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Enrico Biancardi · Tetsuo Tamada Editors Rhizomania Rhizomania Enrico Biancardi • Tetsuo Tamada Editors Rhizomania Editors Enrico Biancardi Stazione Sperimentale di Bieticoltura Rovigo, Italy Tetsuo Tamada Agricultural Research Institute Hokuren Federation of Agricultural Cooperatives Naganuma, Hokkaido, Japan ISBN 978-3-319-30676-6 ISBN 978-3-319-30678-0 DOI 10.1007/978-3-319-30678-0 (eBook) Library of Congress Control Number: 2016946022 © Springer International Publishing Switzerland 2016 Chapter was created within the capacity of an US governmental employment US copyright protection does not apply This work is subject to copyright All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed The use of general descriptive names, registered names, trademarks, service marks, etc in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG Switzerland “To my wife Donatella, who accepted to spend her life not only with me but also with the genus Beta” —Enrico Biancardi “To my wife Sachiko and my daughters Machiko and Chieko who gave warm support to my BNYVV work” —Tetsuo Tamada Foreword An unknown disease of sugar beet was detected in Italy more than 50 years ago Soon the new syndrome displayed devastating effects on yield This greatly concerned the Italian sugar beet growers and processors, especially considering that the syndrome had spread to the most important Italian cultivation areas It was the start of a memorable enterprise for pathologists, breeders, and agronomists The spontaneous and unusual synergy created among the universities, research stations, seed companies, and grower associations led not only at the first very appropriate attempts of prophylaxis measures but also to an awareness that the only possible management would be through the use of resistant varieties In this phase, the Beta maritima germplasm selected at Rovigo and later at Salinas began to display its value against the new disease called “rizomania.” Some resistant varieties were released, thanks to enhanced knowledge of the pathogenic agents (beet necrotic yellow vein virus and Polymyxa betae) obtained in Japan and Germany It also was the beginning of countless research projects and collaborations worldwide, which, in a relatively short time, led to almost complete control of the disease There are perhaps few other diseases, even affecting more important crops, on which so many papers have been published It should be noted that the most significant results in the discovery of rhizomania resistance traits were obtained by public research stations, often without any specific funding The future of sugar beet currently is endangered by the development of resistant strains in the virus, among other things I believe that it also will be possible to overcome these new obstacles with the help of the powerful tools provided by molecular investigation and following the knowledge carefully collected in this very useful book, the first devoted exclusively to rhizomania The issue was much more difficult 50 years ago, when no one knew anything about the syndrome and the researchers only had their eyes to see, a microscope to look closer, and a pencil to take notes Alma Mater Studiorum Bologna, Italy May 2016 Antonio Canova vii Preface This book is the result of an international enterprise among researchers involved in past and present studies on rhizomania, a relatively new and devastating disease of sugar beet In less than 50 years, the disease has become the most damaging biotic factor affecting the crop worldwide Moreover, its spread is still ongoing in every cultivated area Because the traditional management systems were almost ineffective, it was soon evident that the employment of genetic resistances was the only chance for limiting the economic damage The discovery of the pathogenic agents and the release of the first resistant varieties are described by some of the researchers directly involved The breeding efforts led to both the current satisfactory management of the disease and to the survival of the beet sugar industry in several areas The cooperation between the Italian and American Experimental Stations, born spontaneously about 80 years ago and still continuing today, should be remembered The friendly collaboration led to the employment of genetic traits extracted from Beta maritima, which became the sole source so far of the resistances available against the disease The introduction briefly describes sugar beet cultivation, the more common diseases, and the damage caused by rhizomania This is necessary because the book also is addressed to readers who are not directly involved with sugar beet Without these brief explanations, some parts of the text would not be fully comprehensible The following chapters refer to the molecular physiology of the disease agents and their interactions with the environment and the host-plant The knowledge of ecology and epidemiology of rhizomania is, above all else, necessary to understand the means and practices valuable to avoid or at least delay the further spread of the disease into healthy soils Some promising methods of control using concurrent but not damaging viruses, bacteria, and fungi are in progress They could help the action of the genetic resistances, which are not completely effective The integrated protection is useful, especially in the even more frequent occurrences of resistancebreaking strains of BNYVV, where the known types of resistance seem to have partially lost their original efficacy Some almost immune transgenic varieties are already awaiting release For traditional breeding, further efforts will be needed in ix 13 Perspective 267 2010) The TIR domain is thought to have a role in the hypersensitive response, leading to localized cell death and thus restriction of the pathogen’s spread through the plant (de Ronde et al 2014) The status of sugar beet N-terminal domains of R-genes has not been reported exhaustively However, it is tempting to speculate that TIR-based immunity engineered into a sugar beet NB-LRR protein could have a role in creating novel disease resistances, perhaps including rhizomania Review of downstream immunity responses is beyond the scope of this perspective and the reader is referred to the increasing literature related to plant immunity in general Relatively few detailed plant–pathogen interactions have been described to date, and it is not known whether these insights apply to the sugar beet–P betae– BNYVV patho-system It seems likely that some of the processes are shared between sugar beet and other model and crop systems, and that these could be exploited to enhance rhizomania resistance (Nicaise 2014) However, it cannot be overemphasized that these characterizations need to be done for sugar beet, not only for the rhizomania system but also for each of the major sugar beet pathogens worldwide (Biancardi et al 2005) With the advent of sugar beet genome sequences (e.g., Dohm et al 2014), it is anticipated that this task will become more precise and informative with respect to the specific genes involved and thus allow greater precision in choosing targets of opportunity for sugar beet crop protection Some progress has been made in characterizing the rhizomania interaction with sugar beet Using near isogenic lines with and without Rz resistance genes, Larson et al (2008) and Webb et al (2015) were able to identify changes in the proteome in response to challenge with BNYVV versus non-inoculated plants The proteins detected likely represent stable downstream targets and responses of the Rzmediated immunity system and encompass those described in other plant host– pathogen interactions These data reinforce that the sugar beet–rhizomania system is not fundamentally deviant relative to other plant pathogenic processes However, uncertainty as to the putative identities of gene products deduced by homology comparisons with other species, the relative diversity of biological processes detected, and temporal variation in protein abundance across time points assayed make it difficult to draw strong conclusions regarding mechanisms of rhizomania resistance The idea that rhizomania interactions with sugar beet are not fundamentally different than other plant immunity responses is further supported through demonstration that the BNYVV RNA3 P25 pathogenicity component interacts specifically with beet, Arabidopsis, and Nicotiana F-box proteins involved in targeting proteins for degradation, supporting the notion that P25 is involved in the suppression of the beet’s innate immune response (Peltier et al 2011; Thiel et al 2012; Litwiniec et al 2014) An important part of the plant antiviral immune system is destruction of invading viral RNAs such that replication, transcription, and/or translation are prevented; thus, viral titers and gene products not accumulate to damaging concentrations RNA silencing mechanisms exist to recognize host from nonhost RNA, and viruses exploit suppression of this mechanism to replicate Suppression of silencing can be overcome in some cases, such as when virus genes are engineered to express in a plant host and thereby provide a prophylactic copy of a viral gene that presumably 268 J.M McGrath “primes” the immune RNA silencing machinery to high activity prior to infection Beets expressing BNYVV coat protein or replicase genes indeed confer a measure of rhizomania resistance when so configured (Mannerlöf et al 1996; Pavli et al 2010) Extra measures of resistance could be anticipated by combining multiple triggers of the beet’s innate immunity, much like stacking of Rz resistance alleles in current varieties It is logical to think that such resistance would be more difficult for the virus to overcome and thus be more durable Pavli and colleagues (2012) developed an interesting approach toward durable rhizomania resistance In this case, Nicotiana benthamiana was used as a surrogate transformable species The transformed plant received a harpin gene and a BNYVV replicase gene, where the harpin gene acts as a bacterial effector gene involved in pathogen recognition, presumably acting prior to activation of the NB-LRR component of immunity The replicase gene presumably functions in the RNA silencing immune pathway As more components of the immunity system are identified and assessed in sugar beet, it is conceivable that effective components could be stacked in combination, which ideally would confer rhizomania resistance indefinitely Transgenic approaches may be a viable option if the high expense of developing such varieties can be justified In this respect, newer genetic engineering technologies such as targeted gene replacement, perhaps using a CRISPR/Cas9 or similar technology (Belhaj et al 2015), will reduce the cost of developing new germplasm but may not address the high cost of obtaining regulatory approval of such varieties Resistance to BNYVV as the causal agent of rhizomania is the most direct target of intervention, however other targets are also available Resistance to the plasmodiophorid soil-borne vector P betae is another attractive option that would confer indirect rhizomania resistance via precluding virus infection This strategy may be easier to implement as a durable resistance approach versus continually screening germplasm for resistance to newly virulent strains of BNYVV that avoid existing Rz-mediated resistance Three lines of evidence suggest that immunity to could be achieved: • Polymyxa betae has a very restricted host range in nature, affecting only a few species in the genus Beta The only other Polymyxa species described affects wheat (and perhaps beet as well), suggesting that P beta–plant interactions are an exception and that the obligate biotrophic nature of this interaction is highly specific and perhaps easily disrupted (Neuhauser et al 2010) • Closely related Beta species appear immune to P betae infection, again suggesting a highly specific interaction that has perhaps only recently been exploited by BNYVV to vector rhizomania (Tamada and Kondo 2013) Genomics applied to these related species may help to uncover a genetic basis of this immunity, and, by using traditional breeding methods, perhaps this immunity could be transferred to sugar beet • Resistance to P betae may be found within the primary germplasm pool of Beta vulgaris Asher and colleagues described two loci from B vulgaris subsp maritima that confer resistance to P betae opening up the possibility that resistance may be readily incorporated into cultivated materials (Asher et al 2009) 13 Perspective 269 In summary, the dynamics and mechanics of the plant immune system are only beginning to be unraveled Insights gained need to be confirmed in sugar beet (for each of sugar beet’s pathogens) and extended to the rhizomania infection process Opportunities exist to apply these insights to specific interactions with the BNYVV as well as to interactions with the vector of rhizomania It is expected that the beet immune system will follow similar paradigms as in other angiosperms, including the panoply of effector- and plant-mediated pathogen responses However, the recognition of each pathogen is likely a highly specific interaction Thus, modulation of the host response to either the virus or the vector requires an understanding of the specific molecules and mechanisms involved in triggering sugar beet defenses Further, downstream responses may be subject to environmental influences as well as the degree and strength of the interference of the host response by the pathogen’s infection processes Such conditional responses may be difficult to ascertain, and in this respect, model systems may offer an efficient opportunity to examine the molecular interactions that facilitate the development of disease, particularly rhizomania References Asher MJC, Grimmer MK, Mutasa-Goettgens ES (2009) Selection and characterization of resistance to Polymyxa betae, vector of beet necrotic yellow vein virus, derived from wild sea beet Plant Pathol 58:250–260 Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V (2015) Editing plant genomes with CRISPR/Cas9 Curr Opin Biotechnol 32:76–84 Biancardi E, Campbell LG, Skaracis GN, de Biaggi M (eds) (2005) Genetics and breeding of sugar beet Science Publishers, Enfield NH, USA Caplan J, Padmanabhan M, Dinesh-Kumar SP (2008) Plant NB-LRR immune receptors: from recognition to transcriptional reprogramming Cell Host Microbe 3:126–135 David P, Chen NWG, Pedrosa-Harand A, Thareau V, Sévignac M, Cannon SB, Debouck D, Langin T, Geffroy V (2009) A nomadic subtelomeric disease resistance gene cluster in common bean Plant Physiol 151:1048–1065 De Ronde D, Butterbach P, Kormelink R (2014) Dominant resistance against plant viruses Front Plant Sci 5:307 doi:10.3389/fpls.2014.00307 Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Rosleff Sörensen T, Stracke R, Reinhardt R, Goesmann A, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H (2014) The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) Nature 505:546–549 Eitas TK, Dangl JL (2010) NB-LRR proteins: pairs, pieces, perception, partners, and pathways Curr Opin Plant Biol 13:472–477 Hunger S, Di Gaspero G, Möhring S, Bellin D, Schäfer-Pregl R, Borchardt DC, Durel CE, Werber M, Weisshaar B, Salamini F, Schneider K (2003) Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgaris L.) Genome 46:70–82 Larson RL, Wintermantel WM, Hill A, Fortis L, Nunez A (2008) Proteome changes in sugar beet in response to beet necrotic yellow vein virus Physiol Mol Plant Pathol 72:62–72 Litwiniec A, Łukanowski A, Gośka M (2014) RNA silencing mechanisms are responsible for outstanding resistance of some wild beets against rhizomania A preliminary evidence-based hypothesis J Anim Plant Sci 21:3273–3292 270 J.M McGrath Litwiniec A, Gośka M, Choinska B, Kuzdowicz K, Łukanowski A, Skibowska B (2015) Evaluation of rhizomania-resistance segregating sequences and overall genetic diversity pattern among selected accessions of Beta and Patellifolia Potential implications of breeding for genetic bottlenecks in terms of rhizomania resistance Euphytica (published online October 7, 2015) Mandadi KK, Scholthof KG (2013) Plant immune responses against viruses: how does a virus cause disease? Plant Cell 25:1489–1505 Mannerlöf M, Lennerfors BL, Tenning P (1996) Reduced titer of BNYVV in transgenic sugar beets expressing the BNYVV coat protein Euphytica 90:293–299 McGrann GRD, Grimmer MK, Mutasa-Göttgens ES, Stevens M (2009) Progress towards the understanding and control of sugar beet rhizomania disease Mol Plant Pathol 10:129–141 McGrath JM, Panella L, Frese L (2011) Beta In: Kole C (ed) Wild crop relatives: genomic and breeding resources, industrial crops Springer, Berlin Germany, pp 1–28 Meyers BC, Morgante M, Michelmore RW (2002) TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes Plant J 32:77–92 Monosi B, Wisser RJ, Pennill L, Hulbert SH (2004) Full-genome analysis of resistance gene homologues in rice Theor Appl Genet 109:1434–1447 Neuhauser S, Bulman S, Kirchmair M (2010) Plasmodiophorids: the challenge to understand soilborne, obligate biotrophs with a multiphasic life cycle In: Gherbawy Y, Voigt K (eds) Molecular identification of fungi Springer, Heidelberg Germany, pp 51–78 doi:10.1007/978-3-642-05042-8_3 Nicaise V (2014) Crop immunity against viruses: outcomes and future challenges Front Plant Sci 5:660 doi:10.3389/fpls.2014.00660 Pavli OI, Panopoulos NJ, Goldbach R, Skaracis GN (2010) BNYVV-derived dsRNA confers resistance to rhizomania disease of sugar beet as evidenced by a novel transgenic hairy root approach Transgenic Res 19:915–922 Pavli OI, Stevanato P, Biancardi E, Skaracis GN (2011) Achievements and prospects in breeding for rhizomania resistance in sugar beet Field Crops Res 122:165–172 Pavli OI, Tampakaki AP, Skaracis GN (2012) High level resistance against rhizomania disease by simultaneously integrating two distinct defense mechanisms PLoS One 7:e51414 doi:10.1371/ journal.pone.0051414 Peltier C, Schmidlin L, Klein E, Taconnat L, Prinsen E, Erhardt M, Heintz D, Weyens G, Lefebvre M, Renou J-P, Gilmer D (2011) Expression of the beet necrotic yellow vein virus p25 protein induces hormonal changes and a root branching phenotype in Arabidopsis thaliana Transgenic Res 20:443–466 Sarris PF, Duxbury Z, Huh SU, Ma Y, Segonzac C, Sklenar J, Derbyshire P, Cevik V, Rallapalli G, Saucet SB, Wirthmueller L, Menke FLH, Sohn KH, Jones JDG (2015) A plant immune receptor detects pathogen effectors that target WRKY transcription factors Cell 161:1089–1100 Tamada T, Kondo H (2013) Biological and genetic diversity of plasmodiophorid-transmitted viruses and their vectors J Gen Plant Pathol 79:307–320 Thiel H, Hleibieh K, Gilmer D, Varrelmann M (2012) The P25 pathogenicity factor of beet necrotic yellow vein virus targets the sugar beet 26S proteasome involved in the induction of a hypersensitive resistance response via interaction with an f-box protein Mol Plant-Microbe Interact 25:1058–1072 Tian Y, Fan L, Thurau T, Jung C, Cai D (2004) The absence of TIR-Type resistance gene analogues in the sugar beet (Beta vulgaris L.) genome J Mol Evol 58:40–53 Törjèk O, Borchardt D, Mechelke W, Jens C (2014) Rhizomania-resistant gene: WIPO Patent Application WO/2014/202044 Webb KM, Wintermantel WM, Kaur N, Prenni JE, Broccardo CJ, Wolfe LM, Hladky LL (2015) Differential abundance of proteins in response to beet necrotic yellow vein virus during compatible and incompatible interactions in sugar beet containing Rz1 or Rz2 Physiol Mol Plant Pathol 91:96–105 Appendix HINDERED RESISTANT RAPID SUSCEPTIBLE NORMAL TOLERANT POOR NON-TOLERANT BNYVV MULTIPLICATION BEET GROWTH (SUGAR YIELD) Fig A1 Terms generally used (right, underlined) to define the kind and intensity of reactions employed by sugar beet to limit the effects of rhizomania on yield © Springer International Publishing Switzerland 2016 E Biancardi, T Tamada (eds.), Rhizomania, DOI 10.1007/978-3-319-30678-0 271 Appendix 272 Animals Biotic factors Plants Microorganisms Plant diseases and stresses Non-cellular agents Non-biotic factors Mites Insects Nematodes etc Weeds Protozoa Rickettsias Phytoplasmas Spyroplasmas Bacteria Fungi Viruses Viroids Drought Water excess Frost Soil salinity etc Pest Infestation Disease Disease Stress Fig A2 Terms used to define the pathologies affecting the sugar beet crop (right, underlined) according to their origin Index of Names A Abscisic acid, 44 Additive dominance, 18 Agrobacterium rhizogenes, 223, 226 Agrobacterium tumefaciens, 223 Aizoaceae, 58 Alanine scanning mutagenesis, 65 Alba Immobiliare (sc), 196 Alba P (var), 196, 198, 199, 201 Alba type, 196, 203 Alcohol, 182 Alfaflexiviridae, 116 Algae, 110, 114 Alkalinity coefficient (AK), 177 AlkB-like domain, 116 Allelism tests, 264 Alliance, Alpha-amino N, 33, 176–178 Amaranthaceae, 4, 5, 58, 121, 145, 159, 160 Amaranthus retroflexus (A retroflexus), 144, 159, 160 American Crystal Sugar Company (sc), 204 Amino acid, 60, 62, 65, 66, 97, 112, 115, 117, 122–125, 127, 178 residues, 96, 98, 117, 122, 123, 266 Analysis of molecular variance (AMOVA), 203 Angelina (var), 239 Angle-layer aggregates, 69, 70 Anisoploid, 9, 12 Annual beets, 16, 18 Annual cycle, 241 Annuality, Antagonistic ability, 187 Antagonistic action, 187 Antagonistic bacteria, 21 Antagonistic organisms, 187 Anthesis, Antiviral genes, 222, 227 Aphanomyces, 181 Arabidopsis thaliana (A thaliana), 72, 85, 86, 97, 98, 145 Arctium lappa, 116 Asteraceae, 145, 159 Auxin, 44, 72, 98 Auxin-induced gene, 72 Avirulence (Avr), 66, 96–99, 123 B Bacillus amyloliquefaciens, 187 Back-crosses, 235, 241 Bagasse, 13 Bait plants, 74, 121, 156, 157, 237 B annual gene, 14 Beet black scorch virus (BBSV), 74, 76 Beet curly top virus (BCTV), Beet cyst nematode, 9, 32, 161, 186, 198 Beet domestication, 6, 8, 17 Beet necrotic yellow vein virus (BNYVV) A-type, 46, 59, 60, 74, 116, 118, 126, 209 B-type ( = Germany strain), 46, 59, 60, 74, 98, 116, 120, 125–127, 209 China B strain, 118–120 China H strain, 119, 120 China L strain, 120 China X strain, 118–120 China Y strain, 119 European A-type (= Italy strain), 119, 120, 124, 125 Germany strain (= B-type strain), 120 Italy strain (= European A-type), 124 Japan D strain, 120, 125 Japan O strain, 120, 125 © Springer International Publishing Switzerland 2016 E Biancardi, T Tamada (eds.), Rhizomania, DOI 10.1007/978-3-319-30678-0 273 274 Beet necrotic yellow vein virus (BNYVV) (cont.) Japan T strain, 120 J-type, 46, 60, 116 P-type (= France P strain), 46, 60, 118, 126 Beet oak-leaf virus (BOLV), 43, 188 Beet processing, 6, 10, 178 Beet soil-borne mosaic virus (BSBMV), 43, 62, 67, 74, 75, 88–90, 94–96, 115, 127, 136, 147, 187, 188 Beet soil-borne virus (BSBV), 43, 74–76, 127, 136, 147, 226 Beet stand, 236 Beet virus Q (BVQ), 43, 74, 76, 127, 136, 147, 226 Beet yellows virus (BYV), 6, 92, 207, 226 Benyviridae, 64, 92, 110, 115, 147 Benyvirus, 64, 75, 86–88, 90, 92, 110–116, 127, 136, 147, 156 Benyvirus replicase-related sequences (BRLSs), 114 Beta B macrocarpa, 58, 59, 67, 94, 96 B maritima, 4, 12, 13, 15–18, 196–198, 206–211, 235, 240, 241, 250 B nana, B patula, 5, 14 B vulgaris complex, 14 B vulgaris subsp Adanensis, 5, 14 B vulgaris subsp maritima, 121, 122, 268 B vulgaris subsp maritima M8, 58, 67, 70, 71 B vulgaris subsp vulgaris, 57, 59, 115, 135 B vulgaris var cicla, 57 Betaflexiviridae, 116 Betaine, 178 Biennial cycle, 8, 233 Biennial trait, 14, 233 Biogas production, 183 Blinkers, 183 Bolting beets, 14 Bolting resistance, 8, 18 Border rows, 243 Brassicaceae, 145, 159 Breakdown of resistance, 240 Breeding progresses, 244 Brix, 199 Burdock, 116 Burdock mottle virus (BdMoV), 115 Bushel (var), 199 Buszczynski CLR (var), 199 Buszczynski (sc), 40, 199, 200 Bymovirus, 147, 161 Index of Names C C3 photosynthesis, 13 C4 photosynthesis, 13 C37, 207, 208 C47R, 208 C79-1 to C79-11, 208 Campaign, 177, 209, 243 Cane sugar, 13 Canopy, 13, 34, 44, 181, 251 Cariophillaceae, 58, 159, 160 Carlavirus, 66 Cell-to-cell movement, 66, 86, 91–93, 213, 224 Centrifugation, 64, 252 Centro Produzione Seme Cesena (sc), 200 Centro Seme Mezzano (sc), 200 Cercospora leaf spot (CLS), 6, 15, 16, 36, 40, 186, 196–199, 204, 207, 214 Cesena (sc), 198 Chara australis virus (CAV), 110, 114, 127 Chemical control, 18, 211 Chenopodiaceae, 4, 5, 46, 58, 66, 137, 144, 145, 150, 159 Chenopodium C amaranticolor, 58, 144, 159, 250 C quinoa, 58, 64, 65, 67, 73, 87, 93, 94, 96, 188, 226, 237, 250, 254 Chi-square test, 204 Chlorides, 64, 178 Chlorophyll fluorescence, 15 Chloropicrin, 186 Chromosome III, 206, 207 Citoplasmic male sterilty (CMS), 9, 11, 199, 201, 204, 206, 235, 238, 239, 241 Citric acid, 178 Climate change, 16, 24, 46 Coat/capsid protein (CP), 60, 62, 63, 65, 75, 90–93, 99, 101, 102, 111, 112, 116–120, 124, 126, 147, 148, 188, 223, 224, 226, 227, 268 Codominance, 204 Combining ability, 235 Complementary DNA (cDNA) library, 98 Composite seedlings, 226 Coproducts, 182 Coremin, 67, 94–96, 100 Corollinae (ex Patellares), 210 Cortex, 43, 69, 71, 142, 143, 205 Cossettes, 182 Costs/benefits ratio, 236 Crop-to-crop pollination, 14 Crop wild relatives (CWRs), 13, 17, 213, 214 Cross protection, 75, 187, 188 Crown, 176, 197, 204 275 Index of Names C-terminal region, 86 Cysteine-rich protein, 66, 95, 99, 111, 122, 123 D Damping-off, 181 Data processing, 244 Day length, Deep sequencing, 127 Diagnosis, 72–74 Dichloropropene–Dichloropropane (D–D), 186 Dicotyledon, 13, 160 Dimono (var), 200 Diploid, 8, 198–201, 203, 236 Disease index (DI), 199, 205, 234, 254 Distillation, 182 Domestication, 6, 17 Dominant gene, 196, 204 Dora (var), 199 Double resistance, 208, 209, 240 Double-transgenic plants, 228 Drip irrigation, 242 Drought, 12, 15, 16, 242 tolerance, 15 Dry matter (Brix), 175, 178 Durability of resistance, 161, 187, 222, 228 Durable crop protection, 228 E Ecology, 155–169 Economic damage, 22–24, 178 Electron microscopy, 141, 142, 144, 212, 259 Emergence, 122–126, 181, 206, 209, 222, 237, 242, 251 E, N, and Z varieties, 40 Endodermis, 69, 142, 143, 205 Endoplasmic reticulum (ER), 69, 87, 139, 140, 142, 227 Energy, 13, 72, 87, 91, 100, 161 Environmental costs, 18 Enzyme-linked immunosorbent assay (ELISA), 73, 74, 149, 156, 158, 165, 181, 203, 204, 234, 236, 237, 243, 253–255, 259 Epidemiology, 136, 160, 222 Epidermis, 69, 205 Erwinia carotovora, 207 Erwinia root rot, 207 Ethylene, 72 Exchangeable magnesium, 182 Exit-tube differentiation, 142 Experimental designs, 244 Extraction procedures, 178 F Factory waste, 162 Fanginess, 241 Fangy and woody roots, 18 F-box, 98 FC1740, 208 FC1741, 208 Feral beets, 14 Field resistance, Field tolerance, Field trials, 7, 32, 178, 202, 203, 208, 236, 237, 242–244, 250, 253 Flowering physiology, Flowering stage, 14 Fodder beet, 5, 14, 18, 57 Fructose, 176, 178 Furovirus, 110, 147, 161 Furrow irrigation, 162, 183 Fusarium, 181 root rot, 73 Fusarium yellows, 9, 20, 22 G Gabriela (var), 204 Garden beet, 144 Gene flow, 12, 14–15 Genetically modified traits, 187 Genetically modified varieties, 187 Genetic backgrounds, 203, 205, 206 Genetic-cytoplasmic male sterility, Genetic monogermy, 9, 45 Genetic resources, 13, 14, 213, 214 Genetic sources of nonviral origin, 227 Genome sequences, 76, 267 Genotype x environment interactions, 8, 12, 209, 210 Germination ability, 204, 242 Germination of resting spores, 143–144, 167, 168 Global climate change, 15 Glomerulus, 242 Glucose, 176, 178 Glutathione S-transferase (GST), 149, 258 Glyphosate resistance, 15 Gomphrena globosa, 121, 159 Goravirus, 110 Gramineae, 136, 150 Great Western (sc), 204 276 Green fluorescent protein (GFP), 70, 71, 89, 92, 97, 99 Greenhouse systems, Grooves, 176 Gross sugar yield, 176 H Handheld chlorophyll meter, 72 Hand thinning, Harpin gene, 268 Harpin molecule, 228 Harpin proteins, 227 Helicase (HE), 63, 65, 66, 86, 92, 110 Hepeviridae, 111 Herbicides, 8, 9, 160 Heritability, 195, 199 Heterodera schachtii (cyst nematode), 32–34, 161, 186 Heterozygous condition, 239 Hilleshøg (sc), 200, 202, 205 Holly 1-4 (bl), 205, 206 Holly 85C47-06 (bl), 204 Holly Sugar (sc), 203, 204 Holly type, 265 Hordeivirus, 92, 110, 112 Housekeeping genes, 85 Human health, 18 Hybridization of pollinators, 238 Hypersensitive response (HR), 227, 267 I Immune response, 227, 267 Immunity, 7, 95, 211, 223, 264, 267, 268 Immunogold-silver labeling, 212 Immunosorbent electron microscopy (ISEM), 62, 73 Inbreeding, 235 Innate defense mechanism, 95 Innate immunity, 95, 268 Inoculum assessment, 156–157 Inoculum potential, 157–162, 167 Insect-transmitted viruses, 73 Iteroparous, 10 J Jasmonate, 72 K Kelch domain, 98 KWS (sc), 204 Index of Names L Leaf area index (LAI), 22, 175 Leaf beets, 5, 70 Leaves regrowth, 35 Leaves thickness, 238 Lemon, 187 Lena (var), 199 Liberation of zoospores, 141–142 Lion Seeds (sc), 200 Lipopeptides, 187 Long-distance movement, 93, 94, 97, 99–102 Loss of sucrose, 23 Low sugar content syndrome (LSCS), 29, 32–34, 36, 39, 42, 47 Lumbricus terrestris, 187 M Maintainer, 11, 201 Malic acid, 178 Manure, 161, 162, 182 Mass spectrometry, 72, 98 Meloidogyne spp (root-knot nematode), 186 Methyl bromide, 36, 186 Methyltransferase (MT), 110 Mezzano (sc), 198 Mezzano NP (var), 199 Minor genes, 203, 208 Mitochondria, 65, 69, 91, 101 Mitogen-activated protein kinase (MAPK) pathways, 266 Molasses, 182 Monoclonal antibody, 149, 254 Monocotyledon, 13, 121, 145, 160 Monoculture, 42 Monodoro (var), 199 Monogerm trait, 11 Monopoly of sugar, Monosomic addition, 210 Morphological selection, 240 Most probable number (MPN), 156, 158, 237, 259 Mother beets, 196, 201, 240, 253 Multidimensional liquid chromatography, 72 Multiple crowns, 241 Multiple diseases resistance, 16 N Nanae, Natural antiviral defense mechanism, 225 Near isogenic lines, 267 Necrosis, 34, 39, 43, 58, 67, 68, 72, 76, 97, 115, 147, 227, 251 Index of Names Nematode-transmitted virus, 110 Nested PCR (nPCR), 73, 74 Net-CO2 uptake, 238 Nicotiana benthamiana (N benthamiana), 58, 67, 93, 94, 96, 99, 100, 102, 225, 227, 228, 268 Nicotiana velutina mosaic virus (NVMV), 110, 112 Nitrates, 178 Nitrites, 178 Nitrogen availability, 181 Nitrogen compounds, 176, 178 Noncoding RNA (ncRNA), 67, 94 Non-retrovirus RNA viral sequences, 110 Nonselective herbicides, Non-sugars, 176 Normal (N) cytoplasm, 11 N-terminal region, 65, 86, 87, 91–93, 227, 266, 267 Nuclear-cytoplasmic protein, 67 Nuclear export signal (NES), 66, 97 Nuclear localization signal (NLS), 97, 98 Nuclear ribosomal ITS1 sequences, Nucleic acid hybridization assays, 73 Nucleotide diversity, 119 Number of harvests, 243 Nursery, 162, 201, 236, 240–243 O Olpidium brassicae, 74, 76 Open reading frame (ORF), 65, 88, 95, 97–99, 111, 225 Order of emission (leaves), 238, 251 Organic fertilizer, 182 Organic soils, 186 Oryza sativa, 115 O-type, 11, 199, 201, 204, 206 Overwintering, 8, 240 Oxalic acid, 178 P p13, 65, 66, 224 p14, 66, 95, 99 p15, 65, 66, 224 p25, 66, 68, 72, 75, 117, 227, 267 p26, 67, 75, 95–97, 101, 116, 118, 119, 126 p29, 75, 95 p31, 67, 89, 96, 100–102, 116–120 p42, 65, 66 p66, 65, 86, 87 p75, 65, 70, 71, 91 277 p150, 65, 86, 87 p237, 65, 86, 87, 95, 101 Papaveraceae, 159, 160 Papaya, 187 Paper pots, 43, 182 Parenchyma, 69 Partial resistance, Patellares, 210 Patellaris, 5, 210 Patellifolia, 5, 13, 210, 211 Pathogen derived resistance (PDR), 222–224 Pathogen effector, 266 Pathogenicity, 58, 66, 95–99, 127, 212 Peanut clump virus (PCV), 93, 147 Pecluvirus, 66, 110, 113, 147 Pellet, 21, 46, 187 Penetrance, 204 Pesticides, 8, 18 Petioles, 251 Phagomyxida, 136 Phellogen, 43 Phosphoric acid, 178 Photothermal induction, Phylogenetic analysis, 119 Phytohormones, 44 Phytomyxea (phytomyxids), 136 Planchons, 240 Plantibody, 227 Plantlets, 9, 46, 236, 240 Plasmodesmata, 66, 92, 101, 140, 147 Plasmodia, 43, 62, 136–138, 140–143, 148, 209 Plasmodiophora, 136 P brassicae, 136, 145, 149 Plasmodiophoraceae, 60, 136, 147 Plasmodiophorids, 113, 136–141, 143, 145–148, 150, 209, 210, 264, 268 Plasticity of viral genomes, 222 Plot-harvesting machinery, 243 Plot samples, 235, 244, 253 Plowing, 249, 250 Poaceae, 159 Pollen, 8, 14, 15, 18, 162, 240, 241 release, Pollinator, 9, 11, 14, 198, 199, 201, 203, 204, 207, 236, 239, 241 Polyclonal antibody, 149 Polymerase chain reaction (PCR), 145, 255 Polymyxa betae (P betae) P betae f.sp amaranthi, 43, 144 P betae f.sp betae, 144 P betae f.sp portulacaceae, 160 278 Polymyxa graminis (P graminis), 42, 113, 115, 116, 136, 144, 145, 147–150, 161, 167 P graminis f.sp colombiana, 147 P graminis f.sp subtropicalis, 147 P graminis f.sp temperata, 147 P graminis f.sp tepida, 147 P graminis f.sp tropicalis, 147 Pomovirus, 75, 76, 110, 112, 113, 136, 147 Portulaca oleracea, 144, 160 Posttranscriptional gene silencing (PTGS), 224 Potassium, 33, 176, 177 Potato mop-top virus (PMTV), 92, 113, 136, 147 Potexvirus, 66 Potyviridae, 147 Primary gene pool (GP-1), 13 Primary sub-group A: (GP-1A), 13 Primary sub-group B: (GP-1B), 13 Processing of diseased beets, 178 Processing of samples, 74 Processing quality, 18, 22, 40, 175, 176, 196, 203, 241, 242, 253 Procumbens, Procumbentes, 5, 210 Progeny tests, 8, 235 Protease, 63, 65, 86 Proteome, 267 Protist, 110, 136, 142 Protozoa, 42 Pseudomonas, 187, 227 P fluorescens, 187 Purification, 64 Purity of thick juice, 178 Q Quantitative traits, 208 Quarantine, 23, 45, 181, 185 Quasi species, 127 R R104 (wb) R 581 (bl), 206, 207 Randomized block designs, 243 Read-through (RT), 62, 65, 91, 102, 223 Real-time RT-PCR, 74, 149, 150, 256–258 Reassortants, 60, 118, 127 Recombination, 60, 110, 127, 264 Recombinational mutation, 266 Recovery phenotype, 224, 225 Recurrent selection, 199, 207, 235 Reducing sugars, 176, 178 Index of Names Regia Stazione Sperimentale di Bieticoltura (rs), 200 Registration procedure, 18, 196, 243 Remote sensing, 181, 250 Replicase, 112, 115, 116, 268 Replication, 65, 111, 115, 122, 148, 187, 213, 223, 236, 243, 267 Resistance breaking, 16, 18, 23, 110, 117, 122–126, 183, 208, 209, 211, 242 Resistant strains, 18 Resistant winter varieties, 181 Respiration rate, 23 Resting spore, 23, 43, 60–62, 91, 100, 121, 136–138, 141, 143–145, 147–150, 156, 157, 160–164, 166–168, 182, 183, 188, 250 Restriction fragment differential, 72 Restriction fragment length polymorphism (RFLP), 59, 145 Reverse transcriptase (RT), 85, 256–258 Reverse transcriptase polymerase chain reaction (RT-PCR), 73, 74, 159, 255, 256, 258 Rhizaria, 136 Rhizoctonia, 181 Rhizogenic activity, 43 Ribonucleoprotein complex, 90, 148 Ribosomal DNA (rDNA), 136 Rice stripe necrosis virus (RSNV), 115, 116 Ritmo (var), 199, 204 Rizomania–Signal, 177 Rizor (var), 198, 202–208 Rizor type, 203 RNA amplification, 86, 88–89, 93, 99, 100 binding protein, 93 RNA1, 56, 59, 62, 64, 65, 75, 86–90, 93–95, 100, 102, 115, 116 RNA2, 59, 62–66, 70, 71, 74, 75, 86, 88–91, 93–95, 99, 101, 102, 115–117 RNA3, 59, 62, 64, 66–68, 72, 75, 86, 88–91, 93–102, 122, 124–125 RNA4, 56, 59, 62, 64, 67, 68, 86, 88–90, 96, 100–102, 147 RNA5, 46, 60, 62, 64, 67, 68, 74, 75, 86, 88–90, 94–96, 101, 116–118, 125, 126 RNA-dependent RNA polymerase (RdRp), 63, 65, 86 RNAi suppression, 88 RNA-mediated resistance, 223 RNA-RNA interaction, 87, 90, 102, 103 RNase protection assays, 94 RNA silencing, 88, 95, 96, 99–101, 222–226, 267, 268 Index of Names RNA silencing-based resistance, 226 Ro 281 (bl), 203 Ro 401 (bl), 199 Ro 412 (bl), 199 Ro 701 (PI546426) (wb), 207 Rod-shaped virus, 43, 47, 56, 62, 110, 111, 116 Root constriction, 177 Root fanginess, 241 Root grooves, 34, 176 Root homogenate, 237 Rootlet, 7, 33–36, 42–44, 55, 56, 58, 60, 68, 69, 74, 122, 157, 165, 175, 177, 181, 182, 185, 203, 210, 212, 213, 237, 250, 251, 254–255 proliferation, 23, 32, 34, 44, 57, 58, 68, 72, 189 Root sampling, 237, 251 Root system, 15, 65, 69, 122, 226, 249 Root weight, 18, 40, 158, 159, 176, 201, 241, 254 Root woodiness, 241 R-protein, 266 Rz-mediated resistance, 266, 268 Rz1 resistance, 46, 123–126, 206, 209, 211, 264 Rz2 resistance, 207, 264 Rz3 resistance, 241, 264 Rz4 resistance, 208, 264 Rz5 resistance, 207, 264 S Salicylic acid, 186, 266 Salt tolerance, 16 Salty water, 16 Sanamono (var), 199 Saros (var), 35, 40 Scanning electron microscopy, 144, 259 Scarcity of natural genetic sources, 222 Sea beet, 4, 17, 35, 196, 197, 199, 204, 211, 213–215, 237, 265 Secondary gene pool (GP-2), 13 Secondary roots, 34, 177, 181 Secondary sub-group B (GP-1B), 13 Section Corollinae, Section Vulgares Complex, Seed and seedling treatments, 187 Seed-bearers, 9, 18, 45, 201, 238, 239, 241, 242 Seed germination, 182 Seed production, 8, 10, 14, 199, 240–242 Seed stalks, 242 Seed transmission, 60 279 Segregation, 196, 203, 206, 207 Selection pressures, 110, 119 Semelparous, 10 Sequence diversity, 59 Sequencing, 85, 96, 150, 265, 266 SES 2281-R1, 203 SES-Italy, 200 Single-chain antibody fragments (scFv), 227 Single-strand conformation polymorphism (SSCP), 59 Small interfering RNAs (siRNAs), 225 Smooth-root hybrids, 176 Sodium, 33, 176, 253 Sodium chloride, 186 Soil-borne diseases, 16, 186, 195 Soil-borne fungus, 42 Soil-borne RNA virus, 74 Soil-borne wheat mosaic virus (SBWMV), 147, 148 Soil fungicides, 23, 188 Soil mixture, 183, 236, 237, 251 Soil moisture, 45, 143, 163, 166–167, 181, 236 Soil pH, 163, 164, 182 Soil salinity, 12 Soil salinization, 16 Soil sickness, 29, 47 Soil sterilization, 36 Soil temperature, 143, 163, 167, 182, 185–188, 199, 234, 243 Soil tillage, 8, 162 Soil vertical variability, 236 Solanaceae, 58, 159 Solarization, 186 Sources of resistance, 16, 196, 198, 207, 208, 214, 222, 240 Sowing, 8–10, 15, 18, 22, 167, 168, 182–185, 199, 237, 242, 244 time, Spinacia oleracea (Spinach), 57, 58, 144, 159, 160, 259 Spongospora, 136 S subterranea, 113, 136, 147, 149 Sporangial phase, 137, 145 Sporangial plasmodia, 61, 141, 168 Sporogenic phase, 61, 137, 138 Sporogenic plasmodia, 138, 140 Sporosori, 144, 145, 259 Spring varieties, Sprinkler irrigation, 44, 242 Stability of sugar production, 243 Stalk Stazione Sperimentale di Bieticoltura (rs), 8, 13, 18, 20, 242 Stecklings, 239–241 280 Sterilization, 36 Storage of samples, 244 Streptomyces, 187 Suberin, 213 Subfamily Betoideae, Subgenomic RNA, 66, 86, 88, 90, 92, 94, 99, 101 Sublimed sulfur, 182 Sugar (sucrose), 6, 13, 23, 64, 176, 197, 251, 253 Sugar beet cDNA library, 72 Sugar beet gene pool, 214 Sugar beet processing, Sugar beet winter crop, 180 Sugar cane, 11, 13, 24 Sugar content, 15, 18, 22, 23, 29, 30, 33–35, 40, 44, 47, 68, 158, 159, 175, 176, 178, 181, 185, 199, 235, 241 Sugar extraction rate, 178 Sugar yield, 6–9, 11, 15, 18, 22, 158, 159, 167, 176, 186, 196, 203–205, 208, 211, 222, 237, 239, 240, 254 Sulfides, 178 Susceptibility, 7, 15, 68, 145, 204, 236 Susceptible varieties, 22, 23, 122, 160, 161, 178, 180, 186, 203, 204, 211, 242 Swarms of point mutants, 222 Sweet cherry trees, 44 Swiss chard, 57, 160 Synthetic fertilizers, Systemic infection, 67, 103, 177, 224, 234 Systemic perturbation, 266 T Table beet, 56 Tail, 34, 63, 64, 162, 186 Talaromyces, 187 Tandem (var), 239, 264 Tandemly arrayed clusters, 264 Taproot, 6, 13, 17, 34, 38, 39, 43, 44, 57, 58, 71, 73, 122, 126, 197, 203, 251 Tare soil, 23, 32, 176, 182 Taxonomy, 5, 13, 136–137, 213 Temperature, 8, 12, 15, 16, 45, 46, 143, 145, 147, 148, 156, 163, 167, 168, 181–183, 186, 188, 203, 236–238, 251, 255, 259 Terminology of plasmodiophorids, 137 Tertiary gene pool (GP-3), 13 Test-crosses, 235 Tetrad, 66, 98, 123, 125–127 Tetragonia expansa (T expansa), 58, 237 Tetraploid families, 8, 199 Index of Names Thermal stress, 15 Thick juice, 178, 179 Thin juice, 178 TIR-based immunity, 267 Tissue print immunoblotting, 69 Tobacco, 187, 241 Tobacco etch virus (TEV), 224 Tobacco mosaic virus (TMV), 92, 93, 102, 110, 111 Tobamovirus, 110, 112 Togaviridae, 111 Tolerance, 7, 12, 15, 16 Transcriptome, 96, 110 Transduction of signals, 266 Transgenesis, 228 Transgenic approaches, 222, 268 Transgenic hairy roots, 223 Transition substitution, 125 Transmembrane regions, 65, 91, 147 Transversion substitution, 125 Trichoderma, 187 Triple gene block (TGB), 65, 92, 112, 224 Triploid, 9, 199, 236 U Urticaceae, 159 USDA-ARS Beltsville (rs), 198 USDA-ARS East Lansing (rs), 198 USDA-ARS Fort Collins (rs), 198 USDA-ARS Riverside (rs), 200 USDA-ARS Salinas (rs), 198 USDA-ARS Salt Lake City (rs), 200 USDA-ARS Waseca (rs), 200 V Vascular system, 34 Vascular tissue, 69–71, 99, 142, 205 Vector transmission, 65, 67, 68, 92, 111, 113, 147 Vernalization, 8, 18, 241 Viable seed, 8, 18 Vinasses, 182 Viral suppressor of RNA silencing (VSR), 66, 95, 99, 101 Virgaviridae, 75, 76, 110, 116, 147 Virgaviruses, 110–113 Viroplasm-like inclusions, 116 Virulence, 110, 125, 126, 209, 211 Virus concentration, 7, 68, 73, 124, 186, 202, 208, 236, 255 Virus-induced gene silencing (VIGS), 225 Virus-like sequence assembly (VLRAs), 114 281 Index of Names Virus particle, 43, 62–65, 69, 113, 147 Visual root evaluations, 234 Vitamins, 178 Vulgares, 159, 160 Wine glass shape, 177 World Beta Network, 214 World sugar consumption, 11 World sugar production, 11, 23 W Water excesses, 12, 36, 182 Water logging, 29, 40, 183 Water requirement, 13 Water uptake, 57–58, 181, 237 WB41 (wb), 241 WB42 (wb), 241 WB151 (PI546397) (wb), 209 WB258 (wb), 207 Webbiana (species), Weed, 8, 13–15, 121, 159–160, 162, 183 beet, 15 control, 13, 162 Western Sugar Company (sc), 200 Wheat spindle streak mosaic virus (WSSMV), 147, 161 White/extractable sugar, 23, 176, 178, 182, 199, 243, 244 Wild beet populations, 14 Wild Beta species, 214 Wilting, 34, 44, 58, 72, 237 X Xylem, 43, 69–71, 199 Xylematic tissues, 43 Xylem parenchyma, 69 Xylem vessels, 213 Y Yeast, 87, 96, 98, 99 Yeast two-hybrid screen, 72 Yield performances, 239 Z Z, NZ, N etc varieties, 36, 40 Zoosporangium, 138, 140–142 Zoospore, 43, 60–62, 69, 91, 100, 136–139, 141–143, 148–150, 156, 157, 160, 161, 163, 164, 166–168, 182, 183, 185, 186, 188, 203, 204, 210, 225, 237, 250, 251, 258, 259 .. .Rhizomania Enrico Biancardi • Tetsuo Tamada Editors Rhizomania Editors Enrico Biancardi Stazione Sperimentale di Bieticoltura... evolutions of rhizomania agents By means of interdisciplinary approaches, this book was edited above all to provide a broad, comprehensive, and updated overview of the various aspects of rhizomania, ... development and spread of rhizomania and to the development of molecular markers for novel sources of resistance Enrico Biancardi Classified as “Alba type” the multigenic rhizomania resistance carried