APPENDIX C-1 Botanical and Faunal Survey
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Polyploidy and the Evolutionary History of Cotton
POLYPLOIDY AND THE EVOLUTIONARY HISTORY OF COTTON Jonathan F. Wendel1 and Richard C. Cronn2 1Department of Botany, Iowa State University, Ames, Iowa 50011, USA 2Pacific Northwest Research Station, USDA Forest Service, 3200 SW Jefferson Way, Corvallis, Oregon 97331, USA I. Introduction II. Taxonomic, Cytogenetic, and Phylogenetic Framework A. Origin and Diversification of the Gossypieae, the Cotton Tribe B. Emergence and Diversification of the Genus Gossypium C. Chromosomal Evolution and the Origin of the Polyploids D. Phylogenetic Relationships and the Temporal Scale of Divergence III. Speciation Mechanisms A. A Fondness for Trans-oceanic Voyages B. A Propensity for Interspecific Gene Exchange IV. Origin of the Allopolyploids A. Time of Formation B. Parentage of the Allopolyploids V. Polyploid Evolution A. Repeated Cycles of Genome Duplication B. Chromosomal Stabilization C. Increased Recombination in Polyploid Gossypium D. A Diverse Array of Genic and Genomic Interactions E. Differential Evolution of Cohabiting Genomes VI. Ecological Consequences of Polyploidization VII. Polyploidy and Fiber VIII. Concluding Remarks References The cotton genus (Gossypium ) includes approximately 50 species distributed in arid to semi-arid regions of the tropic and subtropics. Included are four species that have independently been domesticated for their fiber, two each in Africa–Asia and the Americas. Gossypium species exhibit extraordinary morphological variation, ranging from herbaceous perennials to small trees with a diverse array of reproductive and vegetative -
Invasive Aphids Attack Native Hawaiian Plants
Biol Invasions DOI 10.1007/s10530-006-9045-1 INVASION NOTE Invasive aphids attack native Hawaiian plants Russell H. Messing Æ Michelle N. Tremblay Æ Edward B. Mondor Æ Robert G. Foottit Æ Keith S. Pike Received: 17 July 2006 / Accepted: 25 July 2006 Ó Springer Science+Business Media B.V. 2006 Abstract Invasive species have had devastating plants. To date, aphids have been observed impacts on the fauna and flora of the Hawaiian feeding and reproducing on 64 native Hawaiian Islands. While the negative effects of some inva- plants (16 indigenous species and 48 endemic sive species are obvious, other species are less species) in 32 families. As the majority of these visible, though no less important. Aphids (Ho- plants are endangered, invasive aphids may have moptera: Aphididae) are not native to Hawai’i profound impacts on the island flora. To help but have thoroughly invaded the Island chain, protect unique island ecosystems, we propose that largely as a result of anthropogenic influences. As border vigilance be enhanced to prevent the aphids cause both direct plant feeding damage incursion of new aphids, and that biological con- and transmit numerous pathogenic viruses, it is trol efforts be renewed to mitigate the impact of important to document aphid distributions and existing species. ranges throughout the archipelago. On the basis of an extensive survey of aphid diversity on the Keywords Aphid Æ Aphididae Æ Hawai’i Æ five largest Hawaiian Islands (Hawai’i, Kaua’i, Indigenous plants Æ Invasive species Æ Endemic O’ahu, Maui, and Moloka’i), we provide the first plants Æ Hawaiian Islands Æ Virus evidence that invasive aphids feed not just on agricultural crops, but also on native Hawaiian Introduction R. -
Methods to Enable the Coexistence of Diverse Cotton Production Systems
AGRICULTURAL BIOTECHNOLOGY IN CALIFORNIA SERIES PUBLICATION 8191 Methods to Enable the Coexistence of Diverse Cotton Production Systems ROBERT B. HUTMACHER, Extension Agronomist, University of California Shafter Research and Extension Center and University of California, Davis, Department of Plant Science; RON N. VARGAS, County Director and Farm Advisor, University of California Cooperative UNIVERSITY OF Extension, Madera and Merced Counties; STEVEN D. WRIGHT, Farm Advisor, University of CALIFORNIA California Cooperative Extension, Tulare and Kings Counties Division of Agriculture Upland cotton (Gossypium hirsutum) and Pima cotton (G. barbadense) are the two and Natural Resources types of cotton produced commercially in California. In acreage as well as crop http://anrcatalog.ucdavis.edu value, over the past 5 years cotton has typically ranked in the top three in agronomic field crops grown in California. During that period, plantings of upland cotton in California have ranged from about 400,000 to over 650,000 acres (160,000 to 260,000 ha), while Pima plantings have ranged from about 140,000 to over 250,000 acres (56,000 to 101,000 ha). Does cross-pollination occur in cotton? Both upland and Pima cotton are variously referred to as “largely self-pollinated” or “partially cross-pollinated.” These descriptions acknowledge that these types of cotton are mostly self-pollinated but some cross-pollination can occur, albeit at relatively low incidence rates, through activity of pollinating insects or by wind dispersion. The pol- len of both wild and cultivated Gossypium species is large in size and among the heaviest among angiosperms, the group of plants that produces flowers, fruit, and seeds. -
*Wagner Et Al. --Intro
NUMBER 60, 58 pages 15 September 1999 BISHOP MUSEUM OCCASIONAL PAPERS HAWAIIAN VASCULAR PLANTS AT RISK: 1999 WARREN L. WAGNER, MARIE M. BRUEGMANN, DERRAL M. HERBST, AND JOEL Q.C. LAU BISHOP MUSEUM PRESS HONOLULU Printed on recycled paper Cover illustration: Lobelia gloria-montis Rock, an endemic lobeliad from Maui. [From Wagner et al., 1990, Manual of flowering plants of Hawai‘i, pl. 57.] A SPECIAL PUBLICATION OF THE RECORDS OF THE HAWAII BIOLOGICAL SURVEY FOR 1998 Research publications of Bishop Museum are issued irregularly in the RESEARCH following active series: • Bishop Museum Occasional Papers. A series of short papers PUBLICATIONS OF describing original research in the natural and cultural sciences. Publications containing larger, monographic works are issued in BISHOP MUSEUM four areas: • Bishop Museum Bulletins in Anthropology • Bishop Museum Bulletins in Botany • Bishop Museum Bulletins in Entomology • Bishop Museum Bulletins in Zoology Numbering by volume of Occasional Papers ceased with volume 31. Each Occasional Paper now has its own individual number starting with Number 32. Each paper is separately paginated. The Museum also publishes Bishop Museum Technical Reports, a series containing information relative to scholarly research and collections activities. Issue is authorized by the Museum’s Scientific Publications Committee, but manuscripts do not necessarily receive peer review and are not intended as formal publications. Institutions and individuals may subscribe to any of the above or pur- chase separate publications from Bishop Museum Press, 1525 Bernice Street, Honolulu, Hawai‘i 96817-0916, USA. Phone: (808) 848-4135; fax: (808) 841-8968; email: [email protected]. Institutional libraries interested in exchanging publications should write to: Library Exchange Program, Bishop Museum Library, 1525 Bernice Street, Honolulu, Hawai‘i 96817-0916, USA; fax: (808) 848-4133; email: [email protected]. -
Cotton Facts
CottonFacts M. Rafiq Chaudhry Andrei Guitchounts International Cotton Advisory Committee CottonFacts CottonFacts Technical Paper No. 25 of the Common Fund for Commodities M. Rafiq Chaudhry Andrei Guitchounts International Cotton Advisory Committee Cotton Producing Areas in the World Europe Americas iv Asia Africa Oceania by Carmen S. León v Copyright © 2003 Common Fund for Commodities International Cotton Advisory Committee All rights are reserved. "Fair use" of the information in this book is permitted provided the reference is properly acknowledged. For additional permission contact the International Cotton Advisory Committee at [email protected]. First Edition 2003 ISBN 0-9704918-3-2 Library of Congress Control No. 2003107604 Contents Cotton Map . .iv Foreword . .xi Introduction . .xiii Acknowledgements . .xv 1. The Cotton Plant and its Organs . .1 The Plant . .1 Taxonomy . .1 Nodes . .3 Branches . .3 Flower . .4 Root . .5 Seed . .6 Leaf . .10 Boll . .13 Yield . .14 Production Technology . .15 Organic Cotton . .15 Precision Agriculture . .16 2. Breeding . .17 Breeding Methods . .18 Hybrid Cotton . .22 Biotechnology . .25 Genetic Engineering . .25 Milestones in Genetic Engineering of Cotton . .31 Natural Outcrossing . .32 Gossypol . .33 Colored Cotton . .34 Contents vii 3. Agronomy and Physiology . .35 Growth and Fruit Formation . .35 Nutrition . .40 Weed Control . .43 4. Diseases . .45 5. Insects . .57 Insect Identification, Biology and Nature of Damage . .57 Sucking Insects . .57 Feeders . .62 Bollworms . .68 Natural Enemies (Beneficials) . .73 Insect Parasites . .76 Pathogens . .77 Insecticide Resistance . .77 Insect Control Methods . .79 Commonly Used Terms in Insect Pest Control . .83 6. Fiber Quality . .85 Fiber Formation . .85 Fiber Quality Parameters . .87 Machine Picking . .90 Ginning . .92 Cotton Cleaning . -
Origin and Evolution of Hawaiian Endemics: New Patterns Revealed by Molecular Phylogenetic Studies
4 Origin and evolution of Hawaiian endemics: new patterns revealed by molecular phylogenetic studies S t e r l i n g C . K e e l e y a n d V i c k i A . F u n k The current high islands of the Hawaiian archipelago are among the most remote land masses in the world. They lie 3500 km from California, the nearest contin- ental source, and approximately 2300 km from the Marquesas , the nearest islands ( Fig. 4.1 ). They are the southernmost islands in the Hawaiian Ridge , formed succes- sively over a ‘hot spot’ that has allowed magma to penetrate the Pacifi c Plate. The plate has moved gradually north and northwestwards over the past 85 Ma, leaving the previously formed islands to gradually erode and subside (Clague, 1996 ). The current high islands ( Fig. 4.1 , inset) range in age from Kauai /Niihau (5.1–4.9 Ma), to Oahu (3.7–2.6 Ma), to Maui Nui (2.2–1.2 Ma), during the Pleistocene compris- ing several islands – West Maui (1.3 Ma), East Maui (0.75 Ma), Molokai (1.76–1.90 Ma), Lanai (1.28 Ma) and Kaho’olawe (1.03 Ma) – and Hawaii (0.5 Ma to present) (Price & Clague, 2002 ). Important for the establishment and evolution of the extant Hawaiian fl ora is the historic pattern of island formation within the archipelago. For example, islands with elevations greater than 1000 m did not exist from 30 to 23 Ma and from c . 8 to 5 Ma when the current high islands began to emerge (Clague, 1996 ; Price & Clague, 2002 ; Clague et al ., 2010 ). -
Evolution and Natural History of the Cotton Genus
Evolution and Natural History of the Cotton Genus Jonathan F. Wendel, Curt Brubaker, Ines Alvarez, Richard Cronn, and James McD. Stewart Abstract We present an overview of the evolution and diversity in Gossypium (the cotton genus). This framework facilitates insight into fundamental aspects of plant biology, provides the necessary underpinnings for effective utilization of cotton genetic resources, and guides exploration of the genomic basis of morphological diversity in the genus. More than 50 species of Gossypium are distributed in arid to semi-arid regions of the tropics and subtropics. Included are four species that independently have been domesticated for their fiber, two each in Africa-Asia and the Americas. Gossypium species exhibit extraordin- ary morphological variation, ranging from trailing herbaceous perennials to 15 m trees with a diverse array of reproductive and vegetative characteris- tics. A parallel level of cytogenetic and genomic diversity has arisen during the global radiation of the genus, leading to the evolution of eight groups of diploid (n 13) species (genome groups A through G, and K). Data implicate an origin for¼Gossypium about 5–10 million years ago and a rapid early diversification of the major genome groups. Allopolyploid cottons appear to have arisen within the last 1–2 million years, as a consequence of trans-oceanic dispersal of an A-genome taxon to the New World followed by hybridization with an indigen- ous D-genome diploid. Subsequent to formation, allopolyploids radiated into three modern lineages, two of which contain the commercially important species G. hirsutum and G. barbadense. 1 Introduction to Gossypium diversity Because the cotton genus (Gossypium L.) is so important to economies around the world, it has long attracted the attention of agricultural scientists, taxono- mists, and evolutionary biologists. -
AFLP Mediated Genetic Diversity of Malvaceae Species
Journal of Medicinal Plants Research Vol. 4(2), pp. 148-154, 18 January, 2010 Available online at http://www.academicjournals.org/JMPR ISSN 1996-0875© 2010 Academic Journals Full Length Research Paper AFLP mediated genetic diversity of malvaceae species Nighat Shaheen1, S. R. Pearce2, Mir Ajab Khan1, Tariq Mahmood1, Ghazalah Yasmin1 and Muhammad Qasim Hayat1 1Department of Plant Sciences, Quaid-i-Azam University, Islamabad-45320, Pakistan. 2School of Life Sciences, JMS Building, University of Sussex, Falmer, Brighton, BN19QG, United Kingdom. Accepted 22 December, 2009 AFLP (Amplified fragment length polymorphism) marker system is a reliable method in the evaluation of genetic diversity among different species. It was used to explore phenetic relationships and diversity within and between 13 Malvaceae species belonging to 5 different genera. The primary objective of the study was to evaluate the taxonomic potential, usefulness and applicability of AFLP marker system to reconstruct genetic relationships at interspecific and intergeneric level in Malvaceae. In total, 28 accessions comprising 13 species were included in the study but for assorted technical reasons five profiles remained incomplete or with ambiguous banding pattern. Therefore 23 accessions comprising 12 species were included in the final analysis. Two primer pairs produced a total of 73 bands, of which 70 were polymorphic. Neighbor Joining (NJ) tree showed that all 23 accessions were basically classified in three main clusters and several sub-clusters. The tree had well supported branches especially at the level of accessions and species. However, it also had poor bootsrap support at some intermediate and deeper branches. The informative value of the technique was evaluated by comparing the current results with earlier morphological and molecular investigations. -
Downloaded from Genbank on That Full Plastid Genomes Are Not Sufficient to Reject Al- February 28, 2012
Ruhfel et al. BMC Evolutionary Biology 2014, 14:23 http://www.biomedcentral.com/1471-2148/14/23 RESEARCH ARTICLE Open Access From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes Brad R Ruhfel1*, Matthew A Gitzendanner2,3,4, Pamela S Soltis3,4, Douglas E Soltis2,3,4 and J Gordon Burleigh2,4 Abstract Background: Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. Results: We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. -
Construction of Microsatellite-Based Linkage Map and Mapping of Nectarilessness and Hairiness Genes in Gossypium Tomentosum
c Indian Academy of Sciences RESEARCH ARTICLE Construction of microsatellite-based linkage map and mapping of nectarilessness and hairiness genes in Gossypium tomentosum MEIYING HOU, CAIPING CAI, SHUWEN ZHANG, WANGZHEN GUO, TIANZHEN ZHANG and BAOLIANG ZHOU∗ State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China Abstract Gossypium tomentosum, a wild tetraploid cotton species with AD genomes, possesses genes conferring strong fibers and high heat tolerance. To effectively transfer these genes into Gossypium hirsutum, an entire microsatellite (simple sequence repeat, SSR)-based genetic map was constructed using the interspecific cross of G. hirsutum × G. tomentosum (HT). We detected 1800 loci from 1347 pairs of polymorphic primers. Of these, 1204 loci were grouped into 35 linkage groups at LOD ≥ 4. The map covers 3320.8 cM, with a mean density of 2.76 cM per locus. We detected 420 common loci (186 in the At subgenome and 234 in Dt) between the HT map and the map of TM-1 (G. hirsutum) and Hai 7124 (G. barbadense; HB map). The linkage groups were assigned chromosome numbers based on location of common loci and the HB map as reference. A comparison of common markers revealed that no significant chromosomal rearrangement exist between G. tomentosum and G. barbadense. Interestingly, however, we detected numerous (33.7%) segregation loci deviating from 3:1 ratio (P < 0.05) in HT, mostly clustering on eight chromosomes in the Dt subgenome, with some on three chromosomes in At. Two morphological traits, leaf hairiness and leaf nectarilessness were mapped on chromosomes 6 (A6) and 26 (D12), respectively. -
Comparative Genomics of Gossypium Spp
COMPARATIVE GENOMICS OF GOSSYPIUM SPP. THROUGH GBS AND CANDIDATE GENES – DELVING INTO THE CONTROLLING FACTORS BEHIND PHOTOPERIODIC FLOWERING A Dissertation by CARLA JO LOGAN YOUNG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Alan E. Pepper Committee Members, Konstantin V. Krutovsky John Z. Yu Keerti S. Rathore Wayne K. Versaw Head of Department, U. J. McMahan August 2013 Major Subject: Biology Copyright 2013 Carla Jo Logan Young ABSTRACT Cotton has been a world-wide economic staple in textiles and oil production. There has been a concerted effort for cotton improvement to increase yield and quality to compete with non-natural man-made fibers. Unfortunately, cultivated cotton has limited genetic diversity; therefore finding new marketable traits within cultivated cotton has reached a plateau. To alleviate this problem, traditional breeding programs have been attempting to incorporate practical traits from wild relatives into cultivated lines. This incorporation has presented a new problem: uncultivated cotton hampered by photoperiodism. Traditionally, due to differing floral times, wild and cultivated cotton species were unable to be bred together in many commercial production areas world-wide. This worldwide breeding problem has inhibited new trait incorporation. Before favorable traits from undomesticated cotton could be integrated into cultivated elite lines using marker-assisted selection breeding, the markers associated with photoperiod independence needed to be discovered. In order to increase information about this debilitating trait, we set out to identify informative markers associated with photoperiodism. This study was segmented into four areas. -
Construction and Characterization of a Bacterial Artificial Chromosome Library for the Allotetraploid Gossypium Tomentosum
Construction and characterization of a bacterial artificial chromosome library for the allotetraploid Gossypium tomentosum F. Liu1,2, Y.H. Wang1, H.Y. Gao1, C.Y. Wang1, Z.L. Zhou1, X.Y. Cai1, X.X. Wang1, Z.S. Zhang2 and K.B. Wang1 1State Key Laboratory of Cotton Biology, China/Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, China 2College of Agronomy and Biotechnology, Southwest University, Chongqing, China Corresponding authors: F. Liu / K.B. Wang E-mail: [email protected] / [email protected] Genet. Mol. Res. 14 (4): 16975-16980 (2015) Received February 18, 2015 Accepted June 25, 2015 Published December 15, 2015 DOI http://dx.doi.org/10.4238/2015.December.15.3 ABSTRACT. Gossypium tomentosum is a wild allotetraploid species with the (AD)5 genome. It is characterized by many useful traits including finer fiber fineness, drought tolerance, and Fusarium and Verticillium resistance. We constructed the first bacterial artificial chromosome library for Gossypium tomentosum. With high quality and broad coverage, this library includes 200,832 clones, with an average insert size of about 122 kb and fewer than 3% empty clones. Our library is approximately 10-fold the size of the (AD)5- genome (2400 Mb) and provides a 99.7% probability of isolating genes of interest or their sequences. Seven of eight simple sequence repeats markers that are located on five different chromosomes and linked with resistance to Verticillium wilt could amplify the 50 superpools and obtained one to five hits. This high capacity library will be an important genomic resource for classifying and analyzing the evolution of allotetraploid cotton species as well as for isolating disease-resistance and drought-tolerance Genetics and Molecular Research 14 (4): 16975-16980 (2015) ©FUNPEC-RP www.funpecrp.com.br F.