelonek
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Ewa Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Cracow, Cracow, Poland
| | - Candida Nibau
- National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Mingjun Gao
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Katja E. Jaeger
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department for Plant Adaptation, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Glyn Jenkins
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - John H. Doonan
- National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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22
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Hu W, Figueroa‐Balderas R, Chi‐Ham C, Lagarias JC. Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B. PLANT DIRECT 2020; 4:e00210. [PMID: 32346668 PMCID: PMC7184922 DOI: 10.1002/pld3.210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/03/2020] [Accepted: 02/25/2020] [Indexed: 05/31/2023]
Abstract
The constitutively active missense allele of Arabidopsis phytochrome B, AtPHYBY276H or AtYHB, encodes a polypeptide that adopts a light-insensitive, physiologically active conformation capable of sustaining photomorphogenesis in darkness. Here, we show that the orthologous OsYHB allele of rice phytochrome B (OsPHYBY283H ) also encodes a dominant "constitutively active" photoreceptor through comparative phenotypic analyses of AtYHB and OsYHB transgenic lines of four eudicot species, Arabidopsis thaliana, Nicotiana tabacum (tobacco), Nicotiana sylvestris and Solanum lycopersicum cv. MicroTom (tomato), and of two monocot species, Oryza sativa ssp. japonica and Brachypodium distachyon. Reciprocal transformation experiments show that the gain-of-function constitutive photomorphogenic (cop) phenotypes by YHB expression are stronger in host plants within the same class than across classes. Our studies also reveal additional YHB-dependent traits in adult plants, which include extreme shade tolerance, both early and late flowering behaviors, delayed leaf senescence, reduced tillering, and even viviparous seed germination. However, the strength of these gain-of-function phenotypes depends on the specific combination of YHB allele and species/cultivar transformed. Flowering and tillering of OsYHB- and OsPHYB-expressing lines of rice Nipponbare and Kitaake cultivars were compared, also revealing differences in YHB/PHYB allele versus genotype interaction on the phenotypic behavior of the two rice cultivars. In view of recent evidence that the regulatory activity of AtYHB is not only light insensitive but also temperature insensitive, selective YHB expression is expected to yield improved agronomic performance of both dicot and monocot crop plant species not possible with wild-type PHYB alleles.
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Affiliation(s)
- Wei Hu
- Department of Molecular and Cellular BiologyUniversity of CaliforniaDavisCAUSA
| | - Rosa Figueroa‐Balderas
- Public Intellectual Property Resource for Agriculture (PIPRA)University of CaliforniaDavisCAUSA
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCAUSA
| | - Cecilia Chi‐Ham
- Public Intellectual Property Resource for Agriculture (PIPRA)University of CaliforniaDavisCAUSA
| | - J. Clark Lagarias
- Department of Molecular and Cellular BiologyUniversity of CaliforniaDavisCAUSA
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23
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Betekhtin A, Hus K, Rojek-Jelonek M, Kurczynska E, Nibau C, Doonan JH, Hasterok R. In Vitro Tissue Culture in Brachypodium: Applications and Challenges. Int J Mol Sci 2020; 21:E1037. [PMID: 32033195 PMCID: PMC7037373 DOI: 10.3390/ijms21031037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/01/2020] [Accepted: 02/03/2020] [Indexed: 01/29/2023] Open
Abstract
Brachypodium distachyon has become an excellent model for plant breeding and bioenergy grasses that permits many fundamental questions in grass biology to be addressed. One of the constraints to performing research in many grasses has been the difficulty with which they can be genetically transformed and the generally low frequency of such transformations. In this review, we discuss the contribution that transformation techniques have made in Brachypodium biology as well as how Brachypodium could be used to determine the factors that might contribute to transformation efficiency. In particular, we highlight the latest research on the mechanisms that govern the gradual loss of embryogenic potential in a tissue culture and propose using B. distachyon as a model for other recalcitrant monocots.
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Affiliation(s)
- Alexander Betekhtin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
| | - Karolina Hus
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
| | - Magdalena Rojek-Jelonek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
| | - Ewa Kurczynska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
| | - Candida Nibau
- National Plant Phenomics Centre, IBERS, Aberystwyth University, Aberystwyth SY23 3EE, UK; (C.N.); (J.H.D.)
| | - John H. Doonan
- National Plant Phenomics Centre, IBERS, Aberystwyth University, Aberystwyth SY23 3EE, UK; (C.N.); (J.H.D.)
| | - Robert Hasterok
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
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24
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Agapit C, Gigon A, Girin T, Leitao L, Blouin M. Split-root system optimization based on the survival, growth and development of the model Poaceae Brachypodium distachyon. PHYSIOLOGIA PLANTARUM 2020; 168:227-236. [PMID: 30950064 DOI: 10.1111/ppl.12971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/21/2019] [Accepted: 03/29/2019] [Indexed: 05/09/2023]
Abstract
Split-root system has been developed to better understand plant response to environmental factors, by exposing two separate parts of a single root system to heterogeneous situations. Surprisingly, there is no study attempting to maximize plant survival, growth and root system structure through a statistically sound comparison of different experimental protocols. Here, we aim at optimizing split-root systems on the model plant for Poaceae and cereals Brachypodium distachyon in terms of plant survival, number of roots and their equal distribution between the two compartments. We tested the effect of hydroponic or soil as growing media, with or without change of media at the transplantation step. The partial or total cutting of roots and/or shoots was also tested in different treatments as it could have an influence on plant access to energy and water and consequently on survival, growth and root development. Growing plants in soil before and after transplantation in split-root system was the best condition to get the highest survival rate, number of coleoptile node axile roots and growth. Cutting the whole root system was the best option to have a high root biomass and length at the end of the experiment. However, cutting shoots was detrimental for plant growth, especially in terms of root biomass production. In well-watered conditions, a plant submitted to a transfer in a split-root system is thus mainly lacking energy to produce new roots thanks to photosynthesis or adaptive autophagy, not water or nutrients.
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Affiliation(s)
- Corinne Agapit
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618), UPEC, Créteil, France
| | - Agnès Gigon
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618), UPEC, Créteil, France
| | - Thomas Girin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Luis Leitao
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618), UPEC, Créteil, France
| | - Manuel Blouin
- Agroécologie, AgroSup Dijon CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
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25
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Brew-Appiah RAT, Peracchi LM, Sanguinet KA. Never the Two Shall Mix: Robust Indel Markers to Ensure the Fidelity of Two Pivotal and Closely-Related Accessions of Brachypodium distachyon. PLANTS 2019; 8:plants8060153. [PMID: 31174296 PMCID: PMC6630600 DOI: 10.3390/plants8060153] [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: 05/20/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 11/25/2022]
Abstract
Brachypodium distachyon is an established model for monocotyledonous plants. Numerous markers intended for gene discovery and population genetics have been designed. However to date, very few indel markers with larger and easily scored length polymorphism differences, that distinguish between the two morphologically similar and highly utilized B. distachyon accessions, Bd21, the reference genome accession, and Bd21-3, the transformation-optimal accession, are publically available. In this study, 22 indel markers were designed and utilized to produce length polymorphism differences of 150 bp or more, for easy discrimination between Bd21 and Bd21-3. When tested on four other B. distachyon accessions, one case of multiallelism was observed. It was also shown that the markers could be used to determine homozygosity and heterozygosity at specific loci in a Bd21 x Bd3-1 F2 population. The work done in this study allows researchers to maintain the fidelity of Bd21 and Bd21-3 stocks for both transgenic and nontransgenic studies. It also provides markers that can be utilized in conjunction with others already available for further research on population genetics, gene discovery and gene characterization, all of which are necessary for the relevance of B. distachyon as a model species.
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Affiliation(s)
- Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Luigi M Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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26
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Wu H, Xue X, Qin C, Xu Y, Guo Y, Li X, Lv W, Li Q, Mao C, Li L, Zhao S, Qi X, An H. An Efficient System for Ds Transposon Tagging in Brachypodium distachyon. PLANT PHYSIOLOGY 2019; 180:56-65. [PMID: 30867334 PMCID: PMC6501085 DOI: 10.1104/pp.18.00875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 03/02/2019] [Indexed: 06/09/2023]
Abstract
Transposon tagging is a powerful tool that has been widely applied in several species for insertional mutagenesis in plants. Several efforts have aimed to create transfer-DNA (T-DNA) insertional mutant populations in Brachypodium distachyon, a monocot plant used as a model system to study temperate cereals, but there has been a lack of research aimed at using transposon strategies. Here, we describe the application of a maize (Zea mays) Dissociation (Ds) transposon tagging system in B distachyon The 35S::AcTPase cassette and Ds element were constructed within the same T-DNA and transformed into B distachyon plants. The Ds element was readily transposed to other chromosomes or to the same chromosome under the function of Activator (Ac) transposase. Through homologous chromosome synapsis, recombination, and segregation, the Ds element separated from the Ac element. We selected stable Ds-only plants using G418 and GFP assays and analyzed 241 T0 lines, some of which were highly efficient at producing Ds-only progeny. Through thermal asymmetric interlaced PCR, we isolated 710 independent Ds flanking sequences from Ds-only plants. Furthermore, we identified a large collection of mutants with visible developmental phenotypes via this transposon tagging system. The system is relatively simple and rapid in comparison to traditional T-DNA insertion strategies, because once efficiency lines are obtained they can be reused to generate more lines from nontransposed plants without the use of time-consuming tissue culture steps.
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Affiliation(s)
- Hongyu Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Xiaodong Xue
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Caihua Qin
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Yi Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Yuyu Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Xiang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Wei Lv
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Qinxia Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Chuangxue Mao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Luzhao Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
| | - Suzhen Zhao
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaoquan Qi
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hailong An
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong 271018, China
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27
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4-Coumarate 3-hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase. Nat Commun 2019; 10:1994. [PMID: 31040279 PMCID: PMC6491607 DOI: 10.1038/s41467-019-10082-7] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 04/15/2019] [Indexed: 12/04/2022] Open
Abstract
Lignin biosynthesis is evolutionarily conserved among higher plants and features a critical 3-hydroxylation reaction involving phenolic esters. However, increasing evidence questions the involvement of a single pathway to lignin formation in vascular plants. Here we describe an enzyme catalyzing the direct 3-hydroxylation of 4-coumarate to caffeate in lignin biosynthesis as a bifunctional peroxidase that oxidizes both ascorbate and 4-coumarate at comparable rates. A combination of biochemical and genetic evidence in the model plants Brachypodium distachyon and Arabidopsis thaliana supports a role for this coumarate 3-hydroxylase (C3H) in the early steps of lignin biosynthesis. The subsequent efficient O-methylation of caffeate to ferulate in grasses is substantiated by in vivo biochemical assays. Our results identify C3H as the only non-membrane bound hydroxylase in the lignin pathway and revise the currently accepted models of lignin biosynthesis, suggesting new gene targets to improve forage and bioenergy crops. Lignin biosynthesis in higher plants relies upon a 3-hydroxylation reaction that can occur via shikimate esters of 4-coumarate. Here, Barros et al. define an alternative biosynthetic pathway via cytosolic ascorbate peroxidase that can catalyze direct 3-hydroxylation of 4-coumarate.
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28
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Chen F, Liu Q, P Vogel J, Wu J. Agrobacterium-Mediated Transformation of Brachypodium distachyon. ACTA ACUST UNITED AC 2019; 4:e20088. [PMID: 30861331 DOI: 10.1002/cppb.20088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Brachypodium distachyon is an excellent model system for the grasses and has been adopted as a research organism by many laboratories around the world. It has all of the biological traits required for a model system, including small stature, short life cycle, small genome, simple growth requirements, and a close relationship to major crop plants (cereals). In addition, numerous resources have been developed for working with this species, including genome sequences for many lines, sequenced mutant collections, and a large, freely available germplasm collection. Fortunately, among grasses B. distachyon is one of the most easily transformed species, an absolute necessity for a model system. Agrobacterium-mediated transformation is the preferred method to transform plants because it usually results in simple insertions of target DNA. In this article, we describe a method for Agrobacterium-mediated transformation of the inbred B. distachyon lines Bd21 and Bd21-3. Embryogenic callus induced from immature embryos is co-cultivated with Agrobacterium tumefaciens strain AGL1 or Agrobacterium rhizogenes strain 18r12v. Hygromycin and paromomycin are used as selective agents, with comparable transformation efficiencies (defined as the percentage of co-cultivated callus that produce transgenic plants) of 40% to 70%. It takes 20 to 30 weeks to obtain T1 seeds starting from the initial step of dissecting out immature embryos. This protocol has been shown to be efficient and facile in several studies that resulted in the creation of over 22,000 T-DNA mutants. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Fengjuan Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China.,College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, China
| | - Qi Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China.,College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, China
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, California.,University of California Berkeley, Berkeley, California
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China.,College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, China
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29
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Subramanyam S, Nemacheck JA, Hargarten AM, Sardesai N, Schemerhorn BJ, Williams CE. Multiple molecular defense strategies in Brachypodium distachyon surmount Hessian fly (Mayetiola destructor) larvae-induced susceptibility for plant survival. Sci Rep 2019; 9:2596. [PMID: 30796321 PMCID: PMC6385206 DOI: 10.1038/s41598-019-39615-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/29/2019] [Indexed: 11/24/2022] Open
Abstract
The Hessian fly is a destructive pest of wheat causing severe economic damage. Numerous genes and associated biological pathways have been implicated in defense against Hessian fly. However, due to limited genetic resources, compounded with genome complexity, functional analysis of the candidate genes are challenging in wheat. Physically, Brachypodium distachyon (Bd) exhibits nonhost resistance to Hessian fly, and with a small genome size, short life cycle, vast genetic resources and amenability to transformation, it offers an alternate functional genomic model for deciphering plant-Hessian fly interactions. RNA-sequencing was used to reveal thousands of Hessian fly-responsive genes in Bd one, three, and five days after egg hatch. Genes encoding defense proteins, stress-regulating transcription factors, signaling kinases, and secondary metabolites were strongly up-regulated within the first 24 hours of larval feeding indicating an early defense, similar to resistant wheat. Defense was mediated by a hypersensitive response that included necrotic lesions, up-regulated ROS-generating and -scavenging enzymes, and H2O2 production. Suppression of cell wall-associated proteins and increased cell permeability in Bd resembled susceptible wheat. Thus, Bd molecular responses shared similarities to both resistant and susceptible wheat, validating its suitability as a model genome for undertaking functional studies of candidate Hessian fly-responsive genes.
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Affiliation(s)
- Subhashree Subramanyam
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA. .,USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA.
| | - Jill A Nemacheck
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
| | - Andrea M Hargarten
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
| | - Nagesh Sardesai
- Corteva Agriscience, Agriculture Division of DowDuPont, Johnston, IA, 50131, USA
| | - Brandon J Schemerhorn
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA.,Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
| | - Christie E Williams
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.,USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907, USA
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30
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O'Connor DL. Live Confocal Imaging of Brachypodium Spikelet Meristems. Bio Protoc 2018; 8:e3026. [PMID: 34395812 DOI: 10.21769/bioprotoc.3026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 11/02/2022] Open
Abstract
Live confocal imaging of fluorescent reporters and stains in plant meristems provides valuable measurements of gene expression, protein dynamics, cell polarity, cell division, and growth. The spikelet meristem in the grass Brachypodium distachyon (Brachypodium) is well suited to live imaging because of the ease of dissection, small meristem size, simple arrangement of organs, and because each plant provides abundant spikelet meristems. Brachypodium is also far easier to genetically transform than other grass species. Presented here is a protocol for the growth, staging, dissection, mounting, and imaging of Brachypodium spikelet meristems for live confocal imaging.
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Affiliation(s)
- Devin Lee O'Connor
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
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31
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van der Schuren A, Voiniciuc C, Bragg J, Ljung K, Vogel J, Pauly M, Hardtke CS. Broad spectrum developmental role of Brachypodium AUX1. THE NEW PHYTOLOGIST 2018; 219:1216-1223. [PMID: 29949662 PMCID: PMC6100110 DOI: 10.1111/nph.15332] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/10/2018] [Indexed: 05/06/2023]
Abstract
Targeted cellular auxin distribution is required for morphogenesis and adaptive responses of plant organs. In Arabidopsis thaliana (Arabidopsis), this involves the prototypical auxin influx facilitator AUX1 and its LIKE-AUX1 (LAX) homologs, which act partially redundantly in various developmental processes. Interestingly, AUX1 and its homologs are not strictly essential for the Arabidopsis life cycle. Indeed, aux1 lax1 lax2 lax3 quadruple knock-outs are mostly viable and fertile, and strong phenotypes are only observed at low penetrance. Here we investigated the Brachypodium distachyon (Brachypodium) AUX1 homolog BdAUX1 by genetic, cell biological and physiological analyses. We report that BdAUX1 is essential for Brachypodium development. Bdaux1 loss-of-function mutants are dwarfs with aberrant flower development, and consequently infertile. Moreover, they display a counter-intuitive root phenotype. Although Bdaux1 roots are agravitropic as expected, in contrast to Arabidopsis aux1 mutants they are dramatically longer than wild type roots because of exaggerated cell elongation. Interestingly, this correlates with higher free auxin content in Bdaux1 roots. Consistently, their cell wall characteristics and transcriptome signature largely phenocopy other Brachypodium mutants with increased root auxin content. Our results imply fundamentally different wiring of auxin transport in Brachypodium roots and reveal an essential role of BdAUX1 in a broad spectrum of developmental processes, suggesting a central role for AUX1 in pooideae.
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Affiliation(s)
- Alja van der Schuren
- Department of Plant Molecular BiologyUniversity of LausanneBiophore BuildingCH‐1015LausanneSwitzerland
| | - Catalin Voiniciuc
- Institute for Plant Cell Biology and BiotechnologyHeinrich‐Heine UniversityD‐40225DuesseldorfGermany
| | - Jennifer Bragg
- DOE Joint Genome Institute2800 Mitchell Dr.Walnut CreekCA94598USA
| | - Karin Ljung
- Umeå Plant Science CenterDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesSE‐901 83UmeåSweden
| | - John Vogel
- DOE Joint Genome Institute2800 Mitchell Dr.Walnut CreekCA94598USA
| | - Markus Pauly
- Institute for Plant Cell Biology and BiotechnologyHeinrich‐Heine UniversityD‐40225DuesseldorfGermany
| | - Christian S. Hardtke
- Department of Plant Molecular BiologyUniversity of LausanneBiophore BuildingCH‐1015LausanneSwitzerland
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32
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Scholthof KBG, Irigoyen S, Catalan P, Mandadi KK. Brachypodium: A Monocot Grass Model Genus for Plant Biology. THE PLANT CELL 2018; 30:1673-1694. [PMID: 29997238 PMCID: PMC6139682 DOI: 10.1105/tpc.18.00083] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/25/2018] [Accepted: 07/11/2018] [Indexed: 05/21/2023]
Abstract
The genus Brachypodium represents a model system that is advancing our knowledge of the biology of grasses, including small grains, in the postgenomics era. The most widely used species, Brachypodium distachyon, is a C3 plant that is distributed worldwide. B. distachyon has a small genome, short life cycle, and small stature and is amenable to genetic transformation. Due to the intensive and thoughtful development of this grass as a model organism, it is well-suited for laboratory and field experimentation. The intent of this review is to introduce this model system genus and describe some key outcomes of nearly a decade of research since the first draft genome sequence of the flagship species, B. distachyon, was completed. We discuss characteristics and features of B. distachyon and its congeners that make the genus a valuable model system for studies in ecology, evolution, genetics, and genomics in the grasses, review current hot topics in Brachypodium research, and highlight the potential for future analysis using this system in the coming years.
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Affiliation(s)
- Karen-Beth G Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843
| | - Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 78596
| | - Pilar Catalan
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071 Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza E-50059, Spain
- Institute of Biology, Tomsk State University, Tomsk 634050, Russia
| | - Kranthi K Mandadi
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 78596
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33
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Jansson C, Vogel J, Hazen S, Brutnell T, Mockler T. Climate-smart crops with enhanced photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3801-3809. [PMID: 30032188 DOI: 10.1093/jxb/ery213] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/29/2018] [Indexed: 05/20/2023]
Abstract
The potential of enhanced photosynthetic efficiency to help achieve the sustainable yield increases required to meet future demands for food and energy has spurred intense research towards understanding, modeling, and engineering photosynthesis. These current efforts, largely focused on the C3 model Arabidopsis thaliana or crop plants (e.g. rice, sorghum, maize, and wheat), could be intensified and broadened using model systems closely related to our food, feed, and energy crops and that allow rapid design-build-test-learn cycles. In this outlooking Opinion, we advocate for a concerted effort to expand our understanding and improve our ability to redesign carbon uptake, allocation, and utilization. We propose two specific research directions that combine enhanced photosynthesis with climate-smart metabolic attributes: (i) engineering pathways for flexible (facultative) C3-C4 metabolism where plants will operate either C3 or C4 photosynthesis based on environmental conditions such as temperature, light, and atmospheric CO2 levels; and (ii) increasing rhizospheric sink strength for carbon utilization, including strategies that allow for augmented transport of carbon to the soil for improved soil properties and carbon storage without jeopardizing aboveground crop biomass. We argue that such ambitious undertakings be first approached and demonstrated by exploring the full genomic potential of two model grasses, the C3Brachypodium distachyon and the C4Setaria viridis. The development of climate-smart crops could provide novel and bold solutions to increase crop productivity while reducing atmospheric carbon and nitrogen emissions.
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Affiliation(s)
- Christer Jansson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - John Vogel
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek CA, USA
| | - Samuel Hazen
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | | | - Todd Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
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Su P, Guo X, Fan Y, Wang L, Yu G, Ge W, Zhao L, Ma X, Wu J, Li A, Wang H, Kong L. Application of Brachypodium genotypes to the analysis of type II resistance to Fusarium head blight (FHB). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:255-266. [PMID: 29807599 DOI: 10.1016/j.plantsci.2018.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
The resistance to Fusarium head blight (FHB) in wheat is mainly via the restrain of fungal expansion through spike rachis (type II resistance). In order to unravel the resistance mechanisms, Brachypodium distachyon 21 (Bd21), a monocotyledonous model plant, was previously proved to interact with F. graminearum, while the disease development in spike still needs to be explored in detail. Herein, it is found that the fungal spores mainly germinate on pistil of Bd21, then the hyphae rapidly extend to the bottom of floret and enter spike rachis, similar with the infection progress in wheat. However, structural difference of spike rachis was found between Brachypodium and wheat. It was found that the spread of the fungus through the rachis node of inoculated spikelets is an important index for the evaluation of type II FHB resistance in Brachypodium under optimal conditions at 28 °C and 50%-70% humidity. To verify the feasibility of this strategy, the transcription factor TaTGA2 was overexpressed in Bd21, and transgenic plants were found to show improved resistance to F. graminearum in both spikes and detached leaves, which was further supported by the increased disease severity when silencing TaTGA2 in the wheat cultivar "Sumai 3" or in tilling "Kronos" mutants. Except for Bd21, another 49 Brachypodium germplasms were further screened for FHB resistance, and three moderately susceptible germplasms, namely, PI 317418, W6-39284, and PI 254868, feasible for transformation, were determined to be better hosts than Bd21 when evaluating heterologous genes that positively regulate FHB resistance. The present study also observed variations in the levels of FHB resistance between coleoptiles and spikes or transgenic plants and natural germplasms.
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Affiliation(s)
- Peisen Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Xiuxiu Guo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Yanhui Fan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Liang Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Guanghui Yu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Wenyang Ge
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Lanfei Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Xin Ma
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Anfei Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China
| | - Hongwei Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China.
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, PR China.
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Alvarez M, Ferreira de Carvalho J, Salmon A, Ainouche ML, Cavé-Radet A, El Amrani A, Foster TE, Moyer S, Richards CL. Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill. Mol Ecol 2018; 27:2986-3000. [PMID: 29862597 DOI: 10.1111/mec.14736] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/16/2022]
Abstract
Despite the severe impacts of the Deepwater Horizon oil spill, the foundation plant species Spartina alterniflora proved resilient to heavy oiling, providing an opportunity to identify mechanisms of response to the anthropogenic stress of crude oil exposure. We assessed plants from oil-affected and unaffected populations using a custom DNA microarray to identify genomewide transcription patterns and gene expression networks that respond to crude oil exposure. In addition, we used T-DNA insertion lines of the model grass Brachypodium distachyon to assess the contribution of four novel candidate genes to crude oil response. Responses in S. alterniflora to hydrocarbon exposure across the transcriptome as well as xenobiotic specific response pathways had little overlap with those previously identified in the model plant Arabidopsis thaliana. Among T-DNA insertion lines of B. distachyon, we found additional support for two candidate genes, one (ATTPS21) involved in volatile production, and the other (SUVH5) involved in epigenetic regulation of gene expression, that may be important in the response to crude oil. The architecture of crude oil response in S. alterniflora is unique from that of the model species A. thaliana, suggesting that xenobiotic response may be highly variable across plant species. In addition, further investigations of regulatory networks may benefit from more information about epigenetic response pathways.
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Affiliation(s)
- Mariano Alvarez
- Department of Integrative Biology, University of South Florida, Tampa, Florida
| | | | - Armel Salmon
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Malika L Ainouche
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Armand Cavé-Radet
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Abdelhak El Amrani
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Tammy E Foster
- Kennedy Space Center Ecological Program, Titusville, Florida
| | - Sydney Moyer
- Department of Integrative Biology, University of South Florida, Tampa, Florida
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Brabham C, Stork J, Barrett M, DeBolt S. Grass cell walls have a role in the inherent tolerance of grasses to the cellulose biosynthesis inhibitor isoxaben. PEST MANAGEMENT SCIENCE 2018; 74:878-884. [PMID: 29087620 DOI: 10.1002/ps.4779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Cellulose biosynthesis inhibitors (CBIs) are pre-emergence herbicides that inhibit anisotropic cell expansion resulting in a severely swollen and stunted growth phenotype. Resistance to group 21 CBIs, such as isoxaben, is conferred by missense mutations in CELLOSE SYNTHASE A (CesA) genes required for primary cell wall synthesis, concluding that this is their in vivo target. RESULTS Herein, we show that grasses exhibit tolerance to group 21 CBIs and explore the mechanism of tolerance to isoxaben in the grass Brachypodium distachyon (L.). Comparative genomics failed to identify synonymous point mutations that have been found to confer isoxaben resistance in the dicot Arabidopsis thaliana (L.). Brachypodium did not metabolize 14 C-isoxaben. We next explored the role of grass-specific non-cellulosic cell wall components, specifically the hemicellulose polysaccharide mix linkage glucans (MLG), as a potential tolerance mechanism by compensating for the loss of cellulose during cell elongation. A partial-transcriptional knockdown T-DNA insertion was found in a key MLG synthesis gene, Cellulose synthase-like F6 (CslF6) and this mutant was found to be 2.1 times more sensitive to isoxaben than wild-type plants. CONCLUSION These data suggest that the composition and compensatory response of grass cell walls may be a factor in conferring tolerance to group 21 CBIs. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Chad Brabham
- Department of Horticulture, University of Kentucky, Lexington, KY, USA
| | - Jozsef Stork
- Department of Horticulture, University of Kentucky, Lexington, KY, USA
| | - Michael Barrett
- Department of Plant and Soil Science, University of Kentucky, Lexington, KY, USA
| | - Seth DeBolt
- Department of Horticulture, University of Kentucky, Lexington, KY, USA
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Kind S, Schurack S, Hinsch J, Tudzynski P. Brachypodium distachyon as alternative model host system for the ergot fungus Claviceps purpurea. MOLECULAR PLANT PATHOLOGY 2018; 19:1005-1011. [PMID: 28452203 PMCID: PMC6638158 DOI: 10.1111/mpp.12563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/19/2017] [Indexed: 05/30/2023]
Abstract
To investigate its susceptibility to ergot infection, we inoculated Brachypodium distachyon with Claviceps purpurea and compared the infection symptoms with those on rye (Secale cereale). We showed that, after inoculation of Brachypodium with Claviceps, the same disease symptoms occurred in comparable temporal and spatial patterns to those on rye. The infection rate of Claviceps on this host was reduced compared with rye, but the disease could be surveyed by fungal genomic DNA quantification. Mutants of Claviceps which were virulence attenuated on rye were also affected on Brachypodium. We were able to show that pathogenesis-related gene expression changed in a typical manner for biotrophic pathogen attack. Our results indicated that the Claviceps-Brachypodium interaction was dependent on salicylic acid, cytokinin and auxin. We consider Brachypodium to be a suitable and useful alternative host; the increased sensitivity compared with rye will be valuable for the identification of infection mechanisms. Future progess in understanding the Claviceps-plant interaction will be facilitated by the use of a well-characterized model host system.
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Affiliation(s)
- Sabine Kind
- Institute for Biology and Biotechnology of PlantsWestphalian Wilhelms UniversitySchlossplatz 8, Muenster D‐48143Germany
| | - Selma Schurack
- Institute for Biology and Biotechnology of PlantsWestphalian Wilhelms UniversitySchlossplatz 8, Muenster D‐48143Germany
- Present address:
Chair of Terrestrial MicrobiologyCEPLAS/Institute of Botany, University of CologneZülpicher Straße 47a, Cologne D‐50674Germany.
| | - Janine Hinsch
- Institute for Biology and Biotechnology of PlantsWestphalian Wilhelms UniversitySchlossplatz 8, Muenster D‐48143Germany
| | - Paul Tudzynski
- Institute for Biology and Biotechnology of PlantsWestphalian Wilhelms UniversitySchlossplatz 8, Muenster D‐48143Germany
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Hao Q, Wang W, Han X, Wu J, Lyu B, Chen F, Caplan A, Li C, Wu J, Wang W, Xu Q, Fu D. Isochorismate-based salicylic acid biosynthesis confers basal resistance to Fusarium graminearum in barley. MOLECULAR PLANT PATHOLOGY 2018; 19:1995-2010. [PMID: 29517854 PMCID: PMC6638154 DOI: 10.1111/mpp.12675] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 05/18/2023]
Abstract
Salicylic acid (SA) plays an important role in signal transduction and disease resistance. In Arabidopsis, SA can be made by either of two biosynthetic branches, one involving isochorismate synthase (ICS) and the other involving phenylalanine ammonia-lyase (PAL). However, the biosynthetic pathway and the importance of SA remain largely unknown in Triticeae. Here, we cloned one ICS and seven PAL genes from barley, and studied their functions by their overexpression and suppression in that plant. Suppression of the ICS gene significantly delayed plant growth, whereas PAL genes, both overexpressed and suppressed, had no significant effect on plant growth. Similarly, suppression of ICS compromised plant resistance to Fusarium graminearum, whereas similar suppression of PAL genes had no significant effect. We then focused on transgenic plants with ICS. In a leaf-based test with F. graminearum, transgenic plants with an up-regulated ICS were comparable with wild-type control plants. By contrast, transgenic plants with a suppressed ICS lost the ability to accumulate SA during pathogen infection and were also more susceptible to Fusarium than the wild-type controls. This suggests that ICS plays a unique role in SA biosynthesis in barley, which, in turn, confers a basal resistance to F. graminearum by modulating the accumulation of H2 O2 , O2- and reactive oxygen-associated enzymatic activities. Although SA mediates systemic acquired resistance (SAR) in dicots, there was no comparable SAR response to F. graminearum in barley. This study expands our knowledge about SA biosynthesis in barley and proves that SA confers basal resistance to fungal pathogens.
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Affiliation(s)
- Qunqun Hao
- State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianShandong271018China
- College of AgronomyShandong Agricultural UniversityTaianShandong271018China
- Department of Plant SciencesUniversity of IdahoMoscowID83844USA
| | - Wenqiang Wang
- State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianShandong271018China
- College of Life SciencesShandong Agricultural UniversityTaianShandong271018China
| | - Xiuli Han
- State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianShandong271018China
- College of AgronomyShandong Agricultural UniversityTaianShandong271018China
- Present address:
College of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Jingzheng Wu
- State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianShandong271018China
- College of AgronomyShandong Agricultural UniversityTaianShandong271018China
| | - Bo Lyu
- Department of Plant SciencesUniversity of IdahoMoscowID83844USA
| | - Fengjuan Chen
- State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianShandong271018China
| | - Allan Caplan
- Department of Plant SciencesUniversity of IdahoMoscowID83844USA
| | - Caixia Li
- State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianShandong271018China
- College of AgronomyShandong Agricultural UniversityTaianShandong271018China
| | - Jiajie Wu
- State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianShandong271018China
- College of AgronomyShandong Agricultural UniversityTaianShandong271018China
| | - Wei Wang
- State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianShandong271018China
- College of Life SciencesShandong Agricultural UniversityTaianShandong271018China
| | - Qian Xu
- State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianShandong271018China
- College of AgronomyShandong Agricultural UniversityTaianShandong271018China
| | - Daolin Fu
- Department of Plant SciencesUniversity of IdahoMoscowID83844USA
- Center for Reproductive BiologyWashington State UniversityPullmanWA99164USA
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Kim SJ, Zemelis-Durfee S, Jensen JK, Wilkerson CG, Keegstra K, Brandizzi F. In the grass species Brachypodium distachyon, the production of mixed-linkage (1,3;1,4)-β-glucan (MLG) occurs in the Golgi apparatus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1062-1075. [PMID: 29377449 DOI: 10.1111/tpj.13830] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/12/2018] [Accepted: 01/18/2018] [Indexed: 05/27/2023]
Abstract
Mixed-linkage (1,3;1,4)-β-glucan (MLG) is a glucose polymer with beneficial effects on human health and high potential for the agricultural industry. MLG is present predominantly in the cell wall of grasses and is synthesized by cellulose synthase-like F or H families of proteins, with CSLF6 being the best-characterized MLG synthase. Although the function of this enzyme in MLG production has been established, the site of MLG synthesis in the cell is debated. It has been proposed that MLG is synthesized at the plasma membrane, as occurs for cellulose and callose; in contrast, it has also been proposed that MLG is synthesized in the Golgi apparatus, as occurs for other matrix polysaccharides of the cell wall. Testing these conflicting possibilities is fundamentally important in the general understanding of the biosynthesis of the plant cell wall. Using immuno-localization analyses with MLG-specific antibody in Brachypodium and in barley, we found MLG present in the Golgi, in post-Golgi structures and in the cell wall. Accordingly, analyses of a functional fluorescent protein fusion of CSLF6 stably expressed in Brachypodium demonstrated that the enzyme is localized in the Golgi. We also established that overproduction of MLG causes developmental and growth defects in Brachypodium as also occur in barley. Our results indicated that MLG production occurs in the Golgi similarly to other cell wall matrix polysaccharides, and supports the broadly applicable model in grasses that tight mechanisms control optimal MLG accumulation in the cell wall during development and growth. This work addresses the fundamental question of where mixed linkage (1,3;1,4)-β-glucan (MLG) is synthesized in plant cells. By analyzing the subcellular localization of MLG and MLG synthase in an endogenous system, we demonstrated that MLG synthesis occurs at the Golgi in Brachypodium and barley. A growth inhibition due to overproduced MLG in Brachypodium supports the general applicability of the model that a tight control of the cell wall polysaccharides accumulation is needed to maintain growth homeostasis during development.
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Affiliation(s)
- Sang-Jin Kim
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 4882, USA
| | - Starla Zemelis-Durfee
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 4882, USA
| | - Jacob Krüger Jensen
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 4882, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Curtis G Wilkerson
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 4882, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kenneth Keegstra
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 4882, USA
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, 48824, USA
| | - Federica Brandizzi
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 4882, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, 48824, USA
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Abstract
TILLING is a low-cost screening method that allows for identification of mutations in a gene-of-interest within a range of few base pairs. TILLING can be applied to mutant populations or to plant collections of cultivars, landraces or crop wild relatives (Eco-TILLING). The method is based on the Cel1 enzyme cleavage of mismatches in PCR products amplified with labeled primers. The cleavage can be detected due to the labeled primers by different methods including capillary electrophoresis. Here, we introduce the development of the mutant population BRACHYLIFE and present a Brachypodium TILLING protocol based on fluorescing primers for PCR, enzymatic cleavage, and detection with Applied Biosystems 3130xl Genetic Analyzer.
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Affiliation(s)
- Louise de Bang
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Anna Maria Torp
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Søren K Rasmussen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark.
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41
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Gill US, Serrani-Yarce JC, Lee HK, Mysore KS. Tissue Culture (Somatic Embryogenesis)-Induced Tnt1 Retrotransposon-Based Mutagenesis in Brachypodium distachyon. Methods Mol Biol 2018; 1667:57-63. [PMID: 29039003 DOI: 10.1007/978-1-4939-7278-4_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Brachypodium distachyon is a model grass species for economically important cereal crops. Efforts are in progress to develop useful functional genomic resources in Brachypodium. A tobacco retrotransposon, Tnt1, has been used successfully in recent past to generate insertional mutagenesis in several dicot plant species. Tnt1 retrotransposon replicates, transposes, and inserts at multiple random genomic locations in the plant genome. Transposition occurs only during somatic embryogenesis but not during seed transmission. We developed Brachypodium transgenic plants that can express the Tnt1 element. Here, we describe an efficient tissue culture-based approach to generate Tnt1 insertional mutant population using transgenic Brachypodium line expressing the Tnt1 retrotransposon.
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Affiliation(s)
- Upinder S Gill
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Juan C Serrani-Yarce
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Hee-Kyung Lee
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Kirankumar S Mysore
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
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Powell JJ, Carere J, Sablok G, Fitzgerald TL, Stiller J, Colgrave ML, Gardiner DM, Manners JM, Vogel JP, Henry RJ, Kazan K. Transcriptome analysis of Brachypodium during fungal pathogen infection reveals both shared and distinct defense responses with wheat. Sci Rep 2017; 7:17212. [PMID: 29222453 PMCID: PMC5722949 DOI: 10.1038/s41598-017-17454-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/26/2017] [Indexed: 11/09/2022] Open
Abstract
Fusarium crown rot (FCR) of wheat and barley, predominantly caused by the fungal pathogen Fusarium pseudograminearum, is a disease of economic significance. The quantitative nature of FCR resistance within cultivated wheat germplasm has significantly limited breeding efforts to enhanced FCR resistance in wheat. In this study, we characterized the molecular responses of Brachypodium distachyon (Brachypodium hereafter) to F. pseudograminearum infection using RNA-seq to determine whether Brachypodium can be exploited as a model system towards better understanding of F. pseudograminearum-wheat interaction. The transcriptional response to infection in Brachypodium was strikingly similar to that previously reported in wheat, both in shared expression patterns of wheat homologs of Brachypodium genes and functional overlap revealed through comparative gene ontology analysis in both species. Metabolites produced by various biosynthetic pathways induced in both wheat and Brachypodium were quantified, revealing a high degree of overlap between these two species in metabolic response to infection but also showed Brachypodium does not produce certain defence-related metabolites found in wheat. Functional analyses of candidate genes identified in this study will improve our understanding of resistance mechanisms and may lead to the development of new strategies to protect cereal crops from pathogen infection.
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Affiliation(s)
- Jonathan J Powell
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, St Lucia, Queensland, 4067, Australia.
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, St Lucia, 4067, Queensland, Australia.
| | - Jason Carere
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, St Lucia, Queensland, 4067, Australia
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Sydney, Australia
| | - Timothy L Fitzgerald
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, St Lucia, Queensland, 4067, Australia
| | - Jiri Stiller
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, St Lucia, Queensland, 4067, Australia
| | - Michelle L Colgrave
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, St Lucia, Queensland, 4067, Australia
| | - Donald M Gardiner
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, St Lucia, Queensland, 4067, Australia
| | - John M Manners
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Black Mountain, Australian Capital Territory, 2601, Australia
| | - John P Vogel
- Joint Genome Institute, United States Department of Energy, Walnut Creek, CA, 94598, USA
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, St Lucia, 4067, Queensland, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, St Lucia, Queensland, 4067, Australia.
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, St Lucia, 4067, Queensland, Australia.
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Pri-Tal O, Shaar-Moshe L, Wiseglass G, Peleg Z, Mosquna A. Non-redundant functions of the dimeric ABA receptor BdPYL1 in the grass Brachypodium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:774-786. [PMID: 28891214 DOI: 10.1111/tpj.13714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 05/05/2023]
Abstract
Abiotic stresses have severe detrimental effects on agricultural productivity worldwide. Abscisic acid (ABA) levels rise in response to abiotic stresses, and play a role in coordinating physiological responses. ABA elicits its effects by binding a family of soluble receptors, increasing affinity of the receptors to type 2C phosphatases (PP2Cs) leading to phosphatase inhibition. In the current study, we conducted a comprehensive analysis of the ABA signaling pathway in the cereal model grass Brachypodium distachyon. The Brachypodium genome encodes a family of 10 functionally conserved ABA receptors. The 10th in the series, BdPYL10, encodes a defective receptor and is likely a pseudogene. Combinatorial protein interaction assay further validated computational analysis, which grouped Brachypodium ABA receptors into three subfamilies, similarly to Arabidopsis classification. Brachypodium subfamily III receptors inhibited PP2C activity in vitro and complemented Arabidopsis quadruple (pyr1/pyl1/pyl2/pyl4) mutant. BdPYL1 T-DNA mutant exhibited clear ABA hyposensitivity phenotypes during seedling establishment and in mature plants. Single receptor predominance is in agreement with high transcriptional abundance of only a small Brachypodium ABA receptors subset, harboring the higher marginal significance of BdPYL1. Our findings suggest that unlike the highly redundant ABA core signaling components of Arabidopsis, Brachypodium encompasses a more compact and specialized ABA receptor apparatus. This organization may contribute to plant adaptations to ecological niches. These results lay the groundwork for targeting the prominent ABA receptors for stress perception in grasses, and reveal functional differences and commonalities between monocots and eudicots.
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Affiliation(s)
- Oded Pri-Tal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Lidor Shaar-Moshe
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Gil Wiseglass
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
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Nahar N, Rahman A, Nawani NN, Ghosh S, Mandal A. Phytoremediation of arsenic from the contaminated soil using transgenic tobacco plants expressing ACR2 gene of Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2017; 218:121-126. [PMID: 28818758 DOI: 10.1016/j.jplph.2017.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 06/07/2023]
Abstract
We have cloned, characterized and transformed the AtACR2 gene (arsenic reductase 2) of Arabidopsis thaliana into the genome of tobacco (Nicotiana tabacum, var Sumsun). Our results revealed that the transgenic tobacco plants are more tolerant to arsenic than the wild type ones. These plants can grow on culture medium containing 200μM arsenate, whereas the wild type can barely survive under this condition. Furthermore, when exposed to 100μM arsenate for 35days the amount of arsenic accumulated in the shoots of transgenic plants was significantly lower (28μg/g d wt.) than that found in the shoots of non-transgenic controls (40μg/g d wt.). However, the arsenic content in the roots of transgenic plants was significantly higher (2400μg/g d. wt.) than that (2100μg/g d. wt.) observed in roots of wild type plants. We have demonstrated that Arabidopsis thaliana AtACR2 gene is a potential candidate for genetic engineering of plants to develop new crop cultivars that can be grown on arsenic contaminated fields to reduce arsenic content of the soil and can become a source of food containing no arsenic or exhibiting substantially reduced amount of this metalloid.
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Affiliation(s)
- Noor Nahar
- Systems Biology Research Center, School of Bioscience, University of Skövde, P.O. Box 408, SE-541 28 Skövde, Sweden
| | - Aminur Rahman
- Systems Biology Research Center, School of Bioscience, University of Skövde, P.O. Box 408, SE-541 28 Skövde, Sweden.
| | - Neelu N Nawani
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Tathawade, Pune-411033, India
| | - Sibdas Ghosh
- School of Arts and Science, Iona College, New Rochelle, NY 10801, USA
| | - Abul Mandal
- Systems Biology Research Center, School of Bioscience, University of Skövde, P.O. Box 408, SE-541 28 Skövde, Sweden
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Hsia MM, O'Malley R, Cartwright A, Nieu R, Gordon SP, Kelly S, Williams TG, Wood DF, Zhao Y, Bragg J, Jordan M, Pauly M, Ecker JR, Gu Y, Vogel JP. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:361-370. [PMID: 28432803 DOI: 10.1111/tpj.13582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 05/07/2023]
Abstract
Due to a large and growing collection of genomic and experimental resources, Brachypodium distachyon has emerged as a powerful experimental model for the grasses. To add to these resources we sequenced 21 165 T-DNA lines, 15 569 of which were produced in this study. This increased the number of unique insertion sites in the T-DNA collection by 21 078, bringing the overall total to 26 112. Thirty-seven per cent (9754) of these insertion sites are within genes (including untranslated regions and introns) and 28% (7217) are within 500 bp of a gene. Approximately 31% of the genes in the v.2.1 annotation have been tagged in this population. To demonstrate the utility of this collection, we phenotypically characterized six T-DNA lines with insertions in genes previously shown in other systems to be involved in cellulose biosynthesis, hemicellulose biosynthesis, secondary cell wall development, DNA damage repair, wax biosynthesis and chloroplast synthesis. In all cases, the phenotypes observed supported previous studies, demonstrating the utility of this collection for plant functional genomics. The Brachypodium T-DNA collection can be accessed at http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/.
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Affiliation(s)
- Mon Mandy Hsia
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Ronan O'Malley
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies and the Howard Hughes Medical Institute, 10010 North Torrey Pines Rd., La Jolla, CA, 92037, USA
- DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA
| | - Amy Cartwright
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
- DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA
| | - Rita Nieu
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Sean P Gordon
- DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA
| | - Sandra Kelly
- Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB, R6M 1Y5, Canada
| | - Tina G Williams
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Delilah F Wood
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Yunjun Zhao
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA
| | - Jennifer Bragg
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - Mark Jordan
- Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB, R6M 1Y5, Canada
| | - Markus Pauly
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies and the Howard Hughes Medical Institute, 10010 North Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Yong Gu
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
| | - John P Vogel
- USDA ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710-1105, USA
- DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA, 94720, USA
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Rioux RA, Van Ryzin BJ, Kerns JP. Brachypodium: A Potential Model Host for Fungal Pathogens of Turfgrasses. PHYTOPATHOLOGY 2017; 107:749-757. [PMID: 28134592 DOI: 10.1094/phyto-08-16-0318-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Brachypodium distachyon is a C3 grass that is an attractive model host system for studying pathogenicity of major turfgrass pathogens due to its genetic similarity to many cool-season turfgrasses. Infection assays with two or more isolates of the casual agents of dollar spot, brown patch, and Microdochium patch resulted in compatible interactions with B. distachyon inbred line Bd21-3. The symptoms produced by these pathogens on Bd21-3 closely resembled those observed on the natural turfgrass host (creeping bentgrass), demonstrating that B. distachyon is susceptible to the fungal pathogens that cause dollar spot, brown patch, and Microdochium patch on turfgrasses. The interaction between Sclerotinia homoeocarpa isolates and Brachypodium ecotypes was also investigated. Interestingly, differential responses of these ecotypes to S. homoeocarpa isolates was found, particularly when comparing B. distachyon to B. hybridum ecotypes. Taken together, these findings demonstrate that B. distachyon can be used as a model host system for these turfgrass diseases and leveraged for studies of molecular mechanisms contributing to host resistance.
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Affiliation(s)
- Renee A Rioux
- First author: Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706; and second and third authors: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh 27695
| | - Benjamin J Van Ryzin
- First author: Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706; and second and third authors: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh 27695
| | - James P Kerns
- First author: Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706; and second and third authors: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh 27695
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Ni F, Qi J, Hao Q, Lyu B, Luo MC, Wang Y, Chen F, Wang S, Zhang C, Epstein L, Zhao X, Wang H, Zhang X, Chen C, Sun L, Fu D. Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species. Nat Commun 2017; 8:15121. [PMID: 28452349 PMCID: PMC5414350 DOI: 10.1038/ncomms15121] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 03/01/2017] [Indexed: 11/30/2022] Open
Abstract
Male sterility is a valuable trait for plant breeding and hybrid seed production. The dominant male-sterile gene Ms2 in common wheat has facilitated the release of hundreds of breeding lines and cultivars in China. Here, we describe the map-based cloning of the Ms2 gene and show that Ms2 confers male sterility in wheat, barley and Brachypodium. MS2 appears as an orphan gene within the Triticinae and expression of Ms2 in anthers is associated with insertion of a retroelement into the promoter. The cloning of Ms2 has substantial potential to assemble practical pipelines for recurrent selection and hybrid seed production in wheat.
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Affiliation(s)
- Fei Ni
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Juan Qi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Qunqun Hao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Bo Lyu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Yan Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Fengjuan Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Shuyun Wang
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Chaozhong Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xiansheng Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Cuixia Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lanzhen Sun
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Daolin Fu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho 83844, USA
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Raissig MT, Matos JL, Anleu Gil MX, Kornfeld A, Bettadapur A, Abrash E, Allison HR, Badgley G, Vogel JP, Berry JA, Bergmann DC. Mobile MUTE specifies subsidiary cells to build physiologically improved grass stomata. Science 2017; 355:1215-1218. [PMID: 28302860 DOI: 10.1126/science.aal3254] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023]
Abstract
Plants optimize carbon assimilation while limiting water loss by adjusting stomatal aperture. In grasses, a developmental innovation-the addition of subsidiary cells (SCs) flanking two dumbbell-shaped guard cells (GCs)-is linked to improved stomatal physiology. Here, we identify a transcription factor necessary and sufficient for SC formation in the wheat relative Brachypodium distachyon. Unexpectedly, the transcription factor is an ortholog of the stomatal regulator AtMUTE, which defines GC precursor fate in Arabidopsis The novel role of BdMUTE in specifying lateral SCs appears linked to its acquisition of cell-to-cell mobility in Brachypodium Physiological analyses on SC-less plants experimentally support classic hypotheses that SCs permit greater stomatal responsiveness and larger range of pore apertures. Manipulation of SC formation and function in crops, therefore, may be an effective approach to enhance plant performance.
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Affiliation(s)
- Michael T Raissig
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA.
| | - Juliana L Matos
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - M Ximena Anleu Gil
- Howard Hughes Medical Institute (HHMI), Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Ari Kornfeld
- Department of Global Ecology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - Akhila Bettadapur
- Howard Hughes Medical Institute (HHMI), Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Emily Abrash
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Hannah R Allison
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Grayson Badgley
- Department of Global Ecology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - John P Vogel
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Joseph A Berry
- Department of Global Ecology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - Dominique C Bergmann
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA. .,Howard Hughes Medical Institute (HHMI), Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
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Luo N, Yu X, Nie G, Liu J, Jiang Y. Specific peroxidases differentiate Brachypodium distachyon accessions and are associated with drought tolerance traits. ANNALS OF BOTANY 2016; 118:259-70. [PMID: 27325900 PMCID: PMC4970367 DOI: 10.1093/aob/mcw104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 02/08/2016] [Accepted: 04/04/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Brachypodium distachyon (Brachypodium) is a model system for studying cereal, bioenergy, forage and turf grasses. The genetic and evolutionary basis of the adaptation of this wild grass species to drought stress is largely unknown. Peroxidase (POD) may play a role in plant drought tolerance, but whether the allelic variations of genes encoding the specific POD isoenzymes are associated with plant response to drought stress is not well understood. The objectives of this study were to examine natural variation of POD isoenzyme patterns, to identify nucleotide diversity of POD genes and to relate the allelic variation of genes to drought tolerance traits of diverse Brachypodium accessions. METHODS Whole-plant drought tolerance and POD activity were examined in contrasting ecotypes. Non-denaturing PAGE and liquid chromatography-mass spectrometry were performed to detect distinct isozymes of POD in 34 accessions. Single nucleotide polymorphisms (SNPs) were identified by comparing DNA sequences of these accessions. Associations of POD genes encoding specific POD isoenzymes with drought tolerance traits were analysed using TASSEL software. KEY RESULTS Variations of POD isoenzymes were found among accessions with contrasting drought tolerance, while the most tolerant and susceptible accessions each had their own unique POD isoenzyme band. Eight POD genes were identified and a total of 90 SNPs were found among these genes across 34 accessions. After controlling population structure, significant associations of Bradi3g41340.1 and Bradi1g26870.1 with leaf water content or leaf wilting were identified. CONCLUSIONS Brachypodium ecotypes have distinct specific POD isozymes. This may contribute to natural variations of drought tolerance of this species. The role of specific POD genes in differentiating Brachypodium accessions with contrasting drought tolerance could be associated with the general fitness of Brachypodium during evolution.
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Affiliation(s)
- Na Luo
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoqing Yu
- Department of Agronomy, Iowa State University, Ames IA 50011, USA
| | - Gang Nie
- Department of Grassland Science, Sichuan Agricultural University, Chengdu 611130, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province & Chinese Academy of Science, Nanjing 210014, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
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50
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Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity. Proc Natl Acad Sci U S A 2016; 113:8326-31. [PMID: 27382177 DOI: 10.1073/pnas.1606728113] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stomata, epidermal valves facilitating plant-atmosphere gas exchange, represent a powerful model for understanding cell fate and pattern in plants. Core basic helix-loop-helix (bHLH) transcription factors regulating stomatal development were identified in Arabidopsis, but this dicot's developmental pattern and stomatal morphology represent only one of many possibilities in nature. Here, using unbiased forward genetic screens, followed by analysis of reporters and engineered mutants, we show that stomatal initiation in the grass Brachypodium distachyon uses orthologs of stomatal regulators known from Arabidopsis but that the function and behavior of individual genes, the relationships among genes, and the regulation of their protein products have diverged. Our results highlight ways in which a kernel of conserved genes may be alternatively wired to produce diversity in patterning and morphology and suggest that the stomatal transcription factor module is a prime target for breeding or genome modification to improve plant productivity.
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