scholarly journals Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations

2020 ◽  
Vol 21 (18) ◽  
pp. 6700
Author(s):  
Aleksandra Skalska ◽  
Christoph Stritt ◽  
Michele Wyler ◽  
Hefin W. Williams ◽  
Martin Vickers ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brachypodium Distachyon ◽  
Growth Conditions ◽  
Grass Species ◽  
Niche Modelling ◽  
Climate Niche ◽  
Population Structure Analysis ◽  
Delayed Flowering ◽  
Model Grass ◽  
The Uk

Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses.

scholarly journals CG methylation covaries with differential gene expression between leaf and floral bud tissues of Brachypodium distachyon

2015 ◽  
Author(s):  
Kyria Roessler ◽  
Shohei Takuno ◽  
Brandon Gaut
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Sequence Data ◽  
Brachypodium Distachyon ◽  
Grass Species ◽  
Specific Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Model Grass ◽  
Floral Bud

DNA methylation has the potential to influence plant growth and development through its influence on gene expression. To date, however, the evidence from plant systems is mixed as to whether patterns of DNA methylation vary significantly among tissues and, if so, whether these differences affect tissue-specific gene expression. To address these questions, we analyzed both bisulfite sequence (BSseq) and transcriptomic sequence data from three biological replicates of two tissues (leaf and floral bud) from the model grass species Brachypodium distachyon. Our first goal was to determine whether tissues were more differentiated in DNA methylation than explained by variation among biological replicates. Tissues were more differentiated than biological replicates, but the analysis of replicated data revealed high (>50%) false positive rates for the inference of differentially methylated sites (DMSs) and differentially methylated regions (DMRs). Comparing methylation to gene expression, we found that differential CG methylation consistently covaried negatively with gene expression, regardless as to whether methylation was within genes, within their promoters or even within their closest transposable element. The relationship between gene expression and either CHG or CHH methylation was less consistent. In total, CG methylation in promoters explained 9% of the variation in tissue-specific expression across genes, suggesting that CG methylation is a minor but appreciable factor in tissue differentiation.

Conserved microRNAs and their targets in model grass species Brachypodium distachyon

Planta ◽  
2009 ◽  
Vol 230 (4) ◽  
pp. 659-669 ◽  
Author(s):  
Turgay Unver ◽  
Hikmet Budak
Keyword(s):  
Brachypodium Distachyon ◽  
Grass Species ◽  
Model Grass

scholarly journals Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

2018 ◽  
Author(s):  
Joelle Sasse ◽  
Josefine Kant ◽  
Benjamin J Cole ◽  
Andrew P Klein ◽  
Borjana Arsova ◽  
...  
Keyword(s):  
Plant Traits ◽  
Brachypodium Distachyon ◽  
Root Hairs ◽  
Plant Morphology ◽  
Growth Conditions ◽  
Soil Extract ◽  
Physiochemical Properties ◽  
Experimental Treatments ◽  
Model Grass ◽  
Soil Influence

There is a dynamic reciprocity between plants and their environment: On one hand, the physiochemical properties of soil influence plant morphology and metabolism, while on the other, root morphology and exudates shape the environment surrounding roots. Here, we investigate both of these aspects as well as the reproducibility of these responses across laboratories. The model grass Brachypodium distachyon was grown in phosphate-sufficient and phosphate-deficient mineral media, as well as in sterile soil extract, within fabricated ecosystem (EcoFAB) devices across four laboratories. Tissue weight and phosphate content, total root length, root tissue and exudate metabolic profiles were found to be consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct in all laboratories, with root hairs four times longer compared to other growth conditions. Further, plants depleted half of the investigated metabolites from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures; they also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high inter-laboratory reproducibility, demonstrating that their value in standardized investigations of plant traits.

scholarly journals Silicon Alters Leaf Surface Morphology and Suppresses Insect Herbivory in a Model Grass Species

Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 643 ◽  
Author(s):  
Casey R. Hall ◽  
Vaibhav Dagg ◽  
Jamie M. Waterman ◽  
Scott N. Johnson
Keyword(s):  
Surface Morphology ◽  
Leaf Surface ◽  
Brachypodium Distachyon ◽  
Insect Herbivory ◽  
Matter Content ◽  
Acheta Domesticus ◽  
Grass Species ◽  
Dry Matter Content ◽  
Leaf Toughness ◽  
Model Grass

Grasses accumulate large amounts of silicon (Si) which is deposited in trichomes, specialised silica cells and cell walls. This may increase leaf toughness and reduce cell rupture, palatability and digestion. Few studies have measured leaf mechanical traits in response to Si, thus the effect of Si on herbivores can be difficult to disentangle from Si-induced changes in leaf surface morphology. We assessed the effects of Si on Brachypodium distachyon mechanical traits (specific leaf area (SLA), thickness, leaf dry matter content (LDMC), relative electrolyte leakage (REL)) and leaf surface morphology (macrohairs, prickle, silica and epidermal cells) and determined the effects of Si on the growth of two generalist insect herbivores (Helicoverpa armigera and Acheta domesticus). Si had no effect on leaf mechanical traits; however, Si changed leaf surface morphology: silica and prickle cells were on average 127% and 36% larger in Si supplemented plants, respectively. Prickle cell density was significantly reduced by Si, while macrohair density remained unchanged. Caterpillars were more negatively affected by Si compared to crickets, possibly due to the latter having a thicker and thus more protective gut lining. Our data show that Si acts as a direct defence against leaf-chewing insects by changing the morphology of specialised defence structures without altering leaf mechanical traits.

scholarly journals Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon

Genome ◽  
2012 ◽  
Vol 55 (7) ◽  
pp. 523-527 ◽  
Author(s):  
Patricia Giraldo ◽  
Marta Rodríguez-Quijano ◽  
José F. Vázquez ◽  
José M. Carrillo ◽  
Elena Benavente
Keyword(s):  
Size Range ◽  
Brachypodium Distachyon ◽  
Grass Species ◽  
Size Difference ◽  
Agarose Gel Electrophoresis ◽  
Chromosome Counting ◽  
Annual Grass ◽  
Amplification Product ◽  
Alternative Approach ◽  
Model Grass

Brachypodium distachyon (L.) P. Beauv. (2n = 2x = 10) is a small annual grass species where the existence of three different cytotypes (10, 20, and 30 chromosomes) has long been regarded as a case of autopolyploid series with x = 5. However, it has been demonstrated that the cytotypes assumed to be polyploids represent two separate Brachypodium species recently named as Brachypodium stacei (2n = 2x = 20) and Brachypodium hybridum (2n = 4x = 30). The aim of this study was to find a PCR-based alternative approach that could replace standard cytotyping methods (i.e., chromosome counting and flow cytometry) to characterize each of the three Brachypodium species. We have analyzed with four microsatellite (SSR) markers 83 B. distachyon-type lines from varied locations in Spain, including the Balearic and Canary Islands. Within this set of lines, 64, 4, and 15 had 10, 20, and 30 chromosomes, respectively. The surveyed markers produced cytotype-specific SSR profiles. So, a single amplification product was generated in the diploid samples, with nonoverlapping allelic ranges between the 2n = 10 and 2n = 20 cytotypes, whereas two bands, one in the size range of each of the diploid cytotypes, were amplified in the 2n = 30 lines. Furthermore, the remarkable size difference obtained with the SSR ALB165 allowed the identification of the Brachypodium species by simple agarose gel electrophoresis.

scholarly journals Grain dormancy and light quality effects on germination in the model grass Brachypodium distachyon

2011 ◽  
Vol 193 (2) ◽  
pp. 376-386 ◽  
Author(s):  
José M. Barrero ◽  
John V. Jacobsen ◽  
Mark J. Talbot ◽  
Rosemary G. White ◽  
Stephen M. Swain ◽  
...  
Keyword(s):  
Light Quality ◽  
Brachypodium Distachyon ◽  
Grain Dormancy ◽  
Model Grass
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