Reference Genome Sequence of the Model Plant Setaria
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Reference Genome Sequence of the Model Plant Setaria
UC Davis UC Davis Previously Published Works Title Reference genome sequence of the model plant Setaria Permalink https://escholarship.org/uc/item/2rv1r405 Journal Nature Biotechnology, 30(6) ISSN 1087-0156 1546-1696 Authors Bennetzen, Jeffrey L Schmutz, Jeremy Wang, Hao et al. Publication Date 2012-05-13 DOI 10.1038/nbt.2196 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ARTICLES Reference genome sequence of the model plant Setaria Jeffrey L Bennetzen1,13, Jeremy Schmutz2,3,13, Hao Wang1, Ryan Percifield1,12, Jennifer Hawkins1,12, Ana C Pontaroli1,12, Matt Estep1,4, Liang Feng1, Justin N Vaughn1, Jane Grimwood2,3, Jerry Jenkins2,3, Kerrie Barry3, Erika Lindquist3, Uffe Hellsten3, Shweta Deshpande3, Xuewen Wang5, Xiaomei Wu5,12, Therese Mitros6, Jimmy Triplett4,12, Xiaohan Yang7, Chu-Yu Ye7, Margarita Mauro-Herrera8, Lin Wang9, Pinghua Li9, Manoj Sharma10, Rita Sharma10, Pamela C Ronald10, Olivier Panaud11, Elizabeth A Kellogg4, Thomas P Brutnell9,12, Andrew N Doust8, Gerald A Tuskan7, Daniel Rokhsar3 & Katrien M Devos5 We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. -
Establishment of a Global Network for the in Situ Conservation of Crop Wild Relatives: Status and Needs
THEMATIC BACKGROUND STUDY Establishment of a Global Network for the In Situ Conservation of Crop Wild Relatives: Status and Needs Nigel Maxted and Shelagh Kell BACKGROUND STUDY PAPER NO. 39 October 2009 COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE ESTABLISHMENT OF A GLOBAL NETWORK FOR THE IN SITU CONSERVATION OF CROP WILD RELATIVES: STATUS AND NEEDS by *By Nigel Maxted and Shelagh Kell The content of this document is entirely the responsibility of the authors, and does not .necessarily represent the views of the FAO, or its Members 2 * School of Biosciences, University of Birmingham. Disclaimer The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the Food and Agriculture Organization of the United Nations (FAO), or its Members. The designations employed and the presentation of material do not imply the expression of any opinion whatsoever on the part of FAO concerning legal or development status of any country, territory, city or area or of its authorities or concerning the delimitation of its frontiers or boundaries. The mention of specific companies or products of manufacturers, whether or not these have been patented, does not imply that these have been endorsed by FAO in preference to others of a similar nature that are not mentioned. CONTENTS SUMMARY 6 ACKNOWLEDGEMENTS 7 PART 1: INTRODUCTION 8 1.1 Background and scope 8 1.2 The global and local importance of crop wild relatives 10 1.3 Definition of a crop wild relative 12 1.4 Global numbers of crop -
24. Tribe PANICEAE 黍族 Shu Zu Chen Shouliang (陈守良); Sylvia M
POACEAE 499 hairs, midvein scabrous, apex obtuse, clearly demarcated from mm wide, glabrous, margins spiny-scabrous or loosely ciliate awn; awn 1–1.5 cm; lemma 0.5–1 mm. Anthers ca. 0.3 mm. near base; ligule ca. 0.5 mm. Inflorescence up to 20 cm; spike- Caryopsis terete, narrowly ellipsoid, 1–1.8 mm. lets usually densely arranged, ascending or horizontally spread- ing; rachis scabrous. Spikelets 1.5–2.5 mm (excluding awns); Stream banks, roadsides, other weedy places, on sandy soil. Guangdong, Hainan, Shandong, Taiwan, Yunnan [Bhutan, Cambodia, basal callus 0.1–0.2 mm, obtuse; glumes narrowly lanceolate, India, Indonesia, Laos, Malaysia, Myanmar, Nepal, Philippines, Sri back scaberulous-hirtellous in rather indistinct close rows (most Lanka, Thailand, Vietnam; Africa (probably introduced), Australia obvious toward lemma base), midvein pectinate-ciliolate, apex (Queensland)]. abruptly acute, clearly demarcated from awn; awn 0.5–1.5 cm. Anthers ca. 0.3 mm. Caryopsis terete, narrowly ellipsoid, ca. 3. Perotis hordeiformis Nees in Hooker & Arnott, Bot. Beech- 1.5 mm. Fl. and fr. summer and autumn. 2n = 40. ey Voy. 248. 1838. Sandy places, along seashores. Guangdong, Hebei, Jiangsu, 麦穗茅根 mai sui mao gen Yunnan [India, Indonesia, Malaysia, Nepal, Myanmar, Pakistan, Sri Lanka, Thailand]. Perotis chinensis Gandoger. This species is very close to Perotis indica and is sometimes in- Annual or short-lived perennial. Culms loosely tufted, cluded within it. No single character by itself is reliable for separating erect or decumbent at base, 25–40 cm tall. Leaf sheaths gla- the two, but the combination of characters given in the key will usually brous; leaf blades lanceolate to narrowly ovate, 2–4 cm, 4–7 suffice. -
Reproductive Phasirna Loci and DICER-LIKE5, but Not Microrna
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.25.061721; this version posted April 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Reproductive phasiRNA loci and DICER‐LIKE5, but not microRNA loci, diversified in monocotyledonous plants Parth Patel2§, Sandra M. Mathioni1§, Reza Hammond2, Alex E. Harkess1, Atul Kakrana2, Siwaret Arikit3, Ayush Dusia2, and Blake C. Meyers1,2,4* 1Donald Danforth Plant Science Center, Saint Louis, Missouri 63132 2Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19716 3Department of Agronomy, Kamphaeng Saen and Rice Science Center, Kasetsart University, Nakhon Pathom 73140, Thailand 4Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211 §These authors contributed equally to this work. *Corresponding author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.04.25.061721; this version posted April 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Abstract (200 words) 2 In monocots other than maize and rice, the repertoire and diversity of microRNAs (miRNAs) and 3 the populations of phased, secondary, small interfering RNAs (phasiRNAs) are poorly 4 characterized. To remedy this, we sequenced small RNAs from vegetative and dissected 5 inflorescence tissue in 28 phylogenetically diverse monocots and from several early‐diverging 6 angiosperm lineages, as well as publicly available data from 10 additional monocot species. -
Interspecific Hybridization Between Durum Wheat and Aegilops Umbellulata (Zhuk.)
713 Bulgarian Journal of Agricultural Science, 18 (No 5) 2012, 713-721 Agricultural Academy INTERSPECIFIC HYBRIDIZATION BETWEEN DURUM WHEAT AND AEGILOPS UMBELLULATA (ZHUK.) B. HADZHIIVANOVA, V. BOZHANOVA and D. DECHEV Field Crops Institute, BG - 6200 Chirpan, Bulgaria Abstract HADZHIIVANOVA, B., V. BOZHANOVA and D. DECHEV, 2012. Interspecific hybridization between durum wheat and Aegilops umbellulata (Zhuk.). Bulg. J. Agric. Sci., 18: 713-721 The possibility for obtaining of interspecific hybrids between three durum wheat genotypes (Triticum durum, 2n = 4x = 28, AABB genomes) and one accession of Aegilops umbellulata (2n = 2x = 18, UU genome) during two different seasons has been studied. A low crossability rate of 3% average for all genotypes over two years was achieved. The observed variation of crossability is due to a greatest extent to the genotype of durum wheat parent with 82.91% from total variation. Hybrid plants were obtained only by means of embryo rescue method. The ability for in vitro regeneration was still independent of crossability of used durum wheat genotypes. All received F1 hybrids plants were identical they exhibited good tillering ability and manifested traits from both parents. In spite of the observed partially fertility in F1 hybrids between durum wheat and Aegilops umbellulata no germination of the hybrid seeds was ascertained. BC1 seeds were obtained from F1 hybrids of hybrid combination Beloslava × Aegilops umbellulata after backcrossing to the durum wheat parent. An increase of crossability with advancing of backcross progenies – from 1.6% in BC1 hybrids to 26.2% in BC2 hybrids has been found. Meiotic abnormalities including dyads and triads at the end of microsporogenesis as well as uninucleate microspores with a different shape and size were observed suggesting production of unreduced gametes in this cross. -
The Setaria Viridis Genome and Diversity Panel Enables Discovery of a Novel
bioRxiv preprint doi: https://doi.org/10.1101/744557; this version posted August 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene Authors: Pu Huang1,5, Sujan Mamidi2, Adam Healey2, Jane Grimwood2, Jerry Jenkins2, Kerrie Barry3, Avinash Sreedasyam2, Shengqiang Shu3, Maximilian Feldman1,6, Jinxia Wu1,7, Yunqing Yu1, Cindy Chen3, Jenifer Johnson3, Hitoshi Sakakibara4,8, Takatoshi Kiba4,9, Tetsuya Sakurai4,9, Daniel Rokhsar3, Ivan Baxter1, Jeremy Schmutz2,3, Thomas P. Brutnell1,7, Elizabeth A. Kellogg1,* 1 Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA 2 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA 3 Department of Energy Joint Genome Institute, Walnut Creek, California, USA 4 RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan 5 present address: BASF Corporation, 26 Davis Dr., Durham, NC 27709, USA 6 present address: USDA-ARS Temperate Tree Fruit and Vegetable Research Unit, 24106 N. Bunn Rd., Prosser, WA 99350, USA 7 Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China 8 present address: Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan 1 bioRxiv preprint doi: https://doi.org/10.1101/744557; this version posted August 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Vascular Plant Diversity of the Alanya Castle Walls and Their Ecological Effects
www.biodicon.com Biological Diversity and Conservation ISSN 1308-8084 Online ISSN 1308-5301 Print Research article/Araştırma makalesi 13/1 (2020) 9-18 DOI: 10.46309/biodicon.2020.731423 Vascular plant diversity of the Alanya Castle walls and their ecological effects Ahmet AKSOY 1, Jale ÇELİK *2 ORCID: 0000-0002-9696-7122; 0000-0002-3624-2146 1 University of Akdeniz, Faculty of Science, Department of Biology, Antalya, Turkey 2 University of Akdeniz, Institute of Science and Technology, Department of Biology, Antalya, Turkey Abstract Since historical buildings are living mirrors of the past, it is very important to preserve and transfer them to future generations. In this study, plants growing on the walls of Alanya Castle were identified and the damages that these plants gave to the historical construction and the precautions to be taken to prevent these damages were emphasized. A total of 94 plant taxa, including five pteridophytes, one gymnosperm and 88 angiosperms, belonging to 35 families were identified on the walls of Alanya Castle. Conyza canadensis, Inula heterolepis, Phagnalon graecum, Arabis verna, Mercurialis annua, Fumaria parviflora, Cymbalaria microcalyx, Galium canum subsp. antalyense, Parietaria judaica, Hyoscyamus aureus, Poa bulbosa were the dominant plant species of Alanya Castle walls. Possible seed dispersion of these plants on the castle walls and the methods for controlling them are discussed in detail. We conclude that the most effective method of combating plants that grow naturally on historical buildings and give damage to these buildings is mechanical excavation. Key words: Alanya, biodiversity, mechanical excavation, urban ecosystems, wall flora ---------- ---------- Alanya Kalesi duvarlarının vasküler bitki çeşitliliği ve ekolojik etkileri Özet Tarihi yapılar geçmişin yaşayan aynaları olduklarından, onları korumak ve gelecek nesillere aktarmak çok önemlidir. -
Genotype-By-Sequencing Facilitates Genetic Mapping of a Stem Rust Resistance Locus in Aegilops Umbellulata, a Wild Relative of Cultivated Wheat Erena A
Edae et al. BMC Genomics (2016) 17:1039 DOI 10.1186/s12864-016-3370-2 RESEARCH ARTICLE Open Access Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat Erena A. Edae1*, Pablo D. Olivera2, Yue Jin1,2, Jesse A. Poland3 and Matthew N. Rouse1,2* Abstract Background: Wild relatives of wheat play a significant role in wheat improvement as a source of genetic diversity. Stem rust disease of wheat causes significant yield losses at the global level and stem rust pathogen race TTKSK (Ug99) is virulent to most previously deployed resistance genes. Therefore, the objective of this study was to identify loci conferring resistance to stem rust pathogen races including Ug99 in an Aegilops umbelluata bi-parental mapping population using genotype-by-sequencing (GBS) SNP markers. Results: A bi-parental F2:3 population derived from a cross made between stem rust resistant accession PI 298905 and stem rust susceptible accession PI 542369 was used for this study. F2 individuals were evaluated with stem rust race TTTTF followed by testing F2:3 families with races TTTTF and TTKSK. The segregation pattern of resistance to both stem rust races suggested the presence of one resistance gene. A genetic linkage map, comprised 1,933 SNP markers, was created for all seven chromosomes of Ae. umbellulata using GBS. A major stem rust resistance QTL that explained 80% and 52% of the phenotypic variations for TTTTF and TTKSK, respectively, was detected on chromosome 2U of Ae. umbellulata. Conclusion: The novel resistance gene for stem rust identified in this study can be transferred to commercial wheat varieties assisted by the tightly linked markers identified here. -
Evaluation and Utilization of Biodiversity in Triticeae for Wheat Lmprovement
Utah State University DigitalCommons@USU Intermountain Herbarium of Utah State Herbarium Publications University 6-24-1994 Evaluation and Utilization of Biodiversity in Triticeae for Wheat lmprovement A. B. Damania University of California, Davis J. Valkoun University of California, Davis Follow this and additional works at: https://digitalcommons.usu.edu/herbarium_pubs Part of the Agriculture Commons, Food Science Commons, and the Plant Sciences Commons Recommended Citation Damania, A. B. and Valkoun, J., "Evaluation and Utilization of Biodiversity in Triticeae for Wheat lmprovement" (1994). Herbarium Publications. Paper 4. https://digitalcommons.usu.edu/herbarium_pubs/4 This Conference Paper is brought to you for free and open access by the Intermountain Herbarium of Utah State University at DigitalCommons@USU. It has been accepted for inclusion in Herbarium Publications by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. Evaluation and Utilization of Biodiversity in Triticeae for Wheat lmpr.ovement A. B. DAMANIA1 and J. VALKOUN International Center for Agricultural Research in the Dry Areas (I CARDA), PO Box 5466, Aleppo, Syria. 1Present address: Genetic Resources Conservation Program, University of California, Davis, CA 95616-8602, USA ABSTRACT A population structure of a species is defined as the totality of ecological and genetical relationships among To adapt new varieties to a wide spectrum of individual members which may co-evolve as a result of environments breeders and farmers have emphasized the gene exchange but may also diverge under localized forces need for broadening the current narrow genetic base of of evolutionary change Qain, 1975). Landraces and obsolete modern varieties of important cereal crops such as wheat cultivars are as a rule products of several years of crop and barley. -
Unearthing Belowground Bud Banks in Fire-Prone Ecosystems
Unearthing belowground bud banks in fire-prone ecosystems 1 2 3 Author for correspondence: Juli G. Pausas , Byron B. Lamont , Susana Paula , Beatriz Appezzato-da- Juli G. Pausas 4 5 Glo'ria and Alessandra Fidelis Tel: +34 963 424124 1CIDE-CSIC, C. Naquera Km 4.5, Montcada, Valencia 46113, Spain; 2Department of Environment and Agriculture, Curtin Email [email protected] University, PO Box U1987, Perth, WA 6845, Australia; 3ICAEV, Universidad Austral de Chile, Campus Isla Teja, Casilla 567, Valdivia, Chile; 4Depto Ci^encias Biologicas,' Universidade de Sao Paulo, Av P'adua Dias 11., CEP 13418-900, Piracicaba, SP, Brazil; 5Instituto de Bioci^encias, Vegetation Ecology Lab, Universidade Estadual Paulista (UNESP), Av. 24-A 1515, 13506-900 Rio Claro, Brazil Summary To be published in New Phytologist (2018) Despite long-time awareness of the importance of the location of buds in plant biology, research doi: 10.1111/nph.14982 on belowground bud banks has been scant. Terms such as lignotuber, xylopodium and sobole, all referring to belowground bud-bearing structures, are used inconsistently in the literature. Key words: bud bank, fire-prone ecosystems, Because soil efficiently insulates meristems from the heat of fire, concealing buds below ground lignotuber, resprouting, rhizome, xylopodium. provides fitness benefits in fire-prone ecosystems. Thus, in these ecosystems, there is a remarkable diversity of bud-bearing structures. There are at least six locations where belowground buds are stored: roots, root crown, rhizomes, woody burls, fleshy -
Foxtail Millet (Setaria Italica), Grain | Feedipedia
Foxtail millet (Setaria italica), grain | Feedipedia Animal feed resources Feedipedia information system Home About Feedipedia Team Partners Get involved Contact us Foxtail millet (Setaria italica), grain Automatic translation Description Nutritional aspects Nutritional tables References Sélectionner une langue ▼ Click on the "Nutritional aspects" tab for recommendations for ruminants, pigs, poultry, rabbits, horses, fish and crustaceans Feed categories All feeds Forage plants Cereal and grass forages Legume forages Forage trees Aquatic plants Common names Other forage plants Plant products/by-products Foxtail millet, dwarf setaria, foxtail bristle grass, German millet, giant setaria, green bristle grass, green foxtail, green foxtail Cereal grains and by-products millet, Hungarian millet, Italian millet, wild foxtail millet, nunbank setaria [English]; mijo, mijo de Italia, mijo menor, moha, moha Legume seeds and by-products de Alemania, moha de Hungria, panizo común, almorejo [Spanish]; painço, milho painço, milho painço de Itália [Portuguese]; Oil plants and by-products millet d'Italie, millet des oiseaux, petit mil, sétaire verte, sétaire d'Italie [French]; Kolbenhirse, Italienische Borstenhirse ذيل الثعلب اإيطالي ;[Fruits and by-products [German]; jawawut, sekoi [Indonesian]; setária-verde [Italian]; juwawut, otèk [Javanese]; setariya [Kinyarwanda Roots, tubers and by-products [Arabic]; 粟 [Chinese]; 조 [Korean]; [Hindi]; アワ [Japanese]; [Kannada]; [Malayalam]; Sugar processing by-products [Nepali]; Щети́ нник италья́нский [Russian]; [Tamil]; [Telugu]; ขาวฟ้ ่ างหางหมา [Thai] Plant oils and fats Other plant by-products Species Feeds of animal origin Animal by-products Setaria italica (L.) P. Beauv. [Poaceae] Dairy products/by-products Animal fats and oils Synonyms Insects Other feeds Chaetochloa italica (L.) Scribn., Chaetochloa viridis (L.) Scribn., Chamaeraphis viridis (L.) Millsp., Panicum italicum L., Minerals Panicum pachystachys Franch. -
On the Taxonomic Position of Panicum Scabridum (Poaceae, Panicoideae, Paspaleae)
Phytotaxa 163 (1): 001–015 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ Article PHYTOTAXA Copyright © 2014 Magnolia Press ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.163.1.1 On the taxonomic position of Panicum scabridum (Poaceae, Panicoideae, Paspaleae) M. AMALIA SCATAGLINI1,2, SANDRA ALISCIONI1 & FERNANDO O. ZULOAGA1 1Instituto de Botánica Darwinion, Labardén 200, Casilla de Correo 22, B1642HYD, San Isidro, Buenos Aires, Argentina. 2Author for correspondence: [email protected] Abstract Panicum scabridum, an incertae sedis species of Panicum s.l., is here included in the genus Coleataenia, following a phylogenetic analysis based on one new ndhF sequence of the species and associated morphological data. Panicum scabridum and species of Coleataenia are cespitose and perennial plants, with a lower glume (1–)3–5-nerved, 1/3 to 3/4 of the spikelet, upper glume and lower lemma 5–9-nerved, and upper anthecium smooth, shiny, and indurate. Within Coleataenia, P. scabridum appeared as the sister taxon of the species pair C. prionitis and C. petersonii; these three species are the only NADP-me taxa of tribe Paspaleae exhibiting two bundle sheaths around the vascular bundles, i.e., with an outer parenchymatous sheath and an inner mestome sheath with specialized chloroplasts. The new combination Coleataenia scabrida is proposed and a lectotype is designated. Key words: Panicum scabridum, phylogeny, combined analysis, anatomy Introduction Panicum scabridum Döll (1877: 201), originally described from a specimen collected in Brazil, grows in Colombia, Venezuela and the Guianas to northern Brazil and Bolivia, in wet open places at low elevations.