Brachypodium distachyon has been proposed as a new model for the temperate grass because it is related to the major cereal grain species (such as wheat, barley, oat, maize, rice, and sorghum) and many forage and turf species. In this study, a multivariate statistical analysis was performed to investigate the characteristics of codon bias and the main factors affecting synonymous codon usage in Brachypodium. We found that low- and high-GC content genes with different codon usage occur frequently in the genome.
Citation: Vogel, J.P., Gu, Y.Q., Twigg, P., Lazo, G.R., Chingcuanco, D.L., Hayden, D.M., Donze, T., Vivia-Lindsay, A., Stamova, B., Coleman-Derr, D. 2006. EST sequencing and phylogenetic analysis of the model grass brachypodium distachyon. Theoretical and Applied Genetics. 113: 186-195. Interpretive Summary: Brachypodium distachyon is a small grass that serves as a model system for the temperate grasses (i.e. forage grasses and cereals). Expressed sequence tags (ESTs) are short DNA sequences from random cDNAs (genes). ESTs are useful tools for many functional and physical genomic experiments including the construction of microarrays and the development of molecular markers. This paper describes the sequencing of a large collection of ESTs from five different cDNA libraries. Analysis of the ESTs included the identification of putative lignin biosynthetic genes and the construction of phylogentic trees that demonstrated the close relationship of Brachypodium to wheat and barley. Technical ...
Proteinase inhibitors (PIs) are established markers for wound- and especially jasmonate-mediated signalling in dicot species such as tomato and potato. Differential screening of a cDNA library constructed from RNA isolated from wounded leaves of the grass Brachypodium distachyon led to the identification of a proteinase inhibitor gene (Bdpin1). Bdpin1 exhibited the highest homology to the subtilisin/chymotrypsin-inhibiting subgroup of the pin1 class of plant PIs. Northern analyses indicated that Bdpin1 was induced within 6 h at the site of wounding and systemically, by 24 h, thereby providing evidence for long-distance signalling in grasses. Bdpin1 also proved to be more rapidly induced in susceptible than in resistant ecotypes of B. distachyon following challenge with the Rice blast pathogen, Magnaporthe grisea. Screening with chemical signals indicated that Bdpin1 could be induced with MeJA but not with the putative mimic of salicylic acid, benzothiadiazole. Genomic Southern hybridization was ...
The main aim of this work is the evaluation of the genetic diversity existing in a collection of 23 wild populations of Brachypodium distachyon, collected in diverse regions of the Iberian Peninsula, using two recently marketed lines as reference. The estimation of this variability has been done with the use of two types of markers. The first is biochemical and consists in the study of the endosperm proteins. The second concerns the molecular analysis of inter-microsatellites (ISSRs). A preliminary evaluation of the response of immature zygotic embryos from samples of all the populations to the in vitro culture has also been carried out. Considering the results obtained and the autogamous reproduction system of Brachypodium distachyon, the collection analysed constitutes an excellent plant material for the production of pure lines, after domestication and mass selection, which would be a valuable resource in the recovery of degraded soils, and to bulk up material for development of ...
Brachypodium distachyon ( Brachypodium) has emerged as a useful model system for studying traits unique to graminaceous species including bioenergy crop grasses owing to its amenability to laboratory experimentation and the availability of extensive genetic and germplasm resources. Considerable natural variation has been uncovered for a variety of traits including flowering time, vernalization responsiveness, and above-ground growth characteristics. However, cell wall composition differences remain underexplored. Therefore, we assessed cell wall-related traits relevant to biomass conversion to biofuels in seven Brachypodium inbred lines that were chosen based on their high level of genotypic diversity as well as available genome sequences and recombinant inbred line (RIL) populations. Senesced stems plus leaf sheaths from these lines exhibited significant differences in acetyl bromide soluble lignin (ABSL), cell wall polysaccharide-derived sugars, hydroxycinnamates content, and ...
Use of the dicot annual Arabidopsis thaliana (Arabidopsis) as a model system continues to revolutionize our understanding of plant biology, but the development of alternative plant models promises to address numerous knowledge gaps. Especially relevant is the development of additional models for the agriculturally important grasses. Leading this charge is the emerging grass model system Brachypodium distachyon (Brachypodium). Brachypodium is a monocotyledonous, C3 temperate grass genus in the family Poaceae, subfamily Pooideae, which is closely related to wheat, oats, and barley [1, 2]. Like Arabidopsis, Brachypodium has many advantageous features for genetic research, including small size, simple growth requirements, and a relatively small genome with diploid accessions [3, 4]. While it would be preferable to directly study food crops (e.g., wheat) and biofuel crops (e.g., switchgrass), they are generally lacking in many of the desirable features that make Brachypodium such an excellent model ...
While many aspects of plant cell wall polymer structure are known, their spatial and temporal distribution within the stem are not well understood. Here, we studied vascular system and fiber development, which has implication for both biofuel feedstock conversion efficiency and crop yield. The subject of this study, Brachypodium distachyon, has emerged as a grass model for food and energy crop research. Here, we conducted our investigation using B. distachyon by applying various histological approaches and Fourier transform infrared spectroscopy to the stem internode from three key developmental stages. While vascular bundle size and number did not change over time, the size of the interfascicular region increased dramatically, as did cell wall thickness. We also describe internal stem internode anatomy and demonstrate that lignin deposition continues after crystalline cellulose and xylan accumulation ceases. The vascular bundle anatomy of B. distachyon appears to be highly similar to domesticated
Interactions between plants and compatible fungal pathogens are spatially and temporally dynamic, posing a major challenge for sampling and data analysis. A protocol is described for the infection of the model grass species Brachypodium distachyon with Magnaporthe grisea (rice blast), together with modifications to extend the use to rice and barley. We outline a method for the preparation of long-term stocks of virulent fungal pathogens and for the generation of fungal inoculants for challenge of host plants. Host plant growth, pathogen inoculation and plant sampling protocols are presented together with methods for assessing the efficiency of both infection and sampling procedures. Included in the anticipated results is a description of the use of metabolite fingerprinting and multivariate data analysis to assess disease synchrony and validate system reproducibility between experiments. The design concepts will have value in any studies using biological systems that contain dynamic variance ...
Plants reduce inorganic carbon to synthesize biomass that is comprised of mostly polysaccharides and lignin. Growth is intricately regulated by external cues such as light, temperature, and water availability and internal cues including those generated by the circadian clock. While many aspects of polymer biosynthesis are known, their regulation and distribution within the stem are poorly understood. Plant biomass is perhaps the most abundant organic substance on Earth and can be used as feedstock for energy production. Various grass species are under development as energy crops yet several of their attributes make them challenging research subjects. Brachypodium distachyon has emerged as a grass model for food and energy crop research. I studied rhythmic growth, a phenomenon important to understanding how plant biomass accumulates through time, and vascular system development, which has biofuel feedstock conversion efficiency and yield. Growth rate changes within the course of a day in a sinusoidal
0.375, 0.500 and 0.625 kg imazapyr/ha and combinations of 5.0 kg atrazine + 1.9 kg amitrole or 8.0 kg diuron + 1.9 kg amitrole/ha were evaluated for roadside control of Cruciferae, Umbelliferae, Compositae, Papilionaceae [Leguminosae] and grasses (mostly Brachypodium distachyon and Lophochloa phleoides). Treatments were applied post-em. to weeds 40-50 cm tall. Imazapyr acted very slowly with the first symptoms visible only 4 weeks after application and complete control evident 4 months later. The highest application rate achieved complete control of all annual weeds and inhibition of growth of the perennial Andropogon distachyos. Atrazine + amitrole and diuron + amitrole provided good control of annual weeds. In further trials on a roadside verge in the Ayalon Valley 0.375, 0.500 and 0.625 kg imazapyr, 4.0 kg diuron + 2.5 kg atrazine and 3.2 kg diuron + 0.8 kg bromacil/ha were applied post-em. to weeds 15-40 cm tall. 6 months after application 0.625 kg imazapyr provided excellent weed control, ...
Brachypodium distachyon is a small annual grass that researchers use as a model for the grasses used to produce biomass, food, feed and forage. Unlike the grasses grown as crops, B. distachyon is well suited to experimental manipulation in the laboratory because of its small size, compact genome, diploid nature, self compatibility, rapid generation time and simple growth requirements. In addition, numerous resources and methods (e.g. complete genome sequence, high efficiency transformation, large collections of natural accessions, many sequenced accessions and several RIL populations) are available that allow researchers to apply a suite of modern research methods to understand the unique aspects of grass biology. See here for a review of B. distachyon as a model system.. In addition to B. distachyon, other species in the genus are being used to study polyploidy (B. hybridum and B. stacei) and perenniality (B. sylvaticum).. Below are links to announcements and experimental resources and ...
International Journal of Genomics is a peer-reviewed, Open Access journal that publishes research articles as well as review articles in all areas of genome-scale analysis. Topics covered by the journal include, but are not limited to: bioinformatics, clinical genomics, disease genomics, epigenomics, evolutionary genomics, functional genomics, genome engineering, and synthetic genomics.
The recent release of the genome sequences of a number of crop and model plant species has made it possible to define the genome organisation and functional characteristics of specific genes and gene families of agronomic importance. For instance, Sorghum bicolor, maize (Zea mays) and Brachypodium distachyon genome sequences along with the model grass species rice (Oryza sativa) enable the comparative analysis of genes involved in plant defence. Germin-like proteins (GLPs) are a small, functionally and taxonomically diverse class of cupin-domain containing proteins that have recently been shown to cluster in an area of rice chromosome 8. The genomic location of this gene cluster overlaps with a disease resistance QTL that provides defence against two rice fungal pathogens (Magnaporthe oryzae and Rhizoctonia solani). Studies showing the involvement of GLPs in basal host resistance against powdery mildew (Blumeria graminis ssp.) have also been reported in barley and wheat. In this mini-review, we ...
Glycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabolites: six-carbon compounds of glucose-6P and fructose-6P and three-carbon compounds of glycerone-P, glyceraldehyde-3P, glycerate-3P, phosphoenolpyruvate, and pyruvate [MD:M00001]. Acetyl-CoA, another important precursor metabolite, is produced by oxidative decarboxylation of pyruvate [MD:M00307]. When the enzyme genes of this pathway are examined in completely sequenced genomes, the reaction steps of three-carbon compounds from glycerone-P to pyruvate form a conserved core module [MD:M00002], which is found in almost all organisms and which sometimes contains operon structures in bacterial genomes. Gluconeogenesis is a synthesis pathway of glucose from noncarbohydrate precursors. It is essentially a reversal of glycolysis with minor variations of alternative paths [MD:M00003 ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Brachypodium distachyon is a small, rapidly growing grass that serves as a model for candidate bioenergy grasses such as Miscanthus and switchgrass. For this reason, in 2010, the B. distachyon genome was sequenced and annotated as part of the U.S. Department of Energys (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility, Community Science Program. To further accelerate research in the development of biofuel feedstocks, a project to sequence thousands of B. distachyon mutants was selected for the 2015 Community Science Program portfolio. The library of sequenced mutants will aid researchers in studying and rapidly identifying and ordering plants with mutations in any gene in its genome. Using a forward genetic screen, a Stanford University team identified a B. distachyonsubsidiary cell identify defective (sid) mutant; this mutant is unable to produce subsidiary cells. By comparing the whole genome sequence of B. distachyon with the sid mutant, a 5-base pair deletion in the ...
Four diploid inbred B. distachyon lines, Bd3-1, Bd21-1, Bd1-1, and Bd29-1 were used to characterize cold induced IRIP gene expression by quantitative real-time polymerase chain reaction (qRT-PCR). The seeds were kindly provided by Dr. David Garvin, University of Minnesota, USA. Bd3-1 and Bd21-1 originate from Iraq and are spring genotypes that do not require vernalization to induce flowering. Bd1-1 and Bd29-1 originate from northern Turkey and the Ukraine, respectively, and are winter genotypes which require long vernalization periods (six and 12 weeks respectively) to flower (http://www.ars.usda.gov/SP2UserFiles/person/1931/GarvinLabCoreBrachypodiumdistachyonLineSet(2).pdf) [34, 35]. For the microarray gene expression experiments only Bd21-1 was used.. In the qRT-PCR experiment 7 weeks old plants were used which had been established from seeds using the following growth conditions: 20/16°C day/night temperature and 16 h photoperiod with a photon flux density of 150 μmol m-2 s-1. Half of the ...
ID I1HCY7_BRADI Unreviewed; 199 AA. AC I1HCY7; DT 13-JUN-2012, integrated into UniProtKB/TrEMBL. DT 13-JUN-2012, sequence version 1. DT 25-OCT-2017, entry version 30. DE RecName: Full=Translation machinery-associated protein 22 {ECO:0000256,RuleBase:RU361273}; GN Name=LOC100838976 {ECO:0000313,EnsemblPlants:BRADI2G05940.1}; GN ORFNames=BRADI_2g05940 {ECO:0000313,EMBL:KQK03160.1}; OS Brachypodium distachyon (Purple false brome) (Trachynia distachya). OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BOP clade; OC Pooideae; Brachypodieae; Brachypodium. OX NCBI_TaxID=15368 {ECO:0000313,EnsemblPlants:BRADI2G05940.1, ECO:0000313,Proteomes:UP000008810}; RN [1] {ECO:0000313,EMBL:KQK03160.1, ECO:0000313,EnsemblPlants:BRADI2G05940.1} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=Bd21 {ECO:0000313,EMBL:KQK03160.1, RC ECO:0000313,EnsemblPlants:BRADI2G05940.1}; RX PubMed=20148030; DOI=10.1038/nature08747; RG ...
Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules ...
1. Brachypodium genome sequenced. A simple model for studying grass cell walls is needed to allow more rapid progress in understanding the potential to alter the properties of cellulosic biomass. ARS scientists in Albany, CA are collaborated with Department of Energy (DOE) and other researchers to complete the analysis and annotation of the entire genome. A paper describing the results was published in the journal Nature and the sequence and annotation is now freely available through several databases. In addition, a project to resequence additional accessions was initiated. To date, four lines have been resequenced and the analysis of the sequences has been initiated. Knowledge of the genome sequence of Brachypodium and the linear order of genes in the genome relative to other grasses will help to make this species useful to researchers studying important agricultural traits in energy crops and grain species. 2. Characterization of diversity in polyploid switchgrass. The genetic make-up of the ...
We use a variety of plant systems including the model flowering plant, Arabidopsis thaliana, tobacco, rice, and the model grass, Brachypodium distachyon to characterize homeostasis mechanisms (i.e. how levels are regulated within the cell) for metabolites that function as signaling compounds. For example, we use stable isotope labeling to examine the regulation of growth and development by the signaling molecule indole-3-acetic acid (IAA), also known as auxin. We are developing analytical tools (primarily high throughput sample prep, quantitative metabolite profiling, and fluorescence-based cell sorting) and mutants that are disrupted in some aspect of metabolite regulation in order to characterize IAA homeostasis. Mass spectrometry features prominently in our experimental approach. Our long-term goal is to understand how auxin biosynthetic pathways interact with biosynthetic pathways for other important signaling molecules such as cytokinins, gibberellins, salicylic acid, ethylene, jasmonic ...
Oxidative stress in plants can be triggered by many environmental stress factors, such as drought and salinity. Brachypodium distachyon is a model organism for the study of biofuel plants and crops, such as wheat. Although recent studies have found many oxidative stress response-related proteins, the mechanism of microRNA (miRNA)-mediated oxidative stress response is still unclear. Using next generation high-throughput sequencing technology, the small RNAs were sequenced from the model plant B. distachyon 21 (Bd21) under H2O2 stress and normal growth conditions. In total, 144 known B. distachyon miRNAs and 221 potential new miRNAs were identified. Further analysis of potential new miRNAs suggested that 36 could be clustered into known miRNA families, while the remaining 185 were identified as B. distachyon-specific new miRNAs. Differential analysis of miRNAs from the normal and H2O2 stress libraries identified 31 known and 30 new H2O2 stress responsive miRNAs. The expression patterns of seven
The Poaceae family includes premier cereal crops such as wheat, rice and maize that currently supply most dietary calories to people worldwide [1], and increased global food output in the past five decades has resulted primarily from improved productivity of these three crops [2,3]. However, our population is predicted to increase by 40 per cent by 2030, which will outpace both the current rate of yield increases for the major cereals, and the availability of arable land [4,5]. Therefore, improved cereal varieties that produce higher yields without increasing land use need to be developed. Global population growth and industrialization are also depleting non-renewable fossil fuel reserves, and several Poaceae family members including sugarcane, miscanthus and switchgrass are currently being used or developed as bioenergy feedstocks [6-8]. Thus, key members of the Poaceae family will probably play a central role in both food and fuel security in the coming decades.. One reason for current, ...
Fine mapping of Yr47 and Lr52 in chromosome arm 5BS of wheat identified close linkage of the marker sun180 to both genes and its robustness for marker-assisted selection was demonstrated. The widely effective and genetically linked rust resistance genes Yr47 and Lr52 have previously been mapped in the short arm of chromosome 5B in two F3 populations (Aus28183/Aus27229 and Aus28187/Aus27229). The Aus28183/Aus27229 F3 population was advanced to generate an F6 recombinant inbred line (RIL) population to identify markers closely linked with Yr47 and Lr52. Diverse genomic resources including flow-sorted chromosome survey sequence contigs representing the orthologous region in Brachypodium distachyon, the physical map of chromosome arm 5BS, expressed sequence tags (ESTs) located in the 5BS6-0.81-1.00 deletion bin and resistance gene analog contigs of chromosome arm 5BS were used to develop markers to saturate the target region. Selective genotyping was also performed using the iSelect 90 K Infinium ...
Artificial microRNAs (amiRNAs) are used for selective gene silencing in plants. However, current methods to produce amiRNA constructs for silencing transcripts in monocot species are not suitable for simple, cost-effective and large-scale synthesis. Here, a series of expression vectors based on Oryza sativa MIR390 (OsMIR390) precursor was developed for high-throughput cloning and high expression of amiRNAs in monocots. Four different amiRNA sequences designed to target specifically endogenous genes and expressed from OsMIR390-based vectors were validated in transgenic Brachypodium distachyon plants. Surprisingly, amiRNAs accumulated to higher levels and were processed more accurately when expressed from chimeric OsMIR390-based precursors that include distal stem-loop sequences from Arabidopsis thaliana MIR390a (AtMIR390a). In all cases, transgenic plants displayed the predicted phenotypes induced by target gene repression, and accumulated high levels of amiRNAs and low levels of the ...
Utility vectors with promoters that confer desired spatial and temporal expression patterns are useful tools for studying gene and cellular function and for industrial applications. To target the expression of DNA sequences of interest to cells forming plant secondary cell walls, which generate most of the vegetative biomass, upstream regulatory sequences of the Brachypodium distachyon lignin biosynthetic gene BdPMT and the cellulose synthase genes BdCESA7 and BdCESA8 were isolated and cloned into binary vectors designed for Agrobacterium-mediated transformation of monocots. Expression patterns were assessed using the β-glucuronidase gene GUSPlus and X-glucuronide staining. All three promoters showed strong expression levels in stem tissue at the base of internodes where cell wall deposition is most active, in both vascular bundle xylem vessels and tracheids, and in interfascicular tissues, with expression less pronounced in developmentally older tissues. In leaves, BdCESA7 and BdCESA8 promoter-driven
Researchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudnas group at UC Berkeley. Read more ...
Patterned after a corn stem, this monocot model shows the various layers of a plant stem and other vital structures. Anatomy of the stem is displayed in two different sections, and includes a detailed key for identification of structures.
My lab is interested in the switch to flower formation and in regulation of flower patterning in a variety of plant species. Most of our work to date has focused on Arabidopsis thaliana, but we are also investigating rice, Brachypodium, soybean and tomato. We are interested in the question how the developmental transition to reproductive development is regulated by integration of exogenous and endogenous cues for optimal reproductive fitness. We are also interested in the question how chromatin state changes regulate cell identity and response to extrinsic (stresses) and intrinsic (hormonal) signals ...
Ears are the seed-bearing inflorescences of maize (Zea mays) plants and represent a crucial component of maize yield. The first step in the formation of ears is the initiation of axillary meristems in the axils of developing leaves. In the classic maize mutant barren stalk fastigiate1 (baf1), first discovered in the 1950s, ears either do not form or, if they do, are partially fused to the main stalk. We positionally cloned Baf1 and found that it encodes a transcriptional regulator containing an AT-hook DNA binding motif. Single coorthologs of Baf1 are found in syntenic regions of brachypodium (Brachypodium distachyon), rice (Oryza sativa), and sorghum (Sorghum bicolor), suggesting that the gene is likely present in all cereal species. Protein-protein interaction assays suggest that BAF1 is capable of forming homodimers and heterodimers with other members of the AT-hook family. Another transcriptional regulator required for ear initiation is the basic helix-loop-helix protein BARREN STALK1 (BA1). ...
Plant root systems and associated symbiotic organisms act as critical links between the growing shoot and the rhizosphere, providing both vital nutrients and water to sustain growth. Many tools have been developed to study plant root systems; however, the efficient quantification of root traits remains a key bottleneck to effectively utilizing expanding collections of genomic and germplasm resources during the study of root system development and function. This dissertation presents results from root system phenotyping research where root phenotyping platforms were developed and used to investigate the genetic components of root system architecture and development in crop plants. It begins with a review chapter that discusses the importance of root system architecture (RSA) during resource acquisition and provides an overview of established root growth and measurement techniques while highlighting modern root phenotyping approaches that have been developed for genetic mapping studies. ...
MAKER-P version 3.1 was used to annotate genes in the Mo17 genome, which used a comprehensive strategy by combining results obtained from protein homology-based prediction, RNA-seq-based prediction, and ab initio prediction. We used the same evidence that was used for previous B73 gene annotations, with addition of Mo17-specific RNA-seq datasets. All annotated proteins from Sorghum bicolor,Oryza sativa, Setaria italica, Brachypodium distachyon and Arabidopsis thaliana were downloaded from Gramene.org release 48 and used for protein homology-based prediction. 74,471 assembled transcripts from Mo17 multiple tissues, full-length transcripts from B73 Iso-seq, another set of 69,163 publicly available full- length cDNAs from B73 deposited in Genbank, a total of 1,574,442 Trinity-assembled transcripts from 94 B73 RNA-Seq experiments, and 112,963 transcripts assembled from deep sequencing of a B73 seedling were collected and included as transcript evidence. Augustus and FGENESH were used to ab initio ...
Scientific conference (2013, February). The metabolic roles of volatile organic compounds (VOCs) emitted by plant growth-promoting rhizobacteria (PGPR) and the identity of the molecules responsible for the growth promotion are still poorly ... [more ▼]. The metabolic roles of volatile organic compounds (VOCs) emitted by plant growth-promoting rhizobacteria (PGPR) and the identity of the molecules responsible for the growth promotion are still poorly documented. As well, the implication of microRNAs in root development is a recent discovery that deserves to be explored. In this study, the implication of microRNAs in the response of Brachypodium distachyon (L.) Beauv. Bd21 root architecture to rhizobacterial VOCs was investigated. Nineteen PGPR strains were screened to select those showing the strongest phenotypic effects. The strain Bacillus subtilis AP305-GB03 induced the most important promotion of biomass production and root development. Total RNA extraction and RT-qPCR analysis of microRNAs ...
Walter Hood Fitch - Illustrations of the British Flora (1924) - Permission granted to use under GFDL by Kurt Stueber. Source: www.biolib.de - Permission is granted to copy, distribute and/or modify this image under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled GNU Free Documentation License. ...
The unprecedented access to rye genomic sequence information provided with this study as well as the detailed genome sequence information recently published for barley (International Barley Genome Sequencing Consortium, 2012) allowed a detailed comparative analysis of conserved orthologous genomic segments between both genomes. This revealed that individual conserved syntenic genomic segments of rye and barley carried strikingly different numbers of putatively conserved orthologous genes in comparison to the model grass genomes of rice, B. distachyon, and sorghum. Furthermore, the genes of defined conserved syntenic rye genome segments exhibited significantly different signatures of sequence conservation if compared with their putatively orthologous barley gene sequences.. Analysis of synonymous and nonsynonymous substitutions did not provide any evidence of different selective pressure among the different genomic regions of rye, but phylogenetic analysis of individual rye genomic segments ...
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As climate change creates new environmental challenges for farmers, Penn State biologists are studying gene variants in a model grass species to help inform better crop planting decisions to increase food production.
Joachim W. Messing (born 1946) is a university professor of Molecular Biology and the fourth director of the Waksman Institute of Microbiology at Rutgers University. Since his arrival at Rutgers in 1985, Jo Messing has initiated research activity on computational and structural biology and further emphasis on molecular genetics of the regulation of gene expression and biomolecular interactions. In the eighties, he provided incubator space for two Biotechnology centers at Rutgers, one in Medicine and one in Agriculture. Subsequently, he also founded two new departments at Rutgers and served as the first chair, the Department of Molecular Biology and Biochemistry and the Department of Genetics. Prof Messing is also involved in the Plant Genome Initiative at Rutgers, which has contributed to the sequencing of the maize, sorghum, and the rice genome. Besides maize, sorghum, and rice, they have also contributed to the sequencing of the Brachypodium and Spirodela genomes. Jo Messing is a pharmacist by ...
We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops…
Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are ...
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The focus in the first part of this exploration malegra power be on how small proteins fold without worrying malegra power the complexities introduced by the larger multidomain entities. Essentially identical areas, known as Wofflin nod- ules, occur in 24 of patients who do not have Down syndrome.
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Centre of Excellence Developments in Platform Technologies Transformation Systems Cell suspension cultures of Lolium multiflorum, Setaria viridis and Brachypodium distachyon have been generated and will be used in conjunction with previously established barley, rice, wheat and Arabidopsis cell culture and transformation systems. The sequenced genomes and genetic resources for rice and Arabidopsis have been supplemented by our access in 2011 to the barley genome scaffold sequence through our colleagues PI Waugh and Dr David Marshall from the James Hutton Institute in Dundee. The genome sequence will greatly accelerate our progress in reverse genetics approaches to the identification of candidate genes. A particular advantage of the Lolium multiflorum cultures, in which cell walls commonly consist of 20-30% (1,3;1,4)-ß-D--glucan, is that we can now generate and rapidly harvest hundreds of grams of biological material, including the cell walls themselves or membrane fractions and proteins that are
Non‐destructive methods to quantify the root system architecture of a plant grown in soil are essential to aid our understanding of the factors that impact plant root development in natural environments
Wheat and barley are the major temperate cereals, being used for food, feed and industrial raw material. However, in all cases the quality may be limited by the amount, composition and properties of...
The flagship monthly journal of SPIE, |i|Optical Engineering|/i| (OE) publishes peer-reviewed papers reporting on research and development in all areas of optics, photonics, and imaging science and engineering.
Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja. Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes (D type
The pendulum swung back the other way in the 60s, when a young post-doctoral associate at the University of Chicago, G.C. Williams, left lecture by Emerson muttering "Something must be done...." (Perhaps apocryphal, from Sober & Wilsons Unto Others). The result was Adaptation and Natural Selection (1966). This marked the rise of the Selfish Gene movement in evolutionary biology, culminating with Richard Dawkins classic, The Selfish Gene. This is not to say that the concept of cooperation was totally abandoned. Actually, it was placed on a more substantial theoretical foundation, particularly by W.D. Hamilton, who developed the notion of kin selection and Hamiltons Rule. Nonetheless the emphasis was definitely on selfish behavior ...
SynMap analysis of Alligator (x-axis) to Chicken (y-axis). Alligator contigs ordered and oriented according to their Syntenic Path to chicken chromosomes, and syntenic gene pairs are colored by their synonymous mutation rates. Note that nearly the entire chicken genome is covered by alligator contigs, but there are many alligator contigs that are not syntenically mapped to chicken. These probably contain few genes to extract a syntenic signal (minimum of three genes required by this analyis) or are made up of only non-genic (repetitive) sequences. Also, the regions of secondary synteny (not on the 45-degree line) are probably due to most recent paleo-tetraploidy event in the vertebrate lineage (1R or 2R). Results may be regenerated at: http://genomevolution.org/r/5ec3 ...