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1. Machine learning approaches to identify core and dispensable genes in pangenomes

Author:
Alan E. Yocca; Patrick P. Edger
Source:
The plant genome 2022 v.15 no.1 pp. e20135
ISSN:
1940-3372
Subject:
Brachypodium distachyon,   etc   ; Oryza sativa; genes; genomics; grasses; models;     Show all 6 Subjects
Abstract:
... A gene in a given taxonomic group is either present in every individual (core) or absent in at least a single individual (dispensable). Previous pangenomic studies have identified certain functional differences between core and dispensable genes. However, identifying if a gene belongs to the core or dispensable portion of the genome requires the construction of a pangenome, which involves sequenci ...
DOI:
10.1002/tpg2.20135

2. Artificial selection of stable rhizosphere microbiota leads to heritable plant phenotype changes

Author:
Samuel Jacquiod; Aymé Spor; Shaodong Wei; Victoria Munkager; David Bru; Søren J. Sørensen; Christophe Salon; Laurent Philippot; Manuel Blouin
Source:
Ecology letters 2022 v.25 no.1 pp. 189-201
ISSN:
1461-023X
Subject:
Brachypodium distachyon,   etc   ; artificial selection; community structure; heritability; leaves; microorganisms; phenotype; rhizosphere;     Show all 8 Subjects
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 greenne ...
DOI:
10.1111/ele.13916

3. Brachypodium: 20 years as a grass biology model system; the way forward?

Author:
Robert Hasterok; Pilar Catalan; Samuel P. Hazen; Anne C. Roulin; John P. Vogel; Kai Wang; Luis A.J. Mur
Source:
Trends in plant science 2022 pp. -
ISSN:
1360-1385
Subject:
Brachypodium distachyon,   etc   ; abiotic stress; bioenergy industry; cell walls; chromosomes; climate change; genomics; grasses; interphase; models;     Show all 10 Subjects
Abstract:
... It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, pol ...
DOI:
10.1016/j.tplants.2022.04.008

4. A genetically encoded biosensor reveals spatiotemporal variation in cellular phosphate content in Brachypodium distachyon mycorrhizal roots

Author:
Shiqi Zhang; Dierdra A. Daniels; Sergey Ivanov; Lucas Jurgensen; Lena M. Müller; Wayne K. Versaw; Maria J. Harrison
Source:
The new phytologist 2022 v.234 no.5 pp. 1817-1831
ISSN:
0028-646X
Subject:
Brachypodium distachyon,   etc   ; biosensors; cortex; energy transfer; fluorescence; hyphae; metabolism; orthophosphates; plant root cells; vesicular arbuscular mycorrhizae;     Show all 10 Subjects
Abstract:
... Arbuscular mycorrhizal (AM) symbiosis is accompanied by alterations to root cell metabolism and physiology, and to the pathways of orthophosphate (Pi) entry into the root, which increase with Pi delivery to cortical cells via arbuscules. How AM symbiosis influences the Pi content and Pi response dynamics of cells in the root cortex and epidermis is unknown. Using fluorescence resonance energy tran ...
DOI:
10.1111/nph.18081

5. Contrasting impacts of herbivore induction and elevated atmospheric CO2 on silicon defences and consequences for subsequent herbivores

Author:
Fikadu N. Biru; Christopher I. Cazzonelli; Rivka Elbaum; Scott N. Johnson
Source:
Entomologia experimentalis et applicata 2022 v.170 no.8 pp. 681-688
ISSN:
0013-8703
Subject:
Brachypodium distachyon,   etc   ; Acheta domesticus; Helicoverpa armigera; carbon dioxide; grasses; greenhouses; host plants; phytomass; phytophagous insects; silicon;     Show all 10 Subjects
Abstract:
... Plants are often sequentially attacked by multiple herbivores; feeding by one herbivore can alter host plant quality that affects the performance of subsequent herbivores. Previous studies suggest that silicon (Si) is a highly inducible defence in grasses (Poaceae) following herbivory, so could mediate such temporally separated insect herbivore interactions. Elevated atmospheric CO₂ concentrations ...
DOI:
10.1111/eea.13168

6. Colonization of Brachypodium distachyon by Gluconacetobacter diazotrophicus and its effect on plant growth promotion

Author:
Xuan Yang; Kathleen Allen Hill; J. Kevin Vessey; Lining Tian
Source:
Canadian journal of plant science 2022 v.102 no.2 pp. 324-335
ISSN:
1918-1833
Subject:
Brachypodium distachyon,   etc   ; Gluconacetobacter diazotrophicus; bacteria; growth promotion; lateral roots; liquids; models; nitrogen; nitrogen fixation; plant growth; sugarcane; Brazil;     Show all 12 Subjects
Abstract:
... Gluconacetobacter diazotrophicus is a nitrogen (N) fixing bacterium originally isolated from sugarcane in Brazil. Understanding the interactions between this bacterium and plants is important to exploit the nitrogen-fixing feature of G. diazotrophicus in different crops. Research was conducted to establish, monitor and optimize methods for introducing G. diazotrophicus into Brachypodium distachyon ...
DOI:
10.1139/cjps-2020-0143

7. Colonization of Brachypodium distachyon by Gluconacetobacter diazotrophicus and its effect on plant growth promotion

Author:
Xuan Yang; Kathleen Allen Hill; J. Kevin Vessey; Lining Tian
Source:
Canadian journal of plant science 2022 v.102 no.2 pp. 324-335
ISSN:
1918-1833
Subject:
Brachypodium distachyon,   etc   ; Gluconacetobacter diazotrophicus; bacteria; growth promotion; lateral roots; liquids; models; nitrogen; nitrogen fixation; plant growth; sugarcane; Brazil;     Show all 12 Subjects
Abstract:
... Gluconacetobacter diazotrophicus is a nitrogen (N) fixing bacterium originally isolated from sugarcane in Brazil. Understanding the interactions between this bacterium and plants is important to exploit the nitrogen-fixing feature of G. diazotrophicus in different crops. Research was conducted to establish, monitor and optimize methods for introducing G. diazotrophicus into Brachypodium distachyon ...
DOI:
10.1139/CJPS-2020-0143

8. A phosphorus‐limitation induced, functionally conserved DUF506 protein is a repressor of root hair elongation in plants

Author:
Sheng Ying; Elison B. Blancaflor; Fuqi Liao; Wolf‐Rüdiger Scheible
Source:
The new phytologist 2022 v.233 no.3 pp. 1153-1171
ISSN:
0028-646X
Subject:
Brachypodium distachyon,   etc   ; Arabidopsis thaliana; biomass; exudation; fluorescence; genes; guanosinetriphosphatase; metabolites; mutants; phosphates; phosphorus; precipitin tests; root hairs; seedlings; soil; soil quality;     Show all 16 Subjects
Abstract:
... Root hairs (RHs) function in nutrient and water acquisition, root metabolite exudation, soil anchorage and plant–microbe interactions. Longer or more abundant RHs are potential breeding traits for developing crops that are more resource‐use efficient and can improve soil health. While many genes are known to promote RH elongation, relatively little is known about genes and mechanisms that constrai ...
DOI:
10.1111/nph.17862

9. Immune gene activation by NPR and TGA transcriptional regulators in the model monocot Brachypodium distachyon

Author:
Kohei Shimizu; Hitomi Suzuki; Takuya Uemura; Akira Nozawa; Yoshitake Desaki; Ryosuke Hoshino; Ayako Yoshida; Hiroshi Abe; Makoto Nishiyama; Chiharu Nishiyama; Tatsuya Sawasaki; Gen‐ichiro Arimura
Source:
plant journal 2022 v.110 no.2 pp. 470-481
ISSN:
0960-7412
Subject:
Brachypodium distachyon,   etc   ; Arabidopsis thaliana; gene activation; genes; immune response; methyl salicylate; pathogenesis-related proteins; pathogens; protoplasts; salicylic acid; transcription (genetics); transcriptional activation;     Show all 12 Subjects
Abstract:
... The nonexpressor of pathogenesis‐related (NPR) gene family is well known to play a crucial role in transactivation of TGA transcription factors for salicylic acid (SA)‐responsive genes, including pathogenesis‐related protein 1 (PR1), during plants' immune response after pathogen attack in the model dicot Arabidopsis thaliana. However, little is known about NPR gene functions in monocots. We theref ...
DOI:
10.1111/tpj.15681

10. Comparison of Antifungal Activity of Bacillus Strains against Fusarium graminearum In Vitro and In Planta

Author:
Catherine Jimenez-Quiros; Emeka C. Okechukwu; Yiguo Hong; Ömür Baysal; Mahmut Tör
Source:
Plants 2022 v.11 no.15 pp. -
ISSN:
2223-7747
Subject:
Brachypodium distachyon,   etc   ; Fusarium graminearum; Fusarium head blight; antifungal properties; barley; biological control; deoxynivalenol; head; heat; leaves; livestock; pathogens; peptidase K; plant growth; wheat;     Show all 15 Subjects
Abstract:
... Fusarium graminearum (Fg) causes Fusarium head blight (FHB) disease in wheat and barley. This pathogen produces mycotoxins including deoxynivalenol (DON), the T-2 and fumorisin B1. Translocation of the mycotoxins in grains causes important losses in yields and contributes to serious health problems in humans and livestock. We tested the Bacillus strains, two commercial, QST713 (Serenade®) and FZB2 ...
DOI:
10.3390/plants11151999

11. KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular‐mycorrhizal symbiosis in Brachypodium distachyon

Author:
Yongjie Meng; Kartikye Varshney; Norbert Incze; Eszter Badics; Muhammad Kamran; Sabrina F. Davies; Larissa M. F. Oppermann; Kévin Magne; Marion Dalmais; Abdel Bendahmane; Richard Sibout; John Vogel; Debbie Laudencia‐Chingcuanco; Charles S. Bond; Vilmos Soós; Caroline Gutjahr; Mark T. Waters
Source:
plant journal 2022 v.109 no.6 pp. 1559-1574
ISSN:
0960-7412
Subject:
Brachypodium distachyon,   etc   ; chlorophyll; grasses; karrikins; leaf development; leaves; ligands; loss-of-function mutation; root hairs; root systems; seed germination; seedling growth; strigolactones; transcription (genetics); transcriptome;     Show all 15 Subjects
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 developme ...
DOI:
10.1111/tpj.15651

12. Characterization and expression of the Pirin gene family in Triticum aestivum

Author:
Sabrina C. Brunetti; Michelle K.M. Arseneault; Patrick J. Gulick
Source:
Genome 2022 v.65 no.6 pp. 349-362
ISSN:
1480-3321
Subject:
Brachypodium distachyon,   etc   ; Aegilops tauschii; Arabidopsis thaliana; Hordeum vulgare; Oryza sativa; Sorghum bicolor; Triticum aestivum; Zea mays; genes; heterotrimeric GTP-binding proteins; sequence analysis; stress response;     Show all 12 Subjects
Abstract:
... Pirins are nuclear bicupin proteins, encoded by genes that are one of several gene families that comprise the cupin superfamily in plants. Pirin genes have been implicated in stress response pathways studied in Arabidopsis and At-Pirin1 has been shown to interact with the heterotrimeric G-protein alpha subunit (GPA1). The aim of this study was to identify the members of the Pirin gene family in Tr ...
DOI:
10.1139/gen-2021-0094

13. Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

Author:
Christoph Stritt; Elena L. Gimmi; Michele Wyler; Abdelmonaim H. Bakali; Aleksandra Skalska; Robert Hasterok; Luis A. J. Mur; Nicola Pecchioni; Anne C. Roulin
Source:
Molecular ecology 2022 v.31 no.1 pp. 70-85
ISSN:
0962-1083
Subject:
Brachypodium distachyon,   etc   ; Pleistocene epoch; evolution; genetic variation; genome; genomics; grasses; meadows; models; population genetics; population structure; seed dispersal; selfing; temporal variation; wild plants; France; Iraq; Italy; Spain;     Show all 19 Subjects
Abstract:
... Wild plant populations show extensive genetic subdivision and are far from the ideal of panmixia which permeates population genetic theory. Understanding the spatial and temporal scale of population structure is therefore fundamental for empirical population genetics – and of interest in itself, as it yields insights into the history and biology of a species. In this study we extend the genomic re ...
DOI:
10.1111/mec.16207

14. Root-TRAPR: a modular plant growth device to visualize root development and monitor growth parameters, as applied to an elicitor response of Cannabis sativa

Author:
Pipob Suwanchaikasem; Alexander Idnurm; Jamie Selby-Pham; Robert Walker; Berin A. Boughton
Source:
Plant methods 2022 v.18 no.1 pp. 46
ISSN:
1746-4811
Subject:
Brachypodium distachyon,   etc   ; Arabidopsis thaliana; Cannabis sativa; chitinase; chitosan; ecosystems; elicitors; growth chambers; hemp; models; nylon; peroxidase; plant hormones; polydimethylsiloxane; printers; root exudates; root growth; root shoot ratio; roots;     Show all 19 Subjects
Abstract:
... BACKGROUND: Plant growth devices, for example, rhizoponics, rhizoboxes, and ecosystem fabrication (EcoFAB), have been developed to facilitate studies of plant root morphology and plant-microbe interactions in controlled laboratory settings. However, several of these designs are suitable only for studying small model plants such as Arabidopsis thaliana and Brachypodium distachyon and therefore requ ...
DOI:
10.1186/s13007-022-00875-1

15. Analysis of Codon Usage Patterns of Six Sequenced Brachypodium distachyon Lines Reveals a Declining CG Skew of the CDSs from the 5′-ends to the 3′-ends

Author:
Jianyong Wang; Yujing Lin; Mengli Xi
Source:
Genes 2021 v.12 no.10 pp. -
ISSN:
2073-4425
Subject:
Brachypodium distachyon,   etc   ; codon usage; genetically modified organisms; hydrogen;     Show all 4 Subjects
Abstract:
... Brachypodium distachyon, a new monocotyledonous model plant, has received wide attention in biological research due to its small genome and numerous genetic resources. Codon usage bias is an important feature of genes and genomes, and it can be used in transgenic and evolutionary studies. In this study, the nucleotide compositions and patterns of codon usage bias were calculated using Codon W. Add ...
DOI:
10.3390/genes12101467

16. Quantitative and dynamic cell polarity tracking in plant cells

Author:
Yan Gong; Rachel Varnau; Eva‐Sophie Wallner; Raghav Acharya; Dominique C. Bergmann; Lily S. Cheung
Source:
new phytologist 2021 v.230 no.2 pp. 867-877
ISSN:
0028-646X
Subject:
Brachypodium distachyon,   etc   ; Arabidopsis thaliana; cell polarity; microscopy; statistical analysis;     Show all 5 Subjects
Abstract:
... Quantitative information on the spatiotemporal distribution of polarised proteins is central for understanding cell‐fate determination, yet collecting sufficient data for statistical analysis is difficult to accomplish with manual measurements. Here we present Polarity Measurement (Pome), a semi‐automated pipeline for the quantification of cell polarity and demonstrate its application to a variety ...
DOI:
10.1111/nph.17165

17. Stacking AsFMT overexpression with BdPMT loss of function enhances monolignol ferulate production in Brachypodium distachyon

Author:
Rebecca A. Smith; Cynthia L. Cass; Deborah L. Petrik; Dharshana Padmakshan; John Ralph; John C. Sedbrook; Steven D. Karlen
Source:
Plant biotechnology journal 2021 v.19 no.9 pp. 1878-1886
ISSN:
1467-7644
Subject:
Brachypodium distachyon,   etc   ; CCR1 receptor; biosynthesis; biotechnology; genes; lignification; lignin; mutants;     Show all 8 Subjects
Abstract:
... To what degree can the lignin subunits in a monocot be derived from monolignol ferulate (ML‐FA) conjugates? This simple question comes with a complex set of variables. Three potential requirements for optimizing ML‐FA production are as follows: (1) The presence of an active FERULOYL‐CoA MONOLIGNOL TRANSFERASE (FMT) enzyme throughout monolignol production; (2) Suppression or elimination of enzymati ...
DOI:
10.1111/pbi.13606

18. Genome-wide identification, expression analyses of Wuschel-related homeobox (WOX) genes in Brachypodium distachyon and functional characterization of BdWOX12

Author:
Hongyu Ren; Shoukun Chen; Jiayuan Hou; Haifeng Li
Source:
Gene 2022 v.836 pp. 146691
ISSN:
0378-1119
Subject:
Brachypodium distachyon,   etc   ; Arabidopsis; genes; growth and development; phylogeny; plant growth; root systems;     Show all 7 Subjects
Abstract:
... As one kind of plant-specific transcription factors (TFs), WOX (Wuschel-related homeobox) plays an essential role in plant growth and development. In this study, 21 WOX TFs were identified in Brachypodium distachyon. They were divided into ancient, intermediate, and WUS clades based on phylogenetic analysis. These 21 BdWOX genes are mapped on 5 chromosomes unevenly. In the promoters, the most abun ...
DOI:
10.1016/j.gene.2022.146691

19. Short‐term exposure to silicon rapidly enhances plant resistance to herbivory

Author:
Jamie M. Waterman; Ximena Cibils‐Stewart; Christopher I. Cazzonelli; Susan E. Hartley; Scott N. Johnson
Source:
Ecology 2021 v.102 no.9 pp. e03438
ISSN:
0012-9658
Subject:
Brachypodium distachyon,   etc   ; Helicoverpa armigera; acute exposure; chronic exposure; grasses; phenolic compounds; silicon;     Show all 7 Subjects
Abstract:
... Silicon (Si) can adversely affect insect herbivores, particularly in plants that evolved the ability to accumulate large quantities of Si. Very rapid herbivore‐induced accumulation of Si has recently been demonstrated, but the level of protection against herbivory this affords plants remains unknown. Brachypodium distachyon, a model Si hyperaccumulating grass, was exposed to the chewing herbivore, ...
DOI:
10.1002/ecy.3438

20. Spatial analysis of the root system coupled to microbial community inoculation shed light on rhizosphere bacterial community assembly

Author:
Shaodong Wei; Samuel Jacquiod; Laurent Philippot; Manuel Blouin; Søren Johannes Sørensen
Source:
Biology and fertility of soils 2021 v.57 no.7 pp. 973-989
ISSN:
0178-2762
Subject:
Brachypodium distachyon,   etc   ; Firmicutes; Verrucomicrobia; bacterial communities; genes; greenhouse experimentation; homogenization; rhizosphere; root systems;     Show all 9 Subjects
Abstract:
... Although studied for more than a century, the spatial distribution of microorganisms in a root system still remains partly understood. In a repeated greenhouse experiment using the model plant Brachypodium distachyon, we investigated the composition and distribution of rhizosphere bacteria and their response to inoculation with artificially selected microbial communities, using two different sampl ...
DOI:
10.1007/s00374-021-01590-0