DOCSLIB.ORG

Title: Painting the Chromosomes of Brachypodium-Current Status and Future Prospects

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Title: Painting the Chromosomes of Brachypodium-Current Status and Future Prospects Title: Painting the chromosomes of Brachypodium-current status and future prospects Author: Dominika Idziak, A. Betekhtin, Elżbieta Wolny, Katarzyna Leśniewska, J. Wright, M. Febrer, M.W. Bevan, G. Jenkins, Robert Hasterok Citation style: Idziak Dominika, Betekhtin A., Wolny Elżbieta, Leśniewska Katarzyna, Wright J., Febrer M., Bevan M. W., Jenkins G., Hasterok Robert. (2011). Painting the chromosomes of Brachypodium-current status and future prospects. ”Chromosoma” (Vol. 120 (2011), s. 469-479), doi: 10.1007/s00412-011-0326-9 Chromosoma (2011) 120:469–479 DOI 10.1007/s00412-011-0326-9 RESEARCH ARTICLE Painting the chromosomes of Brachypodium—current status and future prospects Dominika Idziak & Alexander Betekhtin & Elzbieta Wolny & Karolina Lesniewska & Jonathan Wright & Melanie Febrer & Michael W. Bevan & Glyn Jenkins & Robert Hasterok Received: 7 March 2011 /Revised: 23 May 2011 /Accepted: 25 May 2011 /Published online: 11 June 2011 # The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Chromosome painting is one of the most power- containing relatively little repetitive genomic DNA enabled ful and spectacular tools of modern molecular cytogenetics, the first chromosome painting in dicotyledonous plants. enabling complex analyses of nuclear genome structure and Here, we show for the first time chromosome painting in evolution. For many years, this technique was restricted to three different cytotypes of a monocotyledonous plant—the the study of mammalian chromosomes, as it failed to work model grass, Brachypodium distachyon. Possible directions in plant genomes due mainly to the presence of large of further detailed studies are proposed, such as the amounts of repetitive DNA common to all the chromo- evolution of grass karyotypes, the behaviour of meiotic somes of the complement. The availability of ordered, chromosomes, and the analysis of chromosome distribution chromosome-specific BAC clones of Arabidopsis thaliana at interphase. Communicated by: I. Schubert Introduction Dominika Idziak and Alexander Betekhtin contributed equally to this work. : : : : Chromosome painting (CP), also known as chromosomal D. Idziak (*) A. Betekhtin E. Wolny K. Lesniewska in situ suppression, is one of the most powerful and R. Hasterok spectacular tools of molecular cytogenetics. It refers to the Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, method of visualisation of specific chromosome regions or Jagiellonska 28, entire chromosomes using fluorescence in situ hybrid- 40-032 Katowice, Poland isation (FISH) with chromosome-specific DNA probes e-mail: [email protected] (Pinkel et al. 1988; Ried et al. 1998). For many years, this J. Wright : M. Febrer : M. W. Bevan technique was successfully applied only to studies of Department of Cell and Developmental Biology, animal chromosomes, giving unprecedented insight into John Innes Centre, the structural and functional compartmentalisation of the Colney Lane, nucleus (Cremer et al. 2008; Cremer et al. 1993; Kurz et Norwich NR4 7UH, UK al. 1996). It has also been widely used for molecular G. Jenkins cytotaxonomy, for example of primates (Muller et al. 1999; Institute of Biological, Environmental and Rural Sciences, Wienberg et al. 1990), mutagenicity testing (Marshall and Aberystwyth University, Obe 1998) and radiation biology (Gray et al. 1992). High Edward Llwyd Building, Penglais, Aberystwyth, Wales SY23 3DA( Ceredigion, UK resolution CP-based analyses have become especially important to pre-, neo- and postnatal clinical diagnostics Present Address:: of various chromosomal aberrations associated with J. Wright M. Febrer human diseases and malignancies (Gray and Pinkel 1992; The Genome Analysis Centre, Norwich Research Park, Popp et al. 1991; Tkachuk et al. 1991; Weise et al. 2003; Norwich NR4 7UH, UK Xu et al. 2010). 470 Chromosoma (2011) 120:469–479 For more than a decade, efforts to apply CP in plants Materials and methods failed to yield satisfactory results, which was attributed to the presence of vast amounts of ubiquitous repetitive DNA Plant material and chromosome preparations in most plant genomes (Schubert et al. 2001). The first true painting of plant chromosomes was achieved by Lysak et Three cytotypes of B. distachyon were used in this study. al. (2001) in the dicotyledonous model organism, Arabi- Detailed information on the plant material is provided in dopsis thaliana, whose nuclear genome had just been Table 1. Seeds were sown at high density in compost. All sequenced (Arabidopsis Genome Initiative 2000). The plants were grown as described in Jenkins and Hasterok availability of genome sequence and ordered libraries of (2007). The plants of cytotypes ABR114 and ABR113 did genomic DNA in BAC (Bacterial Artificial Chromosome) not require vernalisation and usually reached the generative vectors, along with some features of A. thaliana genome, stage of their life cycle within 1 month after sowing. such as its compactness, low amount of repetitive DNA and Mitotic chromosome preparations were made using the low number of chromosomes, were key prerequisites for methodology described by Hasterok et al. (2006). Preparation successful painting of its chromosomes. Initially restricted of anther tissue for meiotic chromosome squashes was to the chromosomes of A. thaliana (Pecinka et al. 2004), adopted from Jenkins and Hasterok (2007)withminor CP in later studies was also successfully applied to other modifications. In brief, immature inflorescences were collect- closely related members of the Brassicaceae. This comparative ed, fixed immediately in fresh 3:1 absolute methanol:glacial chromosome painting (CCP) allowed unprecedented analyses acetic acid mixture for 3×24 h at room temperature (RT) and of the evolution of the genomes of this group of plants at the stored at −20°C until required. Individual anthers were chromosomal level (Lysak et al. 2006; Lysak et al. 2010; isolated and washed in 10 mM citric acid–sodium citrate Mandakova and Lysak 2008). buffer and digested enzymatically for 2 h at 37°C in a mixture In contrast to the dicots, chromosome painting has not comprising 10% (v/v) pectinase (Sigma), 0.65% (w/v) been applied so far to any monocotyledonous plant. Despite cellulase Onozuka R-10 (Serva), 0.5% (w/v) cellulase the availability of its long-published genomic sequence (Calbiochem), 0.15% (w/v) cytohelicase and 0.15 % (w/v) (Goff et al. 2002), no chromosome painting has been pectolyase in 10 mM citrate buffer. Several anthers per slide performed in rice. Another species of Poaceae, Brachypo- were squashed in drops of 45% acetic acid, frozen, postfixed dium distachyon, emerged several years ago as a model in 4% formaldehyde for 10 min, washed briefly in distilled system for temperate cereals and grasses. Like A. thaliana, water and air dried. B. distachyon possesses numerous ‘model’ attributes, including inter alia a small (∼300 Mb) genome with a low Selection of BAC clones for chromosome painting (x=5) basic chromosome number, small physical stature, self-fertility, a short life cycle and undemanding growth BAC clones used for CP were selected from the five requirements (Draper et al. 2001; Garvin et al. 2008). The assemblies of FPCs (FingerPrinted Contigs) previously genome of B. distachyon has been extensively studied at aligned to the B. distachyon karyotype (Febrer et al. 2010; the chromosomal level using fluorescence in situ hybrid- International Brachypodium Initiative 2010). Clones from isation (FISH) with a wide range of DNA probes, which enabled unambiguous identification of all the chromosomes and their arms of the complement (Hasterok et al. 2004; Table 1 The original identities, sources, origins and chromosome Hasterok et al. 2006). numbers of the B. distachyon material used in this study The well-established cytogenetic platform, combined Species Accession no. Origin Source 2n with resources such as BAC DNA libraries and bioinfor- matic data from the recently completed genome sequencing B. distachyon Bd21 Iraq a 10 project (Febrer et al. 2010; Gu et al. 2009; International ‘B. distachyon’* ABR114 Spain b 20 Brachypodium Initiative 2010), opened up the possibility of ‘B. distachyon’* ABR113 Portugal b 30 painting for the first time the chromosomes of a monocot a US Department of Agriculture–National Plant Germplasm System, species. In this paper, we present the current status of CP in USA, b Institute of Biological, Environmental and Rural Sciences, B. distachyon, which allows reliable recognition and tracking Aberystwyth University, UK of individual chromosome regions during different stages of * According to our previous cytomolecular studies (Hasterok et al. meiosis. Additionally, we show that CCP with BAC 2004;Hasteroketal.2006) ABR114 and ABR113 represent, pools representing individual B. distachyon chromosomes respectively, a different unnamed diploid and an allotetraploid species can be used as an effective tool for studying karyotype within the Brachypodium genus. As their proposed taxonomical status is not yet officially accepted, we refer in this paper to ABR114 and evolution of its close relatives in the genus Brachypodium. ABR113 as the cytotypes of ‘B. distachyon’. The cytotype with 2n= Possible future prospects are also discussed. 10 chromosomes is referred to as B. distachyon without apostrophes Chromosoma (2011) 120:469–479 471 centromeric and pericentromeric regions were excluded experiment shown on Figs. 1f and 3. The list of BACs from
Load more

Recommended publications
  • The 3Rd International Brachypodium Conference July 29-July 31, 2017, Beijing, China
    The 3rd International Brachypodium Conference Beijing ◌ China July 30-31, 2017 The 3rd International Brachypodium Conference July 29-July 31, 2017, Beijing, China The 3rd International Brachypodium Conference Beijing, CHINA July 30-31, 2017 International Brachypodium Steering Committee Pilar Catalan (University of Zaragoza, Spain) Mhemmed Gandour (Faculty of Sciences and Technology of Sidi Bouzid, Tunisia) Samuel Hazen, (Biology Department, University of Massachusetts,USA) Zhiyong Liu (Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, China) Keiichi Mocida (RIKEN Center for Sustainable Resource Science, Japan) Richard Sibout (INRA, France) John Vogel (Plant Functional Genomics, DOE Joint Genome Institute, USA) Local Organizing Committee Zhiyong Liu, Chair (Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, China) Long Mao, co-Chair (Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, China) Xiaoquan Qi (Institute of Botany, Chinese Academy of Sciences, China) Dawei Li (College of Life Science, China Agricultural University, China) Yueming Yan (College of Life Science, Capital Normal University, China) Hailong An (College of Life Science, Shandong Agricultural University, China) Yuling Jiao (Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, China) Zhaoqing Chu (Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences) Liang Wu (Zhejiang University, China) The 3rd International Brachypodium
    [Show full text]
  • Phenotypic Characterization of Brachypodium Distachyon and a Synthetic Community for Dissecting Plant-Microbial Community Intera
    Phenotypic Characterization of Brachypodium distachyon and a Synthetic Community for Dissecting Plant-Microbial Community Interactions in Fabricated Ecosystems (EcoFAB) Hsiao-Han Lin1 ([email protected]), Trenton K. Owens1, Marta Torres1, Mon O. Yee1, Yifan Li1, Kristine G. Cabugao1, Kateryna Zhalnina1, Lauren K. Jabusch1, Peter F. Andeer1, Romy Chakraborty1, Jenny C. Mortimer1,2([email protected]), Adam M. Deutschbauer1, and Trent R. Northen1 1Lawrence Berkeley National Laboratory, Berkeley CA; 2University of Adelaide, Australia http://mCAFEs.lbl.gov Project Goals: Understanding the interactions, localization, and dynamics of grass rhizosphere communities at the molecular level (genes, proteins, metabolites) to predict responses to perturbations and understand the persistence and fate of engineered genes and microbes for secure biosystems design. To do this, advanced fabricated ecosystems are used in combination with gene editing technologies such as CRISPR-Cas and bacterial virus (phage)-based approaches for interrogating gene and microbial functions in situ—addressing key challenges highlighted in recent DOE reports. This work is integrated with the development of predictive computational models that are iteratively refined through simulations and experimentation to gain critical insights into the functions of engineered genes and interactions of microbes within soil microbiomes as well as the biology and ecology of uncultivated microbes. Together, these efforts lay a critical foundation for developing secure biosystems design strategies, harnessing beneficial microbiomes to support sustainable bioenergy, and improving our understanding of nutrient cycling in the rhizosphere. Plants grow in environments rich with microbes, where negative (pathogenic), neutral, or beneficial plant-microbial interactions may develop. These microbes are found as a complex community, and so interactions must be understood in the context of a community, rather than as an interaction between a single microbe and the plant.
    [Show full text]
  • Natural Variation of Flowering Time and Vernalization Responsiveness in Brachypodium Distachyon
    Bioenerg. Res. (2010) 3:38–46 DOI 10.1007/s12155-009-9069-3 Natural Variation of Flowering Time and Vernalization Responsiveness in Brachypodium distachyon Christopher J. Schwartz & Mark R. Doyle & Antonio J. Manzaneda & Pedro J. Rey & Thomas Mitchell-Olds & Richard M. Amasino Published online: 7 February 2010 # Springer Science+Business Media, LLC. 2010 Abstract Dedicated bioenergy crops require certain char- Keywords Biomass . Bioenergy. Brachypodium . acteristics to be economically viable and environmentally Flowering time . Vernalization sustainable. Perennial grasses, which can provide large amounts of biomass over multiple years, are one option being investigated to grow on marginal agricultural land. Introduction Recently, a grass species (Brachypodium distachyon) has been developed as a model to better understand grass Biomass yield is an important component to consider in any physiology and ecology. Here, we report on the flowering program designed to derive energy from plant material. time variability of natural Brachypodium accessions in Plant size and architecture are important biomass yield response to temperature and light cues. Changes in both parameters, and these parameters are often quite variable environmental parameters greatly influence when a given within a given species. Intraspecies variation in biomass accession will flower, and natural Brachypodium accessions yield can be a product of many factors. One such factor is broadly group into winter and spring annuals. Similar to the timing of the transition from vegetative to reproductive what has been discovered in wheat and barley, we find that growth. The switch to flowering causes a diversion of a portion of the phenotypic variation is associated with resources from the continual production of photosynthetic changes in expression of orthologs of VRN genes, and thus, material (leaves) to the terminal production of reproductive VRN genes are a possible target for modifying flowering tissue (flowers, seeds, and fruit).
    [Show full text]
  • Brachypodium Distachyon Transformation Protocol
    Chapter 2 Brachypodium distachyon Jennifer N. Bragg , Amy Anderton , Rita Nieu , and John P. Vogel Abstract The small grass Brachypodium distachyon has attributes that make it an excellent model for the development and improvement of cereal crops and bioenergy feedstocks. To realize the potential of this system, many tools have been developed (e.g., the complete genome sequence, a large collection of natural accessions, a high density genetic map, BAC libraries, EST sequences, microarrays, etc.). In this chapter, we describe a high-effi ciency transformation system, an essential tool for a modern model system. Our method utilizes the natural ability of Agrobacterium tumefaciens to transfer a well-defi ned region of DNA from its tumor-inducing (Ti) plasmid DNA into the genome of a host plant cell. Immature embryos dissected out of developing B. distachyon seeds generate an embryogenic callus that serves as the source material for transformation and regeneration of transgenic plants. Embryogenic callus is cocultivated with A. tumefaciens carrying a recombinant plasmid containing the desired transformation sequence. Following cocultivation, callus is transferred to selective media to identify and amplify the transgenic tissue. After 2–5 weeks on selection media, transgenic callus is moved onto regeneration media for 2–4 weeks until plantlets emerge. Plantlets are grown in tissue culture until they develop roots and are transplanted into soil. Transgenic plants can be transferred to soil 6–10 weeks after cocultivation. Using this method with hygromycin selection, transformation effi ciencies average 42 %, and it is routinely observed that 50–75 % of cocultivated calluses produce transgenic plants. The time from dissecting out embryos to having the fi rst transgenic plants in soil is 14–18 weeks, and the time to harvesting transgenic seeds is 20–31 weeks.
    [Show full text]
  • Brachypodium Distachyon (L.) Beauv
    A WEED REPORT from the book Weed Control in Natural Areas in the Western United States This WEED REPORT does not constitute a formal recommendation. When using herbicides always read the label, and when in doubt consult your farm advisor or county agent. This WEED REPORT is an excerpt from the book Weed Control in Natural Areas in the Western United States and is available wholesale through the UC Weed Research & Information Center (wric.ucdavis.edu) or retail through the Western Society of Weed Science (wsweedscience.org) or the California Invasive Species Council (cal-ipc.org). Brachypodium distachyon (L.) Beauv. Annual false-brome Family: Poaceae Range: Common in California, but scattered throughout the other western states, including Oregon, Colorado and Texas. Habitat: Dry slopes and fields, roadsides, disturbed grassland, margins of shrub thickets. Tolerates thin rocky soil and partial shade in oak woodlands. Origin: Native to southern Europe. Likely an accidental introduction into North America. Impacts: It is a poor forage grass because of its fibrous stems, little foliage, and firm spikelets with awned florets. California Invasive Plant Council (Cal-IPC) Inventory: Moderate Invasiveness Annual false-brome is a winter annual to 2 ft tall, with spikes that are often tinged purplish. Plants are sometimes branched at the base. The stems are erect or flat with the tips turning upward, usually lacking hairs except at the densely hairy nodes. The ligule is membranous and 2 to 3 mm long, the top irregularly jagged or fringed with short hairs, and the upper surface minutely hairy. The inflorescence is a spike-like raceme, 1 to 3 inches long, with 1 to 6 spikelets per stem.
    [Show full text]
  • Brachypodium Distachyon Genomics for Sustainable Food and Fuel Production Michael W Bevan1, David F Garvin2 and John P Vogel3
    Available online at www.sciencedirect.com Brachypodium distachyon genomics for sustainable food and fuel production Michael W Bevan1, David F Garvin2 and John P Vogel3 Grass crops are the most important sources of human nutrition, The capture of sunlight and its conversion to chemical and their improvement is centrally important for meeting the energy by photosynthesis is the primary biological process challenges of sustainable agriculture, for feeding the world’s available for sustainable biotechnology, and photosyn- population and for developing renewable supplies of fuel and thesis in land plants remains the largest source of renew- industrial products. We describe the complete sequence of the able food and energy [4] that can be produced within a compact genome of Brachypodium distachyon sustainable carbon cycle. Primary production from agri- (Brachypodium) the first pooid grass to be sequenced. We culture therefore assumes an important role in the tran- demonstrate the many favorable characteristics of sition to increasingly sustainable food and industrial Brachypodium as an experimental system and show how it can production methods. Some grass crop species, such as be used to navigate the large and complex genomes of closely maize, sorghum and sugarcane have evolved C4 photo- related grasses. The functional genomics and other synthesis, in which CO2 is concentrated at the sites of experimental resources that are being developed will provide a carboxylation to increase photosynthetic efficiency. Grass key resource for improving food and forage crops, in particular crops are therefore centrally important targets for bio- wheat, barley and forage grasses, and for establishing new technological improvement for food and fuel production.
    [Show full text]
  • Genome Identification and Expression Analysis of GRAS Family Related
    ORIGINAL RESEARCH published: 14 May 2021 doi: 10.3389/fsufs.2021.675177 Genome Identification and Expression Analysis of GRAS Family Related to Development, Hormone and Pathogen Stress in Brachypodium distachyon Zejun Tang 1,2†, Na Song 1,2†, Weiye Peng 1,2, Yang Yang 1,2, Tian Qiu 1,2, Chenting Huang 1,2, Liangying Dai 1,2* and Bing Wang 1,2* 1 Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China, 2 College of Plant Protection, Hunan Agricultural University, Changsha, China Edited by: Wen Xie, GRAS transcription factors are widely present in the plant kingdom and play important Chinese Academy of Agricultural roles in regulating multiple plant physiological processes. Brachypodium distachyon is a Sciences, China model for grasses for researching plant-pathogen interactions. However, little is known Reviewed by: Yong Liu, about the BdGRAS family genes involved in plant response to biotic stress. In this study, Hunan Academy of Agricultural we identified 63 genes of the GRAS family in B. distachyon. The phylogenetic analysis Sciences (CAAS), China showed that BdGRAS genes were divided into ten subfamilies and unevenly distributed Suprasanna Penna, Bhabha Atomic Research Centre on five chromosomes. qRT-PCR results showed that the BdGRAS family genes were (BARC), India involved in the growth and development of B. distachyon. Moreover, the expression of the *Correspondence: HAM subfamily genes of BdGRAS changed during the interaction between B. distachyon Bing Wang [email protected] and Magnaporthe oryzae. Interestingly, BdGRAS31 in the HAM subfamily was regulated Liangying Dai by miR171 after inoculation with M.
    [Show full text]
  • Brachypodium: a Monocot Grass Model Genus for Plant Biology[OPEN]
    The Plant Cell, Vol. 30: 1673–1694, August 2018, www.plantcell.org © 2018 ASPB. REVIEW Brachypodium: A Monocot Grass Model Genus for Plant Biology[OPEN] Karen-Beth G. Scholthof,a,1 Sonia Irigoyen,b Pilar Catalan,c,d,e,1 and Kranthi K. Mandadia,b,1 aDepartment of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843 bTexas A&M AgriLife Research and Extension Center, Weslaco, Texas 78596 cUniversidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071 Huesca, Spain dGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza E-50059, Spain eInstitute of Biology, Tomsk State University, Tomsk 634050, Russia ORCID IDs: 0000-0002-8169-9823 (K.-B.G.S.); 0000-0003-0647-4808 (S.I.); 0000-0001-7793-5259 (P.C.); 0000-0003-2986-4016 (K.K.M.) The genus Brachypodium represents a model system that is advancing our knowledge of the biology of grasses, including small grains, in the postgenomics era. The most widely used species, Brachypodium distachyon, is a C3 plant that is distrib- uted worldwide. B. distachyon has a small genome, short life cycle, and small stature and is amenable to genetic transforma- tion. Due to the intensive and thoughtful development of this grass as a model organism, it is well-suited for laboratory and field experimentation. The intent of this review is to introduce this model system genus and describe some key outcomes of nearly a decade of research since the first draft genome sequence of the flagship species, B. distachyon, was completed. We discuss characteristics and features of B.
    [Show full text]
  • Evaluation of Hall's Panicgrass (<I>Panicum Hallii</I> Vasey)
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Masters Theses Graduate School 5-2017 Evaluation of Hall’s Panicgrass (Panicum hallii Vasey) as a Model System for Genetic Modification of Recalcitrance in Switchgrass (Panicum virgatum (L.)) Joshua Nathaniel Grant University of Tennessee, Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_gradthes Part of the Agriculture Commons, Biotechnology Commons, and the Plant Biology Commons Recommended Citation Grant, Joshua Nathaniel, "Evaluation of Hall’s Panicgrass (Panicum hallii Vasey) as a Model System for Genetic Modification of Recalcitrance in Switchgrass (Panicum virgatum (L.)). " Master's Thesis, University of Tennessee, 2017. https://trace.tennessee.edu/utk_gradthes/4742 This Thesis is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Masters Theses by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a thesis written by Joshua Nathaniel Grant entitled "Evaluation of Hall’s Panicgrass (Panicum hallii Vasey) as a Model System for Genetic Modification of Recalcitrance in Switchgrass (Panicum virgatum (L.))." I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Master of Science, with a major in Plant Sciences. Charles N. Stewart, Major Professor We have read this thesis and recommend its acceptance: Scott C. Lenaghan, Max Chen Accepted for the Council: Dixie L.
    [Show full text]
  • Supplementary Material Brachypodium Distachyon
    10.1071/FP15244_AC © CSIRO 2016 Supplementary Material: Functional Plant Biology, 2016, 43(2), 189–198. Supplementary Material Brachypodium distachyon genotypes vary in resistance to Rhizoctonia solani AG8 Katharina SchneebeliA,B,F,I, Ulrike MathesiusB, Alexander B. ZwartA,G, Jennifer N. BraggC, John P. VogelD,E and Michelle WattA,H ACSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia. BDivision of Plant Science, Research School of Biology, 134 Linnaeus Way, Australian National University, Canberra, ACT 2601, Australia. CJoint BioEnergy Institute, 5885 Hollis St. ESE 4th Floor, Emeryville, CA 94608, USA. DDOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA. EUSDA-ARS Western Regional Research Centre, Albany, CA 94710, USA. FPresent address: NSW Department of Primary Industries, 21 888 Kamilaroi Highway, Narrabri, NSW 2390, Australia. GPresent address: CSIRO Data61, GPO Box 664, Canberra, ACT 2601, Australia. HPresent address: Plant Sciences (IBG-2), Forschungszentrum Jülich, 52 428 Jülich, Germany. ICorresponding author. Email: [email protected] 1 Table S1. Information on tagged genes of T-DNA lines included in R. solani AG8 disease screening experiments Lines were chosen, from those available, based on literature evidence that disruption of putative T-DNA tagged genes could have an effect on disease resistance, root growth or interaction with cell wall degrading enzymes produced by R. solani AG8. NCBI Protein-BLAST sequence JJ line T-DNA tagged Construct A; T-DNA Notes on gene family homologues from cited references and homology with predicted or known number gene location The UniProt Consortium (2012) genes, E-value Predicted: nucleobase-ascorbate NAT6 expressed in Arabidopsis seedling roots and lateral 77 Bradi3g36010 pOL001; in gene transporter 6-like [B.
    [Show full text]
  • Turning a Wild Plant Into a Model – a Déjà Vu Story Daniel Ioan PACURAR 1), 2)
    Available online at www.notulaebotanicae.ro Print ISSN 0255-965X; Electronic ISSN 1842-4309 Not. Bot. Hort. Agrobot. Cluj 37 (1) 2009, 17-24 Notulae Botanicae Horti Agrobotanici Cluj-Napoca Turning a Wild Plant into a Model – A Déjà vu Story Daniel Ioan PACURAR 1), 2) 1)Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90133 Umeå, Sweden 2)University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania; [email protected] Abstract In the past two decades we have witnessed how a useless wild weed has been transformed from an anonymous into a model plant, probably the most widely “cultivated” plant species. The process has been rather slowly in the beginning, very laborious on the way, extremely expensive and time consuming, but the outcome is priceless – the knowledge that is most likely to frame and fill the blueprint of the first artificial plant, as system biology promises. The plant species Arabidopsisis thaliana and the “growers” are highly qualified researchers worldwide. This review introduces a new anonymous – Brachypodium distachyon – that raised big hopes for addressing specific problems of fundamental and practical biology in temperate cereals and forage grasses, and is rapidly becoming a “sweetheart” for the researchers working with these crops, and not only. Keywords: Brachypodium distachyon, Arabidopsis thaliana, Oryza sativa, model plant species Introduction last subgroup has two representatives: the classical model Since the onset of humanity we have domesticated wild Arabidopsis thaliana and the newcomer Brachypodium dis- plants to provide us with food, fibres and oils; we selected tachyon that has been promoted and is being developed as a them for medical purposes, or not less important as orna- model for temperate cereals and forage grasses.
    [Show full text]
  • Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution
    International Journal of Molecular Sciences Article Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution Joanna Lusinska 1 , Alexander Betekhtin 1 , Diana Lopez-Alvarez 2,3 , Pilar Catalan 3,4,5, Glyn Jenkins 6, Elzbieta Wolny 1,* and Robert Hasterok 1,* 1 Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland; [email protected] (J.L.); [email protected] (A.B.) 2 Faculty of Agricultural Sciences, National University of Columbia, Palmira 763533, Colombia; [email protected] 3 Department of Agriculture (Botany), High Polytechnic School of Huesca, University of Zaragoza, 22071 Huesca, Spain; [email protected] 4 Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, 50018 Zaragoza, Spain 5 Institute of Biology, Tomsk State University, Tomsk 634050, Russia 6 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; [email protected] * Correspondence: [email protected] (E.W.); [email protected] (R.H.) Received: 28 September 2019; Accepted: 2 November 2019; Published: 7 November 2019 Abstract: The Brachypodium genus is an informative model system for studying grass karyotype organization. Previous studies of a limited number of species and reference chromosomes have not provided a comprehensive picture of the enigmatic phylogenetic relationships in the genus. Comparative chromosome barcoding, which enables the reconstruction of the evolutionary history of individual chromosomes and their segments, allowed us to infer the relationships between putative ancestral karyotypes of extinct species and extant karyotypes of current species.
    [Show full text]