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Lin X, Xu Y, Wang D, Yang Y, Zhang X, Bie X, Gui L, Chen Z, Ding Y, Mao L, Zhang X, Lu F, Zhang X, Uauy C, Fu X, Xiao J. Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses. MOLECULAR PLANT 2024; 17:438-459. [PMID: 38310351 DOI: 10.1016/j.molp.2024.01.010] [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: 08/14/2023] [Revised: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024]
Abstract
The spike architecture of wheat plays a crucial role in determining grain number, making it a key trait for optimization in wheat breeding programs. In this study, we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages, revealing coordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition. We constructed a core transcriptional regulatory network (TRN) that drives wheat spike formation and experimentally validated a multi-layer regulatory module involving TaSPL15, TaAGLG1, and TaFUL2. By integrating the TRN with genome-wide association studies, we identified 227 transcription factors, including 42 with known functions and 185 with unknown functions. Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time, such as TaMYC2-A1, TaMYB30-A1, and TaWRKY37-A1. Of particular interest, TaMYB30-A1, downstream of and repressed by WFZP, was found to regulate fertile spikelet number. Notably, the excellent haplotype of TaMYB30-A1, which contains a C allele at the WFZP binding site, was enriched during wheat breeding improvement in China, leading to improved agronomic traits. Finally, we constructed a free and open access Wheat Spike Multi-Omic Database (http://39.98.48.156:8800/#/). Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development, with practical value for wheat breeding.
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Affiliation(s)
- Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongxin Xu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongzhi Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiaoyu Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Bie
- Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Lixuan Gui
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan 610000, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan 610000, China
| | - Yiliang Ding
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Long Mao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fei Lu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China
| | - Xiansheng Zhang
- Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiangdong Fu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China.
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2
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Parker GD, Hanley L, Yu XY. Mass Spectral Imaging to Map Plant-Microbe Interactions. Microorganisms 2023; 11:2045. [PMID: 37630605 PMCID: PMC10459445 DOI: 10.3390/microorganisms11082045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Plant-microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.
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Affiliation(s)
- Gabriel D. Parker
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Luke Hanley
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Xiao-Ying Yu
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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3
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Batool TS, Aslam R, Gul A, Paracha RZ, Ilyas M, De Abreu K, Munir F, Amir R, Williams LE. Genome-wide analysis of heavy metal ATPases (HMAs) in Poaceae species and their potential role against copper stress in Triticum aestivum. Sci Rep 2023; 13:7551. [PMID: 37160901 PMCID: PMC10170112 DOI: 10.1038/s41598-023-32023-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/21/2023] [Indexed: 05/11/2023] Open
Abstract
Plants require copper for normal growth and development and have evolved an efficient system for copper management based on transport proteins such as P1B-ATPases, also known as heavy metal ATPases (HMAs). Here, we report HMAs in eleven different Poaceae species, including wheat. Furthermore, the possible role of wheat HMAs in copper stress was investigated. BlastP searches identified 27 HMAs in wheat, and phylogenetic analysis based on the Maximum Likelihood method demonstrated a separation into four distinct clades. Conserved motif analysis, domain identification, gene structure, and transmembrane helices number were also identified for wheat HMAs using computational tools. Wheat seedlings grown hydroponically were subjected to elevated copper and demonstrated toxicity symptoms with effects on fresh weight and changes in expression of selected HMAs TaHMA7, TaHMA8, and TaHMA9 were upregulated in response to elevated copper, suggesting a role in wheat copper homeostasis. Further investigations on these heavy metal pumps can provide insight into strategies for enhancing crop heavy metal tolerance in the face of heavy metal pollution.
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Affiliation(s)
- Tuba Sharf Batool
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Roohi Aslam
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- School of Interdisciplinary Engineering & Sciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Mahnoor Ilyas
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Kathryn De Abreu
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Faiza Munir
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Lorraine E Williams
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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4
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Meng G, Rasmussen SK, Christensen CSL, Fan W, Torp AM. Molecular breeding of barley for quality traits and resilience to climate change. Front Genet 2023; 13:1039996. [PMID: 36685930 PMCID: PMC9851277 DOI: 10.3389/fgene.2022.1039996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
Barley grains are a rich source of compounds, such as resistant starch, beta-glucans and anthocyanins, that can be explored in order to develop various products to support human health, while lignocellulose in straw can be optimised for feed in husbandry, bioconversion into bioethanol or as a starting material for new compounds. Existing natural variations of these compounds can be used to breed improved cultivars or integrated with a large number of mutant lines. The technical demands can be in opposition depending on barley's end use as feed or food or as a source of biofuel. For example beta-glucans are beneficial in human diets but can lead to issues in brewing and poultry feed. Barley breeders have taken action to integrate new technologies, such as induced mutations, transgenics, marker-assisted selection, genomic selection, site-directed mutagenesis and lastly machine learning, in order to improve quality traits. Although only a limited number of cultivars with new quality traits have so far reached the market, research has provided valuable knowledge and inspiration for future design and a combination of methodologies to achieve the desired traits. The changes in climate is expected to affect the quality of the harvested grain and it is already a challenge to mitigate the unpredictable seasonal and annual variations in temperature and precipitation under elevated [CO2] by breeding. This paper presents the mutants and encoded proteins, with a particular focus on anthocyanins and lignocellulose, that have been identified and characterised in detail and can provide inspiration for continued breeding to achieve desired grain and straw qualities.
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Affiliation(s)
- Geng Meng
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark,College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Søren K. Rasmussen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark,*Correspondence: Søren K. Rasmussen,
| | | | - Weiyao Fan
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Anna Maria Torp
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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5
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Gao Y, Qi S, Wang Y. Nitrate signaling and use efficiency in crops. PLANT COMMUNICATIONS 2022; 3:100353. [PMID: 35754172 PMCID: PMC9483113 DOI: 10.1016/j.xplc.2022.100353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Nitrate (NO3-) is not only an essential nutrient but also an important signaling molecule for plant growth. Low nitrogen use efficiency (NUE) of crops is causing increasingly serious environmental and ecological problems. Understanding the molecular mechanisms of NO3- regulation in crops is crucial for NUE improvement in agriculture. During the last several years, significant progress has been made in understanding the regulation of NO3- signaling in crops, and some key NO3- signaling factors have been shown to play important roles in NO3- utilization. However, no detailed reviews have yet summarized these advances. Here, we focus mainly on recent advances in crop NO3- signaling, including short-term signaling, long-term signaling, and the impact of environmental factors. We also review the regulation of crop NUE by crucial genes involved in NO3- signaling. This review provides useful information for further research on NO3- signaling in crops and a theoretical basis for breeding new crop varieties with high NUE, which has great significance for sustainable agriculture.
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Affiliation(s)
- Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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6
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Mass spectral imaging showing the plant growth-promoting rhizobacteria's effect on the Brachypodium awn. Biointerphases 2022; 17:031006. [PMID: 35738921 DOI: 10.1116/6.0001949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The plant growth-promoting rhizobacteria (PGPR) on the host plant surface play a key role in biological control and pathogenic response in plant functions and growth. However, it is difficult to elucidate the PGPR effect on plants. Such information is important in biomass production and conversion. Brachypodium distachyon (Brachypodium), a genomics model for bioenergy and native grasses, was selected as a C3 plant model; and the Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.) were chosen as representative PGPR strains. The PGPRs were introduced to the Brachypodium seed's awn prior to germination, and their possible effects on the seeding and growth were studied using different modes of time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurements, including a high mass-resolution spectral collection and delayed image extraction. We observed key plant metabolic products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and auxin indole-3-acetic acid in the Brachypodium awns. Furthermore, principal component analysis and two-dimensional imaging analysis reveal that the Brachypodium awns are sensitive to the PGPR, leading to chemical composition and morphology changes on the awn surface. Our results show that ToF-SIMS can be an effective tool to probe cell-to-cell interactions at the biointerface. This work provides a new approach to studying the PGPR effects on awn and shows its potential for the research of plant growth in the future.
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7
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Meng Y, Varshney K, Incze N, Badics E, Kamran M, Davies SF, Oppermann LMF, Magne K, Dalmais M, Bendahmane A, Sibout R, Vogel J, Laudencia-Chingcuanco D, Bond CS, Soós V, Gutjahr C, Waters MT. KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular-mycorrhizal symbiosis in Brachypodium distachyon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1559-1574. [PMID: 34953105 DOI: 10.1111/tpj.15651] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
KARRIKIN INSENSITIVE2 (KAI2) is an α/β-hydrolase required for plant responses to karrikins, which are abiotic butenolides that can influence seed germination and seedling growth. Although represented by four angiosperm species, loss-of-function kai2 mutants are phenotypically inconsistent and incompletely characterised, resulting in uncertainties about the core functions of KAI2 in plant development. Here we characterised the developmental functions of KAI2 in the grass Brachypodium distachyon using molecular, physiological and biochemical approaches. Bdkai2 mutants exhibit increased internode elongation and reduced leaf chlorophyll levels, but only a modest increase in water loss from detached leaves. Bdkai2 shows increased numbers of lateral roots and reduced root hair growth, and fails to support normal root colonisation by arbuscular-mycorrhizal (AM) fungi. The karrikins KAR1 and KAR2 , and the strigolactone (SL) analogue rac-GR24, each elicit overlapping but distinct changes to the shoot transcriptome via BdKAI2. Finally, we show that BdKAI2 exhibits a clear ligand preference for desmethyl butenolides and weak responses to methyl-substituted SL analogues such as GR24. Our findings suggest that KAI2 has multiple roles in shoot development, root system development and transcriptional regulation in grasses. Although KAI2-dependent AM symbiosis is likely conserved within monocots, the magnitude of the effect of KAI2 on water relations may vary across angiosperms.
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Affiliation(s)
- Yongjie Meng
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kartikye Varshney
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, 85354, Germany
| | - Norbert Incze
- Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Eszter Badics
- Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, Martonvásár, 2462, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Muhammad Kamran
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Sabrina F Davies
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Larissa M F Oppermann
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Kévin Magne
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France
| | - Marion Dalmais
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France
| | - Abdel Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, 91405, France
| | - Richard Sibout
- Institut Jean-Pierre Bourgin, UMR1318 INRAE-AgroParisTech, Versailles Cedex, F-78026, France
- UR1268 BIA, INRAE, Nantes, 44300, France
| | - John Vogel
- DOE Joint Genome Institute, Berkeley, California, 94720, USA
| | | | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Vilmos Soós
- Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, Martonvásár, 2462, Hungary
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, 85354, Germany
| | - Mark T Waters
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
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8
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Gao Y, Quan S, Lyu B, Tian T, Liu Z, Nie Z, Qi S, Jia J, Shu J, Groot E, Wu J, Wang Y. Barley transcription factor HvNLP2 mediates nitrate signaling and affects nitrogen use efficiency. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:770-783. [PMID: 34050753 DOI: 10.1093/jxb/erab245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Plants have evolved complex mechanisms to adapt to the changing nitrogen levels in the environment. In Arabidopsis, more than a dozen nitrate signaling regulatory genes have been characterized, including the NODULE INCEPTION-LIKE PROTEIN (AtNLP) genes, which play essential roles in nitrate signaling. However, whether NLP genes in the Triticeae crops are involved in nitrate regulation and nitrogen use efficiency (NUE) remains unknown. Here, we isolated a barley (Hordeum vulgare L.) mutant, hvnlp2-1, from a TILLING (Targeting Local Lesions IN Genomes) population and constructed two RNAi lines, hvnlp2-2 and hvnlp2-3, to study the function of HvNLP2. The expression of the nitrate-responsive genes was substantially inhibited after nitrate treatment in the hvnlp2 mutants, indicating that HvNLP2 controls nitrate signaling. Nitrate content was significantly higher in the hvnlp2 mutants, which may result from the decreased assimilation of nitrogen caused by reduced nitrate reductase activity and expression of nitrate assimilatory genes. HvNLP2 is localized to the nucleus in the presence of nitrate. Further investigation showed that HvNLP2 binds to and activates the nitrate-responsive cis-elements. Moreover, hvnlp2 exhibited reduced biomass, seed yield, and NUE. Therefore, HvNLP2 controls nitrate signaling and plays an important role in NUE.
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Affiliation(s)
- Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Bo Lyu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Tian Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Zhiguang Liu
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong, China
| | - Zhentian Nie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jingbo Jia
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jing Shu
- College of Agriculture Science and Technology, Shandong Agriculture and Engineering University, Jinan, Shandong, China
| | - Edwin Groot
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
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9
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Jacquiod S, Spor A, Wei S, Munkager V, Bru D, Sørensen SJ, Salon C, Philippot L, Blouin M. Artificial selection of stable rhizosphere microbiota leads to heritable plant phenotype changes. Ecol Lett 2021; 25:189-201. [PMID: 34749426 DOI: 10.1111/ele.13916] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
Artificial selection of microbiota opens new avenues for improving plants. However, reported results lack consistency. We hypothesised that the success in artificial selection of microbiota depends on the stabilisation of community structure. In a ten-generation experiment involving 1,800 plants, we selected rhizosphere microbiota of Brachypodium distachyon associated with high or low leaf greenness, a proxy of plant performance. The microbiota structure showed strong fluctuations during an initial transitory phase, with no detectable leaf greenness heritability. After five generations, the microbiota structure stabilised, concomitantly with heritability in leaf greenness. Selection, initially ineffective, did successfully alter the selected property as intended, especially for high selection. We show a remarkable correlation between the variability in plant traits and selected microbiota structures, revealing two distinct sub-communities associated with high or low leaf greenness, whose abundance was significantly steered by directional selection. Understanding microbiota structure stabilisation will improve the reliability of artificial microbiota selection.
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Affiliation(s)
- Samuel Jacquiod
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Aymé Spor
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Shaodong Wei
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Victoria Munkager
- Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark
| | - David Bru
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Christophe Salon
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Laurent Philippot
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Manuel Blouin
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
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10
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Sakai K, Citerne S, Antelme S, Le Bris P, Daniel S, Bouder A, D'Orlando A, Cartwright A, Tellier F, Pateyron S, Delannoy E, Laudencia-Chingcuanco D, Mouille G, Palauqui JC, Vogel J, Sibout R. BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon. BMC PLANT BIOLOGY 2021; 21:196. [PMID: 33892630 PMCID: PMC8067424 DOI: 10.1186/s12870-021-02970-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND The vascular system of plants consists of two main tissue types, xylem and phloem. These tissues are organized into vascular bundles that are arranged into a complex network running through the plant that is essential for the viability of land plants. Despite their obvious importance, the genes involved in the organization of vascular tissues remain poorly understood in grasses. RESULTS We studied in detail the vascular network in stems from the model grass Brachypodium distachyon (Brachypodium) and identified a large set of genes differentially expressed in vascular bundles versus parenchyma tissues. To decipher the underlying molecular mechanisms of vascularization in grasses, we conducted a forward genetic screen for abnormal vasculature. We identified a mutation that severely affected the organization of vascular tissues. This mutant displayed defects in anastomosis of the vascular network and uncommon amphivasal vascular bundles. The causal mutation is a premature stop codon in ERECTA, a LRR receptor-like serine/threonine-protein kinase. Mutations in this gene are pleiotropic indicating that it serves multiple roles during plant development. This mutant also displayed changes in cell wall composition, gene expression and hormone homeostasis. CONCLUSION In summary, ERECTA has a pleiotropic role in Brachypodium. We propose a major role of ERECTA in vasculature anastomosis and vascular tissue organization in Brachypodium.
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Affiliation(s)
- Kaori Sakai
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Sébastien Antelme
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Philippe Le Bris
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | | | | | | | - Amy Cartwright
- United States Department of Energy Joint Genome Institute, Berkeley, California, 94598, USA
| | - Frédérique Tellier
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Stéphanie Pateyron
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | | | - Gregory Mouille
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Jean Christophe Palauqui
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - John Vogel
- United States Department of Energy Joint Genome Institute, Berkeley, California, 94598, USA
- University of California, Berkeley, CA, USA
| | - Richard Sibout
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France.
- INRAE, UR BIA, F-44316, Nantes, France.
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11
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Hoang QTN, Tripathi S, Cho JY, Choi DM, Shin AY, Kwon SY, Han YJ, Kim JI. Suppression of Phytochrome-Interacting Factors Enhances Photoresponses of Seedlings and Delays Flowering With Increased Plant Height in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2021; 12:756795. [PMID: 34650585 PMCID: PMC8505764 DOI: 10.3389/fpls.2021.756795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/07/2021] [Indexed: 05/05/2023]
Abstract
Phytochromes are red and far-red photoreceptors that regulate plant growth and development under ambient light conditions. During phytochrome-mediated photomorphogenesis, phytochrome-interacting factors (PIFs) are the most important signaling partners that regulate the expression of light-responsive genes. However, the function of PIFs in monocots has not been studied well. In this study, using RNA interference (RNAi), we investigated the functions of BdPIL1 and BdPIL3, two PIF-like genes identified in Brachypodium distachyon, which are closely related to Arabidopsis PIF1 and PIF3. The expression of their genes is light-inducible, and both BdPIL1 and BdPIL3 proteins interact with phytochromes in an active form-specific manner. Transgenic Brachypodium seedlings with the RNAi constructs of BdPIL1 and BdPIL3 showed decreased coleoptile lengths and increased leaf growth when exposed to both red and far-red light. In addition, the transgenic plants were taller with elongated internodes than wild-type Bd21-3 plant, exhibiting late flowering. Moreover, RNA-seq analysis revealed downregulation of many genes in the transgenic plants, especially those related to the regulation of cell number, floral induction, and chlorophyll biosynthesis, which were consistent with the phenotypes of increased plant height, delayed flowering, and pale green leaves. Furthermore, we demonstrated the DNA-binding ability of BdPIL1 and BdPIL3 to the putative target promoters and that the DNA-binding was inhibited in the presence of phytochromes. Therefore, this study determines a molecular mechanism underlying phytochrome-mediated PIF regulation in Brachypodium, i.e., sequestration, and also elucidates the functions of BdPIL1 and BdPIL3 in the growth and development of the monocot plant.
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Affiliation(s)
- Quyen T. N. Hoang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Sharanya Tripathi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jae-Yong Cho
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Da-Min Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yun-Jeong Han
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
- *Correspondence: Jeong-Il Kim,
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12
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Biru FN, Cazzonelli CI, Elbaum R, Johnson SN. Contrasting effects of Miocene and Anthropocene levels of atmospheric CO 2 on silicon accumulation in a model grass. Biol Lett 2020; 16:20200608. [PMID: 33232651 DOI: 10.1098/rsbl.2020.0608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Grasses are hyper-accumulators of silicon (Si), which they acquire from the soil and deposit in tissues to resist environmental stresses. Given the high metabolic costs of herbivore defensive chemicals and structural constituents (e.g. cellulose), grasses may substitute Si for these components when carbon is limited. Indeed, high Si uptake grasses evolved in the Miocene when atmospheric CO2 concentration was much lower than present levels. It is, however, unknown how pre-industrial CO2 concentrations affect Si accumulation in grasses. Using Brachypodium distachyon, we hydroponically manipulated Si-supply (0.0, 0.5, 1, 1.5, 2 mM) and grew plants under Miocene (200 ppm) and Anthropocene levels of CO2 comprising ambient (410 ppm) and elevated (640 ppm) CO2 concentrations. We showed that regardless of Si treatments, the Miocene CO2 levels increased foliar Si concentrations by 47% and 56% relative to plants grown under ambient and elevated CO2, respectively. This is owing to higher accumulation overall, but also the reallocation of Si from the roots into the shoots. Our results suggest that grasses may accumulate high Si concentrations in foliage when carbon is less available (i.e. pre-industrial CO2 levels) but this is likely to decline under future climate change scenarios, potentially leaving grasses more susceptible to environmental stresses.
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Affiliation(s)
- Fikadu N Biru
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia.,College of Agriculture and Veterinary Medicine, Jimma University, Jimma 307, Ethiopia
| | - Christopher I Cazzonelli
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
| | - Rivka Elbaum
- R H Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Scott N Johnson
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
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13
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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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14
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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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15
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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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16
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Ahkami AH, Wang W, Wietsma TW, Winkler T, Lange I, Jansson C, Lange BM, McDowell NG. Metabolic shifts associated with drought-induced senescence in Brachypodium. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110278. [PMID: 31623774 DOI: 10.1016/j.plantsci.2019.110278] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/05/2019] [Accepted: 09/15/2019] [Indexed: 05/13/2023]
Abstract
The metabolic underpinnings of plant survival under severe drought-induced senescence conditions are poorly understood. In this study, we assessed the morphological, physiological and metabolic responses to sustained water deficit in Brachypodium distachyon, a model organism for research on temperate grasses. Relative to control plants, fresh biomass, leaf water potential, and chlorophyll levels decreased rapidly in plants grown under drought conditions, demonstrating an early onset of senescence. The leaf C/N ratio and protein content showed an increase in plants subjected to drought stress. The concentrations of several small molecule carbohydrates and amino acid-derived metabolites previously implicated in osmotic protection increased rapidly in plants experiencing water deficit. Malic acid, a low molecular weight organic acid with demonstrated roles in stomatal closure, also increased rapidly as a response to drought treatment. The concentrations of prenyl lipids, such as phytol and α-tocopherol, increased early during the drought treatment but then dropped dramatically. Surprisingly, continued changes in the quantities of metabolites were observed, even in samples harvested from visibly senesced plants. The data presented here provide insights into the processes underlying persistent metabolic activity during sustained water deficit and can aid in identifying mechanisms of drought tolerance in plants.
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Affiliation(s)
- Amir H Ahkami
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA.
| | - Wenzhi Wang
- Earth Systems Science Division, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Thomas W Wietsma
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Tanya Winkler
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
| | - Christer Jansson
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
| | - Nate G McDowell
- Earth Systems Science Division, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA.
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17
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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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18
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Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20092348. [PMID: 31083584 PMCID: PMC6540107 DOI: 10.3390/ijms20092348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/27/2022] Open
Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.
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Affiliation(s)
- Yoshihiko Onda
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Minami Shimizu
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yukiko Uehara-Yamaguchi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Masami Y Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - David F Garvin
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Institute of Plant Science and Resource, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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19
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Lenk I, Fisher LHC, Vickers M, Akinyemi A, Didion T, Swain M, Jensen CS, Mur LAJ, Bosch M. Transcriptional and Metabolomic Analyses Indicate that Cell Wall Properties are Associated with Drought Tolerance in Brachypodium distachyon. Int J Mol Sci 2019; 20:E1758. [PMID: 30974727 PMCID: PMC6479473 DOI: 10.3390/ijms20071758] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/03/2019] [Accepted: 04/08/2019] [Indexed: 01/07/2023] Open
Abstract
Brachypodium distachyon is an established model for drought tolerance. We previously identified accessions exhibiting high tolerance, susceptibility and intermediate tolerance to drought; respectively, ABR8, KOZ1 and ABR4. Transcriptomics and metabolomic approaches were used to define tolerance mechanisms. Transcriptional analyses suggested relatively few drought responsive genes in ABR8 compared to KOZ1. Linking these to gene ontology (GO) terms indicated enrichment for "regulated stress response", "plant cell wall" and "oxidative stress" associated genes. Further, tolerance correlated with pre-existing differences in cell wall-associated gene expression including glycoside hydrolases, pectin methylesterases, expansins and a pectin acetylesterase. Metabolomic assessments of the same samples also indicated few significant changes in ABR8 with drought. Instead, pre-existing differences in the cell wall-associated metabolites correlated with drought tolerance. Although other features, e.g., jasmonate signaling were suggested in our study, cell wall-focused events appeared to be predominant. Our data suggests two different modes through which the cell wall could confer drought tolerance: (i) An active response mode linked to stress induced changes in cell wall features, and (ii) an intrinsic mode where innate differences in cell wall composition and architecture are important. Both modes seem to contribute to ABR8 drought tolerance. Identification of the exact mechanisms through which the cell wall confers drought tolerance will be important in order to inform development of drought tolerant crops.
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Affiliation(s)
- Ingo Lenk
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge, Denmark.
| | - Lorraine H C Fisher
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Martin Vickers
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Aderemi Akinyemi
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Thomas Didion
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge, Denmark.
| | - Martin Swain
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | | | - Luis A J Mur
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
| | - Maurice Bosch
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3EE, UK.
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David LC, Girin T, Fleurisson E, Phommabouth E, Mahfoudhi A, Citerne S, Berquin P, Daniel-Vedele F, Krapp A, Ferrario-Méry S. Developmental and physiological responses of Brachypodium distachyon to fluctuating nitrogen availability. Sci Rep 2019; 9:3824. [PMID: 30846873 PMCID: PMC6405861 DOI: 10.1038/s41598-019-40569-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 02/12/2019] [Indexed: 02/03/2023] Open
Abstract
The Nitrogen Use Efficiency (NUE) of grain cereals depends on nitrate (NO3-) uptake from the soil, translocation to the aerial parts, nitrogen (N) assimilation and remobilization to the grains. Brachypodium distachyon has been proposed as a model species to identify the molecular players and mechanisms that affects these processes, for the improvement of temperate C3 cereals. We report on the developmental, physiological and grain-characteristic responses of the Bd21-3 accession of Brachypodium to variations in NO3- availability. As previously described in wheat and barley, we show that vegetative growth, shoot/root ratio, tiller formation, spike development, tissue NO3- and N contents, grain number per plant, grain yield and grain N content are sensitive to pre- and/or post-anthesis NO3- supply. We subsequently described constitutive and NO3--inducible components of both High and Low Affinity Transport Systems (HATS and LATS) for root NO3- uptake, and BdNRT2/3 candidate genes potentially involved in the HATS. Taken together, our data validate Brachypodium Bd21-3 as a model to decipher cereal N nutrition. Apparent specificities such as high grain N content, strong post-anthesis NO3- uptake and efficient constitutive HATS, further identify Brachypodium as a direct source of knowledge for crop improvement.
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Affiliation(s)
- L C David
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - T Girin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France.
| | - E Fleurisson
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - E Phommabouth
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - A Mahfoudhi
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - S Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - P Berquin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - F Daniel-Vedele
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - A Krapp
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - S Ferrario-Méry
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
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21
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Wang J, Hüner N, Tian L. Identification and molecular characterization of the Brachypodium distachyon NRT2 family, with a major role of BdNRT2.1. PHYSIOLOGIA PLANTARUM 2019; 165:498-510. [PMID: 29498420 DOI: 10.1111/ppl.12716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/09/2018] [Accepted: 02/27/2018] [Indexed: 05/28/2023]
Abstract
The small monocot plant Brachypodium distachyon is rapidly emerging as a powerful model system to study questions unique to the monocot crops. An extensive BLAST search was carried to identify putative orthologues of the Arabidopsis NRT2 genes in the fully sequenced Brachypodium genome. Seven genes encoding putative high-affinity nitrate transporters (BdNRT2) were identified. Transcriptional analysis of individual BdNRT2 gene under various nitrogen sources and levels in the wild-type and a T-DNA mutant of BdNRT2.1 were performed. A transgenic approach was taken to complement the bdnrt2.1 mutant. BdNRT2.1 and BdNRT2.2 were strongly induced by nitrate resupply to nitrogen-starved plants and were classified as inducible genes. BdNRT2.5 was found to be repressed by nitrate resupply whereas other members were constitutively expressed in the root. Interestingly, higher ammonium concentrations also triggered similar gene expression regulation, suggesting BdNRT2 gene expression was also governed by internal nitrogen status, not just external nitrate concentrations. In bdnrt2.1 mutant, the high-affinity transporter system (HATS) was reduced by 30% and BdNRT2.2 and BdNRT2.6 were differentially regulated. This pioneering research demonstrates that genes in the BdNRT2 family have diverse roles, differing from the Arabidopsis AtNRT2 family, in response to various nitrogen conditions. BdNRT2.1 serves as a key member of the family.
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Affiliation(s)
- Jiang Wang
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Norman Hüner
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Lining Tian
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- London Research and Development Center, Agriculture and Agri-Food Canada, London, Ontario, Canada
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22
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Khan Z, Karamahmutoğlu H, Elitaş M, Yüce M, Budak H. THROUGH THE LOOKING GLASS: Real-Time Imaging in Brachypodium Roots and Osmotic Stress Analysis. PLANTS (BASEL, SWITZERLAND) 2019; 8:E14. [PMID: 30625995 PMCID: PMC6358813 DOI: 10.3390/plants8010014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/23/2018] [Accepted: 01/04/2019] [Indexed: 01/01/2023]
Abstract
To elucidate dynamic developmental processes in plants, live tissues and organs must be visualised frequently and for extended periods. The development of roots is studied at a cellular resolution not only to comprehend the basic processes fundamental to maintenance and pattern formation but also study stress tolerance adaptation in plants. Despite technological advancements, maintaining continuous access to samples and simultaneously preserving their morphological structures and physiological conditions without causing damage presents hindrances in the measurement, visualisation and analyses of growing organs including plant roots. We propose a preliminary system which integrates the optical real-time visualisation through light microscopy with a liquid culture which enables us to image at the tissue and cellular level horizontally growing Brachypodium roots every few minutes and up to 24 h. We describe a simple setup which can be used to track the growth of the root as it grows including the root tip growth and osmotic stress dynamics. We demonstrate the system's capability to scale down the PEG-mediated osmotic stress analysis and collected data on gene expression under osmotic stress.
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Affiliation(s)
- Zaeema Khan
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey.
| | - Hande Karamahmutoğlu
- Mechatronics Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey.
| | - Meltem Elitaş
- Mechatronics Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey.
| | - Meral Yüce
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Istanbul 34956, Turkey.
| | - Hikmet Budak
- Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA.
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23
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24
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Lawas LMF, Zuther E, Jagadish SK, Hincha DK. Molecular mechanisms of combined heat and drought stress resilience in cereals. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:212-217. [PMID: 29673612 DOI: 10.1016/j.pbi.2018.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/26/2018] [Accepted: 04/04/2018] [Indexed: 05/22/2023]
Abstract
Global climate change leads to increased temperatures and decreased precipitation in many parts of the world. The simultaneous occurrence of high temperature and water deficit results in heat stress damage in plants. Cereals provide the majority of calories for human consumption, making this stress scenario particularly threatening for global food security. Several studies in both dicots and cereals indicate that the molecular reactions of plants to combined stresses cannot be predicted from reactions to single stresses. Recent results indicate that the regulation of heat shock proteins and of sugar transport and accumulation in flowers are crucial factors determining resilience of tolerant genotypes to combined heat and drought stress.
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Affiliation(s)
- Lovely Mae F Lawas
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Ellen Zuther
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | | | - Dirk K Hincha
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany.
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25
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Germination and the Early Stages of Seedling Development in Brachypodium distachyon. Int J Mol Sci 2018; 19:ijms19102916. [PMID: 30257527 PMCID: PMC6212949 DOI: 10.3390/ijms19102916] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 01/27/2023] Open
Abstract
Successful germination and seedling development are crucial steps in the growth of a new plant. In this study, we investigated the course of the cell cycle during germination in relation to grain hydration in the model grass Brachypodium distachyon (Brachypodium) for the first time. Flow cytometry was performed to monitor the cell cycle progression during germination and to estimate DNA content in embryo tissues. The analyses of whole zygotic embryos revealed that the relative DNA content was 2C, 4C, 8C, and 16C. Endoreplicated nuclei were detected in the scutellum and coleorhiza cells, whereas the rest of the embryo tissues only had nuclei with a 2C and 4C DNA content. This study was accompanied by a spatiotemporal profile analysis of the DNA synthetic activity in the organs of Brachypodium embryos during germination using EdU labelling. Upon imbibition, nuclear DNA replication was initiated in the radicle within 11 h and subsequently spread towards the plumule. The first EdU-labelled prophases were observed after 14 h of imbibition. Analysis of selected genes that are involved in the regulation of the cell cycle, such as those encoding cyclin-dependent kinases and cyclins, demonstrated an increase in their expression profiles.
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26
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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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27
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Głazowska S, Murozuka E, Persson DP, Castro PH, Schjoerring JK. Silicon affects seed development and leaf macrohair formation in Brachypodium distachyon. PHYSIOLOGIA PLANTARUM 2018; 163:231-246. [PMID: 29215732 DOI: 10.1111/ppl.12675] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 11/27/2017] [Indexed: 05/11/2023]
Abstract
Silicon (Si) has many beneficial effects in plants, especially for the survival from biotic and abiotic stresses. However, Si may negatively affect the quality of lignocellulosic biomass for bioenergy purposes. Despite many studies, the regulation of Si distribution and deposition in plants remains to be fully understood. Here, we have identified the Brachypodium distachyon mutant low-silicon 1 (Bdlsi1-1), with impaired channeling function of the Si influx transporter BdLSI1, resulting in a substantial reduction of Si in shoots. Bioimaging by laser ablation-inductively coupled plasma-mass spectrometry showed that the wild-type plants deposited Si mainly in the bracts, awns and leaf macrohairs. The Bdlsi1-1 mutants showed substantial (>90%) reduction of Si in the mature shoots. The Bdlsi1-1 leaves had fewer, shorter macrohairs, but the overall pattern of Si distribution in bracts and leaf tissues was similar to that in the wild-type. The Bdlsi1-1 plants supplied with Si had significantly lower seed weights, compared to the wild-type. In low-Si media, the seed weight of wild-type plants was similar to that of Bdlsi1-1 mutants supplied with Si, while the Bdlsi1-1 seed weight decreased further. We conclude that Si deficiency results in widespread alterations in leaf surface morphology and seed formation in Brachypodium, showing the importance of Si for successful development in grasses.
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Affiliation(s)
- Sylwia Głazowska
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
| | - Emiko Murozuka
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
| | - Daniel P Persson
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
| | - Pedro Humberto Castro
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
| | - Jan K Schjoerring
- Plant and Soil Science Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
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28
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Xu X, Sharma R, Tondelli A, Russell J, Comadran J, Schnaithmann F, Pillen K, Kilian B, Cattivelli L, Thomas WTB, Flavell AJ. Genome-Wide Association Analysis of Grain Yield-Associated Traits in a Pan-European Barley Cultivar Collection. THE PLANT GENOME 2018; 11:170073. [PMID: 29505630 DOI: 10.3835/plantgenome2017.08.0073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with two and six row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6,810 segregating gene-based single nucleotide polymorphism (SNP) loci and corresponding field trial data were obtained for eight traits related to grain yield at four European sites in three countries over two growth years. The combined data were analyzed and statistically significant associations between the traits and regions of the barley genomes were obtained. Combining this information with the high resolution gene map for barley allowed the identification of candidate genes underlying all scored traits and superposition of this information with the known genomics of grain trait genes in rice resulted in the assignation of 13 putative barley genes controlling grain traits in European cultivated barley. Several of these genes are associated with grain traits in both winter and spring barley.
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29
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Onda Y, Takahagi K, Shimizu M, Inoue K, Mochida K. Multiplex PCR Targeted Amplicon Sequencing (MTA-Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:201. [PMID: 29628929 PMCID: PMC5876661 DOI: 10.3389/fpls.2018.00201] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/02/2018] [Indexed: 05/20/2023]
Abstract
Next-generation sequencing (NGS) technologies have enabled genome re-sequencing for exploring genome-wide polymorphisms among individuals, as well as targeted re-sequencing for the rapid and simultaneous detection of polymorphisms in genes associated with various biological functions. Therefore, a simple and robust method for targeted re-sequencing should facilitate genotyping in a wide range of biological fields. In this study, we developed a simple, custom, targeted re-sequencing method, designated "multiplex PCR targeted amplicon sequencing (MTA-seq)," and applied it to the genotyping of the model grass Brachypodium distachyon. To assess the practical usability of MTA-seq, we applied it to the genotyping of genome-wide single-nucleotide polymorphisms (SNPs) identified in natural accessions (Bd1-1, Bd3-1, Bd21-3, Bd30-1, Koz-1, Koz-3, and Koz-4) by comparing the re-sequencing data with that of reference accession Bd21. Examination of SNP-genotyping accuracy in 443 amplicons from eight parental accessions and an F1 progeny derived by crossing of Bd21 and Bd3-1 revealed that ~95% of the SNPs were correctly called. The assessment suggested that the method provided an efficient framework for accurate and robust SNP genotyping. The method described here enables easy design of custom target SNP-marker panels in various organisms, facilitating a wide range of high-throughput genetic applications, such as genetic mapping, population analysis, molecular breeding, and genomic diagnostics.
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Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kotaro Takahagi
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Minami Shimizu
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resource, Okayama University, Okayama, Japan
- *Correspondence: Keiichi Mochida
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30
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Imaging cellulose synthase motility during primary cell wall synthesis in the grass Brachypodium distachyon. Sci Rep 2017; 7:15111. [PMID: 29118446 PMCID: PMC5678151 DOI: 10.1038/s41598-017-14988-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/19/2017] [Indexed: 12/02/2022] Open
Abstract
The mechanism of cellulose synthesis has been studied by characterizing the motility of cellulose synthase complexes tagged with a fluorescent protein; however, this approach has been used exclusively on the hypocotyl of Arabidopsis thaliana. Here we characterize cellulose synthase motility in the model grass, Brachypodium distachyon. We generated lines in which mEGFP is fused N-terminal to BdCESA3 or BdCESA6 and which grew indistinguishably from the wild type (Bd21-3) and had dense fluorescent puncta at or near the plasma membrane. Measured with a particle tracking algorithm, the average speed of GFP-BdCESA3 particles in the mesocotyl was 164 ± 78 nm min−1 (error gives standard deviation [SD], n = 1451 particles). Mean speed in the root appeared similar. For comparison, average speed in the A. thaliana hypocotyl expressing GFP-AtCESA6 was 184 ± 86 nm min−1 (n = 2755). For B. distachyon, we quantified root diameter and elongation rate in response to inhibitors of cellulose (dichlorobenylnitrile; DCB), microtubules (oryzalin), or actin (latrunculin B). Neither oryzalin nor latrunculin affected the speed of CESA complexes; whereas, DCB reduced average speed by about 50% in B. distachyon and by about 35% in A. thaliana. Evidently, between these species, CESA motility is well conserved.
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31
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Aslam R, Williams LE, Bhatti MF, Virk N. Genome-wide analysis of wheat calcium ATPases and potential role of selected ACAs and ECAs in calcium stress. BMC PLANT BIOLOGY 2017; 17:174. [PMID: 29078753 PMCID: PMC5658947 DOI: 10.1186/s12870-017-1112-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/09/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND P2- type calcium ATPases (ACAs-auto inhibited calcium ATPases and ECAs-endoplasmic reticulum calcium ATPases) belong to the P- type ATPase family of active membrane transporters and are significantly involved in maintaining accurate levels of Ca2+, Mn2+ and Zn2+ in the cytosol as well as playing a very important role in stress signaling, stomatal opening and closing and pollen tube growth. Here we report the identification and possible role of some of these ATPases from wheat. RESULTS In this study, ACA and ECA sequences of six species (belonging to Poaceae) were retrieved from different databases and a phylogenetic tree was constructed. A high degree of evolutionary relatedness was observed among P2 sequences characterized in this study. Members of the respective groups from different plant species were observed to fall under the same clade. This pattern highlights the common ancestry of P2- type calcium ATPases. Furthermore, qRT-PCR was used to analyse the expression of selected ACAs and ECAs from Triticum aestivum (wheat) under calcium toxicity and calcium deficiency. The data indicated that expression of ECAs is enhanced under calcium stress, suggesting possible roles of these ATPases in calcium homeostasis in wheat. Similarly, the expression of ACAs was significantly different in plants grown under calcium stress as compared to plants grown under control conditions. This gives clues to the role of ACAs in signal transduction during calcium stress in wheat. CONCLUSION Here we concluded that wheat genome consists of nine P2B and three P2A -type calcium ATPases. Moreover, gene loss events in wheat ancestors lead to the loss of a particular homoeolog of a gene in wheat. To elaborate the role of these wheat ATPases, qRT-PCR was performed. The results indicated that when plants are exposed to calcium stress, both P2A and P2B gene expression get enhanced. This further gives clues about the possible role of these ATPases in wheat in calcium management. These findings can be useful in future for genetic manipulations as well as in wheat genome annotation process.
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Affiliation(s)
- Roohi Aslam
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000 Pakistan
| | | | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000 Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000 Pakistan
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Oliveira EJ, Koehler AD, Rocha DI, Vieira LM, Pinheiro MVM, de Matos EM, da Cruz ACF, da Silva TCR, Tanaka FAO, Nogueira FTS, Otoni WC. Morpho-histological, histochemical, and molecular evidences related to cellular reprogramming during somatic embryogenesis of the model grass Brachypodium distachyon. PROTOPLASMA 2017; 254:2017-2034. [PMID: 28290060 DOI: 10.1007/s00709-017-1089-9] [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: 11/20/2016] [Accepted: 02/13/2017] [Indexed: 05/25/2023]
Abstract
The wild grass species Brachypodium distachyon (L.) has been proposed as a new model for temperate grasses. Among the biotechnological tools already developed for the species, an efficient induction protocol of somatic embryogenesis (SE) using immature zygotic embryos has provided the basis for genetic transformation studies. However, a systematic work to better understanding the basic cellular and molecular mechanisms that underlie the SE process of this grass species is still missing. Here, we present new insights at the morpho-histological, histochemical, and molecular aspects of B. distachyon SE pathway. Somatic embryos arose from embryogenic callus formed by cells derived from the protodermal-dividing cells of the scutellum. These protodermal cells showed typical meristematic features and high protein accumulation which were interpreted as the first observable steps towards the acquisition of a competent state. Starch content decreased along embryogenic callus differentiation supporting the idea that carbohydrate reserves are essential to morphogenetic processes. Interestingly, starch accumulation was also observed at late stages of SE process. Searches in databanks revealed three sequences available annotated as BdSERK, being two copies corresponding to SERK1 and one showing greater identity to SERK2. In silico analysis confirmed the presence of characteristic domains in a B. distachyon Somatic Embryogenesis Receptor Kinase genes candidates (BdSERKs), which suggests SERK functions are conserved in B. distachyon. In situ hybridization demonstrated the presence of transcripts of BdSERK1 in all development since globular until scutellar stages. The results reported in this study convey important information about the morphogenetic events in the embryogenic pathway which has been lacking in B. distachyon. This study also demonstrates that B. distachyon provides a useful model system for investigating the genetic regulation of SE in grass species.
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Affiliation(s)
- Evelyn Jardim Oliveira
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Andréa Dias Koehler
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Diego Ismael Rocha
- Instituto de Biociências, Universidade Federal de Goiás, Regional Jataí, BR 364, km 195, 75801-615, Jataí, GO, Brazil
| | - Lorena Melo Vieira
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Marcos Vinícius Marques Pinheiro
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Elyabe Monteiro de Matos
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Ana Claudia Ferreira da Cruz
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Thais Cristina Ribeiro da Silva
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil
| | - Francisco André Ossamu Tanaka
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo/ESALQ, Av. Pádua Dias, 13418-900, Piracicaba, SP, Brazil
| | - Fabio Tebaldi Silveira Nogueira
- Laboratorio de Genética Molecular do Desenvolvimento Vegetal (LGMDV), Universidade de São Paulo/ESALQ, Av. Pádua Dias, 13418-900, Piracicaba, SP, Brazil.
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos/BIOAGRO, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida P. H. Rolfs s/n, 36570-900, Viçosa, MG, Brazil.
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Comparative and Evolutionary Analysis of Grass Pollen Allergens Using Brachypodium distachyon as a Model System. PLoS One 2017; 12:e0169686. [PMID: 28103252 PMCID: PMC5245863 DOI: 10.1371/journal.pone.0169686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 11/23/2022] Open
Abstract
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional characterization in related grass species.
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Corvalán C, Choe S. Identification of brassinosteroid genes in Brachypodium distachyon. BMC PLANT BIOLOGY 2017; 17:5. [PMID: 28061864 PMCID: PMC5217202 DOI: 10.1186/s12870-016-0965-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 12/23/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND Brassinosteroids (BRs) are steroidal phytohormones that are involved in diverse physiological processes and affect many important traits, such as plant stature, stress tolerance, leaf angle, fertility, and grain filling. BR signaling and biosynthetic pathways have been studied in various plants, such as the model dicot Arabidopsis thaliana; however, relatively little is known about these pathways in monocots. RESULTS To characterize BR-related processes in the model grass Brachypodium distachyon, we studied the response of these plants to the specific BR biosynthesis inhibitor, propiconazole (Pcz). We found that treatments with Pcz produced a dwarf phenotype in B. distachyon seedlings, similar to that observed in Pcz-treated Arabidopsis plants and in characterized BR-deficient mutants. Through bioinformatics analysis, we identified a list of putative homologs of genes known to be involved in BR biosynthesis and signaling in Arabidopsis, such as DWF4, BR6OX2, CPD, BRI1, and BIN2. Evaluating the response of these genes to Pcz treatments revealed that candidates for BdDWF4, BR6OX2 and, CPD were under feedback regulation. In addition, Arabidopsis plants heterologously expressing BdDWF4 displayed tall statures and elongated petioles, as would be expected in plants with elevated levels of BRs. Moreover, heterologous expression of BdBIN2 in Arabidopsis resulted in dwarfism, suggesting that BdBIN2 functions as a negative regulator of BR signaling. However, the dwarf phenotypes of Arabidopsis bri1-5, a weak BRI1 mutant allele, were not complemented by overexpression of BdBRI1, indicating that BdBRI1 and BRI1 are not functionally equivalent. CONCLUSION We identified components of the BR biosynthetic and signaling pathways in Brachypodium, and provided examples of both similarities and differences in the BR biology of these two plants. Our results suggest a framework for understanding BR biology in monocot crop plants such as Zea mays (maize) and Oryza sativa (rice).
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Affiliation(s)
- Claudia Corvalán
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Sunghwa Choe
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, 08826 South Korea
- Convergence Research Lab for Plant Functional Products, Advanced Institutes of Convergence Technology, Suwon, 16229 Gyeonggi-do South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
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Gombos M, Zombori Z, Szécsényi M, Sándor G, Kovács H, Györgyey J. Characterization of the LBD gene family in Brachypodium: a phylogenetic and transcriptional study. PLANT CELL REPORTS 2017; 36:61-79. [PMID: 27686461 DOI: 10.1007/s00299-016-2057-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/07/2016] [Indexed: 05/20/2023]
Abstract
An unambiguous nomenclature is proposed for the twenty-eight-member LOB domain transcription factor family in Brachypodium . Expression analysis provides unique transcript patterns that are characteristic of a wide range of organs and plant parts. LOB (lateral organ boundaries)-domain proteins define a family of plant-specific transcription factors involved in developmental processes from embryogenesis to seed production. They play a crucial role in shaping the plant architecture through coordinating cell fate at meristem to organ boundaries. Despite their high potential importance, our knowledge of them is limited, especially in the case of monocots. In this study, we characterized LOB domain protein coding genes (LBDs) of Brachypodium distachyon, a model plant for grasses, and present their phylogenetic relationships and an overall spatial expression study. In the Brachypodium genome database, 28 LBDs were found and then classified based on the presence of highly conserved LOB domain motif. Their transcript amounts were measured via quantitative real-time RT-PCR in 37 different plant parts from root tip to generative organs. Comprehensive phylogenetic analysis suggests that there are neither Brachypodium- nor monocot-specific lineages among LBDs, but there are differences in terms of complexity of subclasses between monocots and dicots. Although LBDs in Brachypodium have wide variation of tissue-specific expression and relative transcript levels, overall expression patterns show similarity to their counterparts in other species. The varying transcript profiles we observed support the hypothesis that Brachypodium LBDs have diverse but conserved functions in plant organogenesis.
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Affiliation(s)
- Magdolna Gombos
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Zoltán Zombori
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Mária Szécsényi
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Györgyi Sándor
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Hajnalka Kovács
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, Szeged, 6726, Hungary
| | - János Györgyey
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, Szeged, 6726, Hungary.
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Bhalla PL, Sharma A, Singh MB. Enabling Molecular Technologies for Trait Improvement in Wheat. Methods Mol Biol 2017; 1679:3-24. [PMID: 28913791 DOI: 10.1007/978-1-4939-7337-8_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Wheat is the major staple food crop and a source of calories for humans worldwide. A steady increase in the wheat production is essential to meet the demands of an ever-increasing global population and to achieve food security. The large size and structurally intricate genome of polyploid wheat had hindered the genomic analysis. However, with the advent of new genomic technologies such as next generation sequencing has led to genome drafts for bread wheat and its progenitors and has paved the way to design new strategies for crop improvement. Here we provide an overview of the advancements made in wheat genomics together with the available "omics approaches" and bioinformatics resources developed for wheat research. Advances in genomic, transcriptomic, and metabolomic technologies are highlighted as options to circumvent existing bottlenecks in the phenotypic and genomic selection and gene transfer. The contemporary reverse genetics approaches, including the novel genome editing techniques to inform targeted manipulation of a single/multiple genes and strategies for generating marker-free transgenic wheat plants, emphasize potential to revolutionize wheat improvement shortly.
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Affiliation(s)
- Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Akanksha Sharma
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Fisher LHC, Han J, Corke FMK, Akinyemi A, Didion T, Nielsen KK, Doonan JH, Mur LAJ, Bosch M. Linking Dynamic Phenotyping with Metabolite Analysis to Study Natural Variation in Drought Responses of Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2016; 7:1751. [PMID: 27965679 PMCID: PMC5126067 DOI: 10.3389/fpls.2016.01751] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/07/2016] [Indexed: 05/23/2023]
Abstract
Drought is an important environmental stress limiting the productivity of major crops worldwide. Understanding drought tolerance and possible mechanisms for improving drought resistance is therefore a prerequisite to develop drought-tolerant crops that produce significant yields with reduced amounts of water. Brachypodium distachyon (Brachypodium) is a key model species for cereals, forage grasses, and energy grasses. In this study, initial screening of a Brachypodium germplasm collection consisting of 138 different ecotypes exposed to progressive drought, highlighted the natural variation in morphology, biomass accumulation, and responses to drought stress. A core set of ten ecotypes, classified as being either tolerant, susceptible or intermediate, in response to drought stress, were exposed to mild or severe (respectively, 15 and 0% soil water content) drought stress and phenomic parameters linked to growth and color changes were assessed. When exposed to severe drought stress, phenotypic data and metabolite profiling combined with multivariate analysis revealed a remarkable consistency in separating the selected ecotypes into their different pre-defined drought tolerance groups. Increases in several metabolites, including for the phytohormones jasmonic acid and salicylic acid, and TCA-cycle intermediates, were positively correlated with biomass yield and with reduced yellow pixel counts; suggestive of delayed senescence, both key target traits for crop improvement to drought stress. While metabolite analysis also separated ecotypes into the distinct tolerance groupings after exposure to mild drought stress, similar analysis of the phenotypic data failed to do so, confirming the value of metabolomics to investigate early responses to drought stress. The results highlight the potential of combining the analyses of phenotypic and metabolic responses to identify key mechanisms and markers associated with drought tolerance in both the Brachypodium model plant as well as agronomically important crops.
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Affiliation(s)
- Lorraine H. C. Fisher
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Jiwan Han
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Fiona M. K. Corke
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Aderemi Akinyemi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | | | | | - John H. Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
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Missihoun TD, Kotchoni SO, Bartels D. Active Sites of Reduced Epidermal Fluorescence1 (REF1) Isoforms Contain Amino Acid Substitutions That Are Different between Monocots and Dicots. PLoS One 2016; 11:e0165867. [PMID: 27798665 PMCID: PMC5087895 DOI: 10.1371/journal.pone.0165867] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 10/19/2016] [Indexed: 11/22/2022] Open
Abstract
Plant aldehyde dehydrogenases (ALDHs) play important roles in cell wall biosynthesis, growth, development, and tolerance to biotic and abiotic stresses. The Reduced Epidermal Fluorescence1 is encoded by the subfamily 2C of ALDHs and was shown to oxidise coniferaldehyde and sinapaldehyde to ferulic acid and sinapic acid in the phenylpropanoid pathway, respectively. This knowledge has been gained from works in the dicotyledon model species Arabidopsis thaliana then used to functionally annotate ALDH2C isoforms in other species, based on the orthology principle. However, the extent to which the ALDH isoforms differ between monocotyledons and dicotyledons has rarely been accessed side-by-side. In this study, we used a phylogenetic approach to address this question. We have analysed the ALDH genes in Brachypodium distachyon, alongside those of other sequenced monocotyledon and dicotyledon species to examine traits supporting either a convergent or divergent evolution of the ALDH2C/REF1-type proteins. We found that B. distachyon, like other grasses, contains more ALDH2C/REF1 isoforms than A. thaliana and other dicotyledon species. Some amino acid residues in ALDH2C/REF1 isoforms were found as being conserved in dicotyledons but substituted by non-equivalent residues in monocotyledons. One example of those substitutions concerns a conserved phenylalanine and a conserved tyrosine in monocotyledons and dicotyledons, respectively. Protein structure modelling suggests that the presence of tyrosine would widen the substrate-binding pocket in the dicotyledons, and thereby influence substrate specificity. We discussed the importance of these findings as new hints to investigate why ferulic acid contents and cell wall digestibility differ between the dicotyledon and monocotyledon species.
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Affiliation(s)
- Tagnon D. Missihoun
- Department of Biology, Rutgers University, Camden, New Jersey, United States of America
- * E-mail: (SOK); (TDM)
| | - Simeon O. Kotchoni
- Department of Biology, Rutgers University, Camden, New Jersey, United States of America
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, United States of America
- * E-mail: (SOK); (TDM)
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
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Peng FY, Hu Z, Yang RC. Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants. BMC Genomics 2016; 17:573. [PMID: 27503086 PMCID: PMC4977670 DOI: 10.1186/s12864-016-2916-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/07/2016] [Indexed: 11/14/2022] Open
Abstract
Background Many genes involved in responses to photoperiod and vernalization have been characterized or predicted in Arabidopsis (Arabidopsis thaliana), Brachypodium (Brachypodium distachyon), wheat (Triticum aestivum) and barley (Hordeum vulgare). However, little is known about the transcription regulation of these genes, especially in the large, complex genomes of wheat and barley. Results We identified 68, 60, 195 and 61 genes that are known or postulated to control pathways of photoperiod (PH), vernalization (VE) and pathway integration (PI) in Arabidopsis, Brachypodium, wheat and barley for predicting transcription factor binding sites (TFBSs) in the promoters of these genes using the FIMO motif search tool of the MEME Suite. The initial predicted TFBSs were filtered to confirm the final numbers of predicted TFBSs to be 1066, 1379, 1528, and 789 in Arabidopsis, Brachypodium, wheat and barley, respectively. These TFBSs were mapped onto the PH, VE and PI pathways to infer about the regulation of gene expression in Arabidopsis and cereal species. The GC contents in promoters, untranslated regions (UTRs), coding sequences and introns were higher in the three cereal species than those in Arabidopsis. The predicted TFBSs were most abundant for two transcription factor (TF) families: MADS-box and CSD (cold shock domain). The analysis of publicly available gene expression data showed that genes with similar numbers of MADS-box and CSD TFBSs exhibited similar expression patterns across several different tissues and developmental stages. The intra-specific Tajima D-statistics of TFBS motif diversity showed different binding specificity among different TF families. The inter-specific Tajima D-statistics suggested faster TFBS divergence in TFBSs than in coding sequences and introns. Mapping TFBSs onto the PH, VE and PI pathways showed the predominance of MADS-box and CSD TFBSs in most genes of the four species, and the difference in the pathway regulations between Arabidopsis and the three cereal species. Conclusion Our approach to associating the key flowering genes with their potential TFs through prediction of putative TFBSs provides a framework to explore regulatory mechanisms of photoperiod and vernalization responses in flowering plants. The predicted TFBSs in the promoters of the flowering genes provide a basis for molecular characterization of transcription regulation in the large, complex genomes of important crop species, wheat and barley. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2916-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fred Y Peng
- Feed Crops Section, Alberta Agriculture and Forestry, 7000 - 113 Street, Edmonton, AB, T6H 5T6, Canada
| | - Zhiqiu Hu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Rong-Cai Yang
- Feed Crops Section, Alberta Agriculture and Forestry, 7000 - 113 Street, Edmonton, AB, T6H 5T6, Canada. .,Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
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40
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Li Q, Wang Y, Wang F, Guo Y, Duan X, Sun J, An H. Functional conservation and diversification of APETALA1/FRUITFULL genes in Brachypodium distachyon. PHYSIOLOGIA PLANTARUM 2016; 157:507-518. [PMID: 26856680 DOI: 10.1111/ppl.12427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
The duplicated grass APETALA1/FRUITFULL (AP1/FUL) genes have distinct but overlapping patterns of expression, suggesting their discrete roles in transition to flowering, specification of spikelet meristem identity and specification of floral organ identity. In this study, we analyzed the expression patterns and functions of four AP1/FUL paralogs (BdVRN1, BdFUL2, BdFUL3 and BdFUL4) in Brachypodium distachyon, a model plant for the temperate cereals and related grasses. Among the four genes tested, only BdVRN1 could remember the prolonged cold treatment. The recently duplicated BdVRN1 and BdFUL2 genes were expressed in a highly consistent manner and ectopic expressions of them caused similar phenotypes such as extremely early flowering and severe morphological alterations of floral organs, indicating their redundant roles in floral transition, inflorescence development and floral organ identity. In comparison, ectopic expressions of BdFUL3 and BdFUL4 only caused a moderate early flowering phenotype, suggesting their divergent function. In yeast two-hybrid assay, both BdVRN1 and BdFUL2 physically interact with SEP proteins but only BdFUL2 is able to form a homodimer. BdVRN1 also interacts weakly with BdFUL2. Our results indicate that, since the separation of AP1/FUL genes in grasses, the process of sub- or neo-functionalization has occurred and paralogs function redundantly and/or separately in flowering competence and inflorescence development.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Ye Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Fuxiang Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Yuyu Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Xueqing Duan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Jinhao Sun
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
| | - Hailong An
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, P. R. China
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Tyler L, Lee SJ, Young ND, DeIulio GA, Benavente E, Reagon M, Sysopha J, Baldini RM, Troìa A, Hazen SP, Caicedo AL. Population Structure in the Model Grass Is Highly Correlated with Flowering Differences across Broad Geographic Areas. THE PLANT GENOME 2016; 9. [PMID: 27898828 DOI: 10.3835/plantgenome2015.08.0074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The small, annual grass (L.) Beauv., a close relative of wheat ( L.) and barley ( L.), is a powerful model system for cereals and bioenergy grasses. Genome-wide association studies (GWAS) of natural variation can elucidate the genetic basis of complex traits but have been so far limited in by the lack of large numbers of well-characterized and sufficiently diverse accessions. Here, we report on genotyping-by-sequencing (GBS) of 84 , seven , and three accessions with diverse geographic origins including Albania, Armenia, Georgia, Italy, Spain, and Turkey. Over 90,000 high-quality single-nucleotide polymorphisms (SNPs) distributed across the Bd21 reference genome were identified. Our results confirm the hybrid nature of the genome, which appears as a mosaic of -like and -like sequences. Analysis of more than 50,000 SNPs for the accessions revealed three distinct, genetically defined populations. Surprisingly, these genomic profiles are associated with differences in flowering time rather than with broad geographic origin. High levels of differentiation in loci associated with floral development support the differences in flowering phenology between populations. Genome-wide association studies combining genotypic and phenotypic data also suggest the presence of one or more photoperiodism, circadian clock, and vernalization genes in loci associated with flowering time variation within populations. Our characterization elucidates genes underlying population differences, expands the germplasm resources available for , and illustrates the feasibility and limitations of GWAS in this model grass.
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Francin-Allami M, Lollier V, Pavlovic M, San Clemente H, Rogniaux H, Jamet E, Guillon F, Larré C. Understanding the Remodelling of Cell Walls during Brachypodium distachyon Grain Development through a Sub-Cellular Quantitative Proteomic Approach. Proteomes 2016; 4:E21. [PMID: 28248231 PMCID: PMC5217356 DOI: 10.3390/proteomes4030021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 12/18/2022] Open
Abstract
Brachypodiumdistachyon is a suitable plant model for studying temperate cereal crops, such as wheat, barley or rice, and helpful in the study of the grain cell wall. Indeed, the most abundant hemicelluloses that are in the B. distachyon cell wall of grain are (1-3)(1-4)-β-glucans and arabinoxylans, in a ratio similar to those of cereals such as barley or oat. Conversely, these cell walls contain few pectins and xyloglucans. Cell walls play an important role in grain physiology. The modifications of cell wall polysaccharides that occur during grain development and filling are key in the determination of the size and weight of the cereal grains. The mechanisms required for cell wall assembly and remodelling are poorly understood, especially in cereals. To provide a better understanding of these processes, we purified the cell wall at three developmental stages of the B. distachyon grain. The proteins were then extracted, and a quantitative and comparative LC-MS/MS analysis was performed to investigate the protein profile changes during grain development. Over 466 cell wall proteins (CWPs) were identified and classified according to their predicted functions. This work highlights the different proteome profiles that we could relate to the main phases of grain development and to the reorganization of cell wall polysaccharides that occurs during these different developmental stages. These results provide a good springboard to pursue functional validation to better understand the role of CWPs in the assembly and remodelling of the grain cell wall of cereals.
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Affiliation(s)
| | - Virginie Lollier
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Marija Pavlovic
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borderouge-Auzeville, BP42617, Castanet-Tolosan 31326, France.
| | - Hélène Rogniaux
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borderouge-Auzeville, BP42617, Castanet-Tolosan 31326, France.
| | - Fabienne Guillon
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Colette Larré
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
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Sharma A, Singh MB, Bhalla PL. Ultrastructure of microsporogenesis and microgametogenesis in Brachypodium distachyon. PROTOPLASMA 2015; 252:1575-86. [PMID: 25772681 DOI: 10.1007/s00709-015-0793-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 03/02/2015] [Indexed: 05/05/2023]
Abstract
Brachypodium distachyon has emerged as a model system for forage grass and cereal grain species. Here, we report B. distachyon pollen development at the ultrastructural level. The process of microsporogenesis and microgametogenesis in B. distachyon follows the typical angiosperm pollen development sequence. Pronounced evaginations of the nuclear envelope are observed prior to meiosis, indicating active nucleocytoplasmic exchange processes. The microspore mother cells undergo meiosis and subsequent cytokinesis, forming isobilateral tetrads. Following dissolution of the callose wall and release of free and vacuolated microspores, mitotic divisions lead to the formation of mature, three-celled pollen grains. In B. distachyon, pollen wall formation begins at the tetrad stage by the formation of the exine template (primexine). The exine is tectate-columellate, comprising a foot layer and endexine. Development of the tectum and the foot layer is complete by the free microspore stage of development, with the tectum formed discontinuously. The endexine initiates in the free microspore stage but becomes compressed in mature grains. The intine layer is deposited after mitosis and comprises three layers during the mature pollen stage of development. Pore development initiates during early free microspore development stage and Brachypodium pollen has a single germination pore consisting of a slightly raised annulus surrounding a central operculum. The tapetum is of the secretory type with loss of the tapetal cell walls beginning at about the time of microsporocyte meiosis. This is the first report on ultrastructure of microsporogenesis and microgametogenesis in B. distachyon. In general, Brachypodium microsporogenesis and microgametogenesis conform to a typical grass pollen development pattern.
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Affiliation(s)
- Akanksha Sharma
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
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Delaplace P, Delory BM, Baudson C, Mendaluk-Saunier de Cazenave M, Spaepen S, Varin S, Brostaux Y, du Jardin P. Influence of rhizobacterial volatiles on the root system architecture and the production and allocation of biomass in the model grass Brachypodium distachyon (L.) P. Beauv. BMC PLANT BIOLOGY 2015; 15:195. [PMID: 26264238 PMCID: PMC4531529 DOI: 10.1186/s12870-015-0585-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/03/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plant growth-promoting rhizobacteria are increasingly being seen as a way of complementing conventional inputs in agricultural systems. The effects on their host plants are diverse and include volatile-mediated growth enhancement. This study sought to assess the effects of bacterial volatiles on the biomass production and root system architecture of the model grass Brachypodium distachyon (L.) Beauv. RESULTS An in vitro experiment allowing plant-bacteria interaction throughout the gaseous phase without any physical contact was used to screen 19 bacterial strains for their growth-promotion ability over a 10-day co-cultivation period. Five groups of bacteria were defined and characterised based on their combined influence on biomass production and root system architecture. The observed effects ranged from unchanged to greatly increased biomass production coupled with increased root length and branching. Primary root length was increased only by the volatile compounds emitted by Enterobacter cloacae JM22 and Bacillus pumilus T4. Overall, the most significant results were obtained with Bacillus subtilis GB03, which induced an 81 % increase in total biomass, as well as enhancing total root length, total secondary root length and total adventitious root length by 88.5, 201.5 and 474.5 %, respectively. CONCLUSIONS This study is the first report on bacterial volatile-mediated growth promotion of a grass plant. Contrasting modulations of biomass production coupled with changes in root system architecture were observed. Most of the strains that increased total plant biomass also modulated adventitious root growth. Under our screening conditions, total biomass production was strongly correlated with the length and branching of the root system components, except for primary root length. An analysis of the emission kinetics of the bacterial volatile compounds is being undertaken and should lead to the identification of the compounds responsible for the observed growth-promotion effects. Within the context of the inherent characteristics of our in vitro system, this paper identifies the next critical experimental steps and discusses them from both a fundamental and an applied perspective.
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Affiliation(s)
- Pierre Delaplace
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | - Benjamin M Delory
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | - Caroline Baudson
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | | | - Stijn Spaepen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
| | - Sébastien Varin
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | - Yves Brostaux
- University of Liège, Gembloux Agro-Bio Tech, Applied Statistics, Computer Science and Modeling, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | - Patrick du Jardin
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
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González-Calle V, Barrero-Sicilia C, Carbonero P, Iglesias-Fernández R. Mannans and endo-β-mannanases (MAN) in Brachypodium distachyon: expression profiling and possible role of the BdMAN genes during coleorhiza-limited seed germination. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3753-64. [PMID: 25922488 PMCID: PMC4473977 DOI: 10.1093/jxb/erv168] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Immunolocalization of mannans in the seeds of Brachypodium distachyon reveals the presence of these polysaccharides in the root embryo and in the coleorhiza in the early stages of germination (12h), decreasing thereafter to the point of being hardly detected at 27h. Concurrently, the activity of endo-β-mannanases (MANs; EC 3.2.1.78) that catalyse the hydrolysis of β-1,4 bonds in mannan polymers, increases as germination progresses. The MAN gene family is represented by six members in the Brachypodium genome, and their expression has been explored in different organs and especially in germinating seeds. Transcripts of BdMAN2, BdMAN4 and BdMAN6 accumulate in embryos, with a maximum at 24-30h, and are detected in the coleorhiza and in the root by in situ hybridization analyses, before root protrusion (germination sensu stricto). BdMAN4 is not only present in the embryo root and coleorhiza, but is abundant in the de-embryonated (endosperm) imbibed seeds, while BdMAN2 and BdMAN6 are faintly expressed in endosperm during post-germination (36-42h). BdMAN4 and BdMAN6 transcripts are detected in the aleurone layer. These data indicate that BdMAN2, BdMAN4 and BdMAN6 are important for germination sensu stricto and that BdMAN4 and BdMAN6 may also influence reserve mobilization. Whether the coleorhiza in monocots and the micropylar endosperm in eudicots have similar functions, is discussed.
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Affiliation(s)
- Virginia González-Calle
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and ETSI Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Cristina Barrero-Sicilia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and ETSI Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and ETSI Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and ETSI Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
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Vesty EF, Kessler RW, Wichard T, Coates JC. Regulation of gametogenesis and zoosporogenesis in Ulva linza (Chlorophyta): comparison with Ulva mutabilis and potential for laboratory culture. FRONTIERS IN PLANT SCIENCE 2015; 6:15. [PMID: 25674100 PMCID: PMC4306291 DOI: 10.3389/fpls.2015.00015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/07/2015] [Indexed: 05/23/2023]
Abstract
Green Ulvophyte macroalgae represent attractive model systems for understanding growth, development, and evolution. They are untapped resources for food, fuel, and high-value compounds, but can also form nuisance blooms. To fully analyze green seaweed morphogenesis, controlled laboratory-based culture of these organisms is required. To date, only a single Ulvophyte species, Ulva mutabilis Føyn, has been manipulated to complete its whole life cycle in laboratory culture and to grow continuously under axenic conditions. Such cultures are essential to address multiple key questions in Ulva development and in algal-bacterial interactions. Here we show that another Ulva species, U. linza, with a broad geographical distribution, has the potential to be grown in axenic culture similarly to U. mutabilis. U. linza can be reliably induced to sporulate (form gametes and zoospores) in the laboratory, by cutting the relevant thallus tissue into small pieces and removing extracellular inhibitors (sporulation and swarming inhibitors). The germ cells work as an ideal feed stock for standardized algae cultures. The requirement of U. linza for bacterial signals to induce its normal morphology (particularly of the rhizoids) appears to have a species-specific component. The axenic cultures of these two species pave the way for future comparative studies of algal-microbial interactions.
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Affiliation(s)
| | - Ralf W. Kessler
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University JenaJena, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University JenaJena, Germany
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Rancour DM, Hatfield RD, Marita JM, Rohr NA, Schmitz RJ. Cell wall composition and digestibility alterations in Brachypodium distachyon achieved through reduced expression of the UDP-arabinopyranose mutase. FRONTIERS IN PLANT SCIENCE 2015; 6:446. [PMID: 26136761 PMCID: PMC4470266 DOI: 10.3389/fpls.2015.00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/31/2015] [Indexed: 05/09/2023]
Abstract
Nucleotide-activated sugars are essential substrates for plant cell-wall carbohydrate-polymer biosynthesis. The most prevalent grass cell wall (CW) sugars are glucose (Glc), xylose (Xyl), and arabinose (Ara). These sugars are biosynthetically related via the UDP-sugar interconversion pathway. We sought to target and generate UDP-sugar interconversion pathway transgenic Brachypodium distachyon lines resulting in CW carbohydrate composition changes with improved digestibility and normal plant stature. Both RNAi-mediated gene-suppression and constitutive gene-expression approaches were performed. CWs from 336 T0 transgenic plants with normal appearance were screened for complete carbohydrate composition. RNAi mutants of BdRGP1, a UDP-arabinopyranose mutase, resulted in large alterations in CW carbohydrate composition with significant decreases in CW Ara content but with minimal change in plant stature. Five independent RNAi-RGP1 T1 plant lines were used for in-depth analysis of plant CWs. Real-time PCR analysis indicated that gene expression levels for BdRGP1, BdRGP2, and BdRGP3 were reduced in RNAi-RGP1 plants to 15-20% of controls. CW Ara content was reduced by 23-51% of control levels. No alterations in CW Xyl and Glc content were observed. Corresponding decreases in CW ferulic acid (FA) and ferulic acid-dimers (FA-dimers) were observed. Additionally, CW p-coumarates (pCA) were decreased. We demonstrate the CW pCA decrease corresponds to Ara-coupled pCA. Xylanase-mediated digestibility of RNAi-RGP1 Brachypodium CWs resulted in a near twofold increase of released total carbohydrate. However, cellulolytic hydrolysis of CW material was inhibited in leaves of RNAi-RGP1 mutants. Our results indicate that targeted manipulation of UDP-sugar biosynthesis can result in biomass with substantially altered compositions and highlights the complex effect CW composition has on digestibility.
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Affiliation(s)
- David M. Rancour
- U.S. Dairy Forage Research Center, United States Department of Agriculture – Agricultural Research Service, MadisonWI, USA
| | - Ronald D. Hatfield
- U.S. Dairy Forage Research Center, United States Department of Agriculture – Agricultural Research Service, MadisonWI, USA
- *Correspondence: Ronald D. Hatfield, U.S. Dairy Forage Research Center, United States Department of Agriculture – Agricultural Research Service, 1925 Linden Drive, Madison, WI 53706, USA,
| | - Jane M. Marita
- U.S. Dairy Forage Research Center, United States Department of Agriculture – Agricultural Research Service, MadisonWI, USA
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