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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. -
CATALOGUE of the GRASSES of CUBA by A. S. Hitchcock
CATALOGUE OF THE GRASSES OF CUBA By A. S. Hitchcock. INTRODUCTION. The following list of Cuban grasses is based primarily upon the collections at the Estaci6n Central Agron6mica de Cuba, situated at Santiago de las Vegas, a suburb of Habana. The herbarium includes the collections made by the members of the staff, particularly Mr. C. F. Baker, formerly head of the department of botany, and also the Sauvalle Herbarium deposited by the Habana Academy of Sciences, These specimens were examined by the writer during a short stay upon the island in the spring of 1906, and were later kindly loaned by the station authorities for a more critical study at Washington. The Sauvalle Herbarium contains a fairly complete set of the grasses col- lected by Charles Wright, the most important collection thus far obtained from Cuba. In addition to the collections at the Cuba Experiment Station, the National Herbarium furnished important material for study, including collections made by A. H. Curtiss, W. Palmer and J. H. Riley, A. Taylor (from the Isle of Pines), S. M. Tracy, Brother Leon (De la Salle College, Habana), and the writer. The earlier collections of Wright were sent to Grisebach for study. These were reported upon by Grisebach in his work entitled "Cata- logus Plant arum Cubensium," published in 1866, though preliminary reports appeared earlier in the two parts of Plantae Wrightianae. * During the spring of 1907 I had the opportunity of examining the grasses in the herbarium of Grisebach in Gottingen.6 In the present article I have, with few exceptions, accounted for the grasses listed by Grisebach in his catalogue of Cuban plants, and have appended a list of these with references to the pages in the body of this article upon which the species are considered. -
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. -
Breeding System Diversification and Evolution in American Poa Supersect. Homalopoa (Poaceae: Poeae: Poinae)
Annals of Botany Page 1 of 23 doi:10.1093/aob/mcw108, available online at www.aob.oxfordjournals.org Breeding system diversification and evolution in American Poa supersect. Homalopoa (Poaceae: Poeae: Poinae) Liliana M. Giussani1,*, Lynn J. Gillespie2, M. Amalia Scataglini1,Marıa A. Negritto3, Ana M. Anton4 and Robert J. Soreng5 1Instituto de Botanica Darwinion, San Isidro, Buenos Aires, Argentina, 2Research and Collections Division, Canadian Museum of Nature, Ottawa, Ontario, Canada, 3Universidad de Magdalena, Santa Marta, Colombia, 4Instituto Multidisciplinario de Biologıa Vegetal (IMBIV), CONICET-UNC, Cordoba, Argentina and 5Department of Botany, Smithsonian Institution, Washington, DC, USA *For correspondence. E-mail [email protected] Received: 11 December 2015 Returned for revision: 18 February 2016 Accepted: 18 March 2016 Downloaded from Background and Aims Poa subgenus Poa supersect. Homalopoa has diversified extensively in the Americas. Over half of the species in the supersection are diclinous; most of these are from the New World, while a few are from South-East Asia. Diclinism in Homalopoa can be divided into three main types: gynomonoecism, gynodioe- cism and dioecism. Here the sampling of species of New World Homalopoa is expanded to date its origin and diver- sification in North and South America and examine the evolution and origin of the breeding system diversity. Methods A total of 124 specimens were included in the matrix, of which 89 are species of Poa supersect. http://aob.oxfordjournals.org/ Homalopoa sections Acutifoliae, Anthochloa, Brizoides, Dasypoa, Dioicopoa, Dissanthelium, Homalopoa sensu lato (s.l.), Madropoa and Tovarochloa, and the informal Punapoa group. Bayesian and parsimony analyses were conducted on the data sets based on four markers: the nuclear ribosomal internal tanscribed spacer (ITS) and exter- nal transcribed spacer (ETS), and plastid trnT-L and trnL-F. -
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. -
Proso and Foxtail Millet Production
Proso and foxtail millet production R.L. Croissant and J.F. Shanahan1 no. 0.118 self-pollinated, but some outcrossing may occur when two Quick Facts varieties are planted side by side. Foxtail millet (Setaria italica) is an annual warm Proso and foxtail millet grain may be used as season grass with slender leafy stems up to 40 inches tall. livestock feed or in birdseed mixture. The inflorescence is a dense, cylindrical, bristly panicle. Foxtail millet produces a high-quality forage when The lemma and palea covering the threshed seed may be harvested at the bloom stage. white, yellow, orange or other shades including green and Millet is a very efficient utilizer of soil water and purple. Like proso, foxtail millet is highly self-pollinated, can produce grain or forage in drought but may show some outcrosses when different varieties are conditions. planted side by side. Proso millet and foxtail millet generally require swathing when harvested for grain. Acreage planted to millet annually depends on soil Climatic Requirements moisture at planting time, the price and demand for millet grain and millet hay, and Proso millet is a short season crop requiring 50 to 90 government acreage control for other crops. days from sowing to maturity for early to midseason varieties while foxtail millet requires 55 to 70 days to reach a suitable stage for hay, and 75 to 90 days for seed production. The millets, grown world-wide, are important as feed Both types of millet require relatively warm weather and food sources. During 1965 to 1985, millet production for germination and plant growth. -
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. -
Genetic Glass Ceilings Gressel, Jonathan
Genetic Glass Ceilings Gressel, Jonathan Published by Johns Hopkins University Press Gressel, Jonathan. Genetic Glass Ceilings: Transgenics for Crop Biodiversity. Johns Hopkins University Press, 2008. Project MUSE. doi:10.1353/book.60335. https://muse.jhu.edu/. For additional information about this book https://muse.jhu.edu/book/60335 [ Access provided at 2 Oct 2021 23:39 GMT with no institutional affiliation ] This work is licensed under a Creative Commons Attribution 4.0 International License. Genetic Glass Ceilings Transgenics for Crop Biodiversity This page intentionally left blank Genetic Glass Ceilings Transgenics for Crop Biodiversity Jonathan Gressel Foreword by Klaus Ammann The Johns Hopkins University Press Baltimore © 2008 The Johns Hopkins University Press All rights reserved. Published 2008 Printed in the United States of America on acid-free paper 987654321 The Johns Hopkins University Press 2715 North Charles Street Baltimore, Maryland 21218-4363 www.press.jhu.edu Library of Congress Cataloging-in-Publication Data Gressel, Jonathan. Genetic glass ceilings : transgenics for crop biodiversity / Jonathan Gressel. p. cm. Includes bibliographical references and index. ISBN 13: 978-0-8018-8719-2 (hardcover : alk. paper) ISBN 10: 0-8018-8719-4 (hardcover : alk. paper) 1. Crops—Genetic engineering. 2. Transgenic plants. 3. Plant diversity. 4. Crop improvement. I. Title. II. Title: Transgenics for crop biodiversity. SB123.57.G74 2008 631.5Ј233—dc22 20007020365 A catalog record for this book is available from the British Library. Special discounts are available for bulk purchases of this book. For more information, please contact Special Sales at 410-516-6936 or [email protected]. Dedicated to the memory of Professor Leroy (Whitey) Holm, the person who stimulated me to think differently. -
31295002021987.Pdf (16.44Mb)
POPULATION DYNAMICS OF RODENTS OF THE MESQUITE PLAINS-HIGH PLAINS ECOTONE by DANIEL ROBERT WOMOCHEL, B.S. A THESIS IN ZOOLOGY Submitted to the Graduate Faculty of Texas Technological College in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE Approved Accepted June, 1968 I' % nc. 7T ACKNOWLEDGMENTS I am grateful to Dr. Robert L. Packard for his di rection of my research and preparation of this thesis, and to my parents and grandmother for their encouragement and assistance. Thanks also are due Mr. Allan Wallace, vjho kindly permitted me to conduct this study on his ranch. ii TABLE OF CONTENTS Page ACKNOWLEDGMENTS ii LIST OF TABLES iv LIST OP ILLUSTRATIONS vi CHAPTER I. INTRODUCTION 1 II. DESCRIPTION OF THE AREA 3 III. METHODS AND MATERIALS 12 IV. SPECIES ACCOUNTS l6 Sigmodon hispidus l6 Perognathus flavus 33 "Perognathus hispidus 47 Reithrodontomys montanus 59 Peromyscus maniculatus 64 Dipodomys ordii 65 Peromyscus leucopus 65 Citellus spilosoma 66 V. POPULATION RELATIONSHIPS 67 VI. SUMI4ARY AND CONCLUSIONS 73 LITERATURE CITED 77 iii LIST OF TABLES TABLE Page 1. Plants of the Study Area 10 2. Density of Cotton Rats Based on Average Num ber Trapped Per Acre 17 3. Population Density of Cotton Rats Based on the Lincoln Index l8 h. Monthly Distribution of Immature and Re- productively Active Nonresident Males and Females 21 5. Monthly Distribution of Immature and Re- productively Active Resident Males and Females 22 6. Home Ranges of Adult Male Cotton Rats ... 26 7. Home Ranges of Adult Female Cotton Rats ... 27 8. Average Home Ranges of All Cotton Rats .. -
Millet Forage Management
Millets IOWA STATE UNIVERSITY University Extension Forage Management By Brian Lang, Extension Crop Specialist Fact Sheet BL-55, June 2001 Introduction Forage Selection for Livestock Millets are major grain crops world wide, but in Iowa All millet forages are good feed for beef and sheep. The their use is mainly as annual summer forage production choice of millet is largely dependent on seasonal needs as hay, silage, green-chop, and pasture. The and intended harvest management @ silage, pasture, sudan/sorghum forages are often the first choice for green-chop, hay, etc. summer annual forage production, but millets have been Dairy -- There is some evidence1 that Pearl Millet may gaining in popularity. cause butterfat depression in milk. Therefore, Millets grown in Iowa include: recommendations for use of Pearl Millet with lactating · Pearl Millet -- also called Cattail Millet. dairy are either to: · limit feed the millet and monitor butterfat levels · Japanese Millet -- also called Barnyard Millet. Seed · or simply avoid its use for lactating dairy shatter may lead to Barnyardgrass weed problems. · Foxtail Millet -- German and Siberian varieties seem Horses -- Do not feed Foxtail Millet as a major 2 to be the most popular for forage use. component of their diet. Foxtail Millet acts as a laxative and contains a glucoside called setarian that may damage · Proso Millet -- also called hog, hershey, and the kidneys, liver, and bones3. broomcorn millet. Table 1. Establishment and Harvest Information for Millet Forages. Typical dry matter Days from planting Harvest at boot Height when to graze, Forage Seeding yield & cutting to 36-inch height stage or 36-inch Height to graze to, millet rate schedule or boot stage height down to… Grazing interval lbs./ac. -
MILLET in Your Meals
MILLET in your Meals Issued in public interest by - An ISO 22000 Company Publication supported by NABARD (National Bank for Agriculture and Rural Development) Let’s welcome Millets back into our meals Millets - Millet is the name given to a group of cereals other than wheat, rice, maize & barley. They are mostly tiny in size, round in shape & ready for usage as it is. It is acknowledged that during the Stone Age, the Millet plant was grown by the lake inhabitants of Switzerland. History reveals that since the Neolithic Era, millet, a prehistoric seed was cultivated in the dry climates of Africa and northern China. Interestingly it was millets and not rice that was a staple food in Indian, Chinese Neolithic and Korean civilizations. Eventually, millets spread all over the world. It was heavy, it was tall, It sprouted, it eared, It nodded, it hung, Indeed the lucky grains were sent down to us The black millet, the double kernelled, millet, pink sprouted and white. So goes the folk song from China- a melodious litany to the treasure trove of nutrition, the oldest food know to mankind! There are about 6,000 varieties of millet throughout the world with grains varying in colour from pale yellow, to gray, white, and red. Archaeologists say that foxtail millet is so old that no wild plant of the species is known to exist today. The Millet Story - The origin of millet is diverse with varieties coming from both Africa and Asia. Pearl millet for example comes from tropical West Africa and finger millet from Uganda or neighboring areas. -
Sudan Grass, Millets, and So'rghums At
FJJCATF Sudan Grass, Millets, and So'rghums at H. A. Schofh H. H. Rampton Agricultural Experiment Station, Oregon State College, Corvallis. Cooperating: Division of Forage Crops and Diseases, Station Bulletin 425 Bureau of Plant Industry, Soils and Agri- March 1945 cultural Engineering, United States De- Revised January 1949 partment of Agriculture. Toble of Con±en±s Page Introduction 3 Adaptations in Oregon 4 Seedbed Preparation 7 Rodents and Birds 7 Diseases Insects Sudan Grass 11 Proso 17 Foxtail Millet 20 Japanese Barnyard Millet 22 Sorghum 24 ACKNOWLEDGMENT: Forage crop work at thc Oregon Agricultural Experiment Station conducted in cooperation with the Division of Forage Crops and Diseases. Buieau of Plant Industry, Soils and Agricultural Engineering, United States Department ot Agricul- ture; creditis hcreby acknowledged as jointly due to the above named clivson am! bureau and the Oregon Agricultural Experiment Station. Figure 1. A good crop of sorghum in western Oregon. Sudan Grass, MiIIeIs, and Sorghums By H. A. SCHOTH, Senior Agronomist, and H. H. RAMPTON, Associate Agronomist Introd uction grass, millets, and sorghurns ha\Te been grown in varying SUDANacreages in several sections of Oregon for many years. These crops are of relatively minor importance but the acreage is gradually increasing as adapted and improved varieties are obtained, more satis- factory cultural practices are determined, and wider utility is devel- oped. In some sections they are now considered to be standard field crops. In others, some of them are grown as temporary or emergency crops during seasons that are unfavorable for other crops. Use of Sudan grass is increasing more rapidly than use of millets and other sorghums.it has been estimated that in 1948, the acreage had increased to approximately 45,500.