TU Darmstadt / ULB / TUbiblio

Genetic Structure of Cydia pomonella Granulovirus Isolates and their Potential in Overcoming Resistance in Codling Moth

Fan, Jiangbin (2019)
Genetic Structure of Cydia pomonella Granulovirus Isolates and their Potential in Overcoming Resistance in Codling Moth.
Technische Universität Darmstadt
doi: 10.25534/tuprints-00008864
Dissertation, Erstveröffentlichung

Kurzbeschreibung (Abstract)

Cydia pomonella granulovirus (CpGV) is a highly virulent pathogen of codling moth (CM, Cydia pomonella L.) larvae. It has been developed to one of the most successful commercial baculovirus biocontrol agents used on hundred thousands of hectares of pome fruit production worldwide. In recent years, however, three types (I to III) of field resistance to CpGV as well as the existence of resistance-breaking CpGV isolates have been discovered, providing an ideal model for studying baculovirus-host adaptation. This thesis aims to elucidate the potential of recently collected isolates of CpGV from northwest China to infect susceptible and resistant CM colonies and to study the stability and restoration of type I resistance in laboratory rearing by mass-crossing and selection. To further explore the genotypic and biological differences of CpGV, the population structure of 20 CpGV isolates was analyzed on the basis of Illumina next generation sequence (NGS) data. The isolates included seven new Chinese CpGV isolates, termed CpGV-ZY, -JQ, -ALE, -KS1, -KS2, -ZY2 and -WW, the re-sequenced isolates CpGV-M, -S, -E2, -I12 and the Iranian isolate CpGV-I0X, as well as the active ingredients of commercial virus selections from MadexPlus, MadexMAX, MadexTOP (V15), V14, V34, V45 and Carpovirusine EVO2. First, resistance testing or full range bioassays were conducted to determine the resistance-breaking capacity or the median lethal concentration (LC50) of the Chinese CpGV isolates against susceptible and three resistant CM strains, representing type I to III resistance (Chapter 2). The isolates were further screened for the presence of the additional 2×12 bp repeat insertion in CpGV gene pe38 (ORF24), which had been proposed to be the target of type I resistance in the Mexican isolate CpGV-M. It was found that the isolates CpGV-JQ, -KS1 and -ZY2 could break type I resistance, though a distinct delay was observed in the infection process. The isolates followed the previously established “pe38 model” of resistance-breaking, except CpGV-WW, which lacked the 2×12 bp repeat involved in resistance-breaking but failed to overcome type I resistance. However, CpGV-WW was able to overcome type II and type III resistance. Correlation of bioassay results and the isolates’ pe38 repeat structure were in agreement with the potential role of pe38 as the major target for resistance in CpRR1, except for CpGV-WW. Second, resistance tests with CpGV-M revealed a certain decline of the resistance level of CM strain CpRR1, expressing type I resistance, after it had been reared for several years without virus pressure (Chapter 3). Therefore, two newly selected lines, CpRR1_F5 and CpRR1_F7, were established by mass crossing experiments combined with virus selection on CpGV-M. Resistance level of the newly selected lines was determined by full range bioassays. The successful selection process resulted in a 15- to 160-fold increase of the LC50 of CpRR1_F5 resistance compared to CpRR1, suggesting that the rearing in absence of virus selection was most likely the main factor involved the observed resistance decline of CpRR1. Additionally, some fitness costs of fecundity were recorded in the re-selected CpRR1_F5. Single-pair crossing of CpRR1_F5 and CpRR1-F7 with susceptible CM, followed by a resistance testing with a discriminating concentration of CpGV-M occlusion bodies, revealed a dominant but not fully sex-linked inheritance arguing for a partial change of previous genetic traits in CpRR1. Third, in Chapter 4 the genomic difference among seven new Chinese CpGV isolates could provide some answers for the virulence difference observed in bioassays. After Illumina NGS sequencing, the genome annotation and phylogenetic analyses of these isolates indicated that the genomes were highly conserved and related to known CpGV isolates, despite a considerable geographic distance. However, two new phylogenetic lineages, termed genome groups F (CpGV-JQ and -ZY2) and G (CpGV-ALE), were proposed in addition to previous phylogenetic genome groups A to E. The genetic composition of the isolates was further quantified on the basis of previously identified genome group specific single nucleotide polymorphisms (SNPs). In addition of 223 new SNP positions out of total 563 SNPs were detected against CpGV-M reference sequence, which represented virus characteristics of Chinese isolates. Whereas CpGV-WW was proposed to be genetically highly homogeneous, belonging to genome group E, the other six isolates were mixtures of at least two genotypes. Thereof CpGV-ZY, -KS1 and -KS2 were highly similar and were composed of variable ratios of genome group A (CpGV-M) and genome group E (CpGV-WW). Detailed quantification of the 12 bp repeat unit of pe38 corresponded to the results obtained from PCR and Sanger sequence analyses (Chapter 2). Fourth, to achieve a fully comprehensive perspective of CpGVs of different origin, 20 CpGV isolates, including twelve natural isolates from different geographic locations and eight selected CpGV strains, were analyzed together for the distribution and frequency of single nucleotide polymorphisms (SNPs) in NGS genome data and for the abundance of the 12 bp repeat unit in pe38 (Chapter 5). The results indicated that CpGV-M, -WW, -S and MadexPlus were genetically highly homogenous isolates with a low rate of polymorphisms, while other isolates were composed of two or more genome groups at different ratios. Based on hierarchical clustering on principal components (HCPC) analysis, six distinct clusters were proposed, which represents the previously proposed main phylogenetic lineages, though the insertions and deletions were not included in cluster analysis. Relative location of different isolates in HCPC further reflected the ratio of variable compositions of different genome groups. For the quantification of the proportions of 1-5×12 bp repeat units in the different CpGV isolates a “read counting” method was developed and showed a high diversity and less conserved characteristics in pe38 than literature reported before. The established methods for SNP quantification and HCPC analysis provide novel tools to decipher the molecular complexity of genome mixtures in virus isolates, thus depicting the population structure of baculovirus isolates in a more adequate form than genome consensus based analyses. In summary, the results in this thesis showed that resistance loss in CpRR1 is developing in laboratory under continuous rearing without virus pressure. Newly discovered CpGV isolates exhibited high potential for control of known types of field resistance of CM. The established methods to determine positional SNP distribution can be easily extended to other (baculo)viruses to assess isolate composition and genetic diversity and to study quality and stability of virus mixtures during propagation. It can be further applied to determine its potential for control of resistant CM on molecular level, since CpGV isolates with the similar virulence patterns were found to be grouped together considering their spatial location in factor map of HCPC. Understanding CpGV population structure and the genetic adaption between baculovirus and host insect give a crucial blueprint to improve current strategies of CpGV resistance management in the field.

Typ des Eintrags: Dissertation
Erschienen: 2019
Autor(en): Fan, Jiangbin
Art des Eintrags: Erstveröffentlichung
Titel: Genetic Structure of Cydia pomonella Granulovirus Isolates and their Potential in Overcoming Resistance in Codling Moth
Sprache: Englisch
Referenten: Jehle, Prof. Dr. Johannes ; Thiel, Prof. Dr. Gerhard
Publikationsjahr: 8 Mai 2019
Ort: Darmstadt
Datum der mündlichen Prüfung: 8 Mai 2019
DOI: 10.25534/tuprints-00008864
URL / URN: https://tuprints.ulb.tu-darmstadt.de/8864
Kurzbeschreibung (Abstract):

Cydia pomonella granulovirus (CpGV) is a highly virulent pathogen of codling moth (CM, Cydia pomonella L.) larvae. It has been developed to one of the most successful commercial baculovirus biocontrol agents used on hundred thousands of hectares of pome fruit production worldwide. In recent years, however, three types (I to III) of field resistance to CpGV as well as the existence of resistance-breaking CpGV isolates have been discovered, providing an ideal model for studying baculovirus-host adaptation. This thesis aims to elucidate the potential of recently collected isolates of CpGV from northwest China to infect susceptible and resistant CM colonies and to study the stability and restoration of type I resistance in laboratory rearing by mass-crossing and selection. To further explore the genotypic and biological differences of CpGV, the population structure of 20 CpGV isolates was analyzed on the basis of Illumina next generation sequence (NGS) data. The isolates included seven new Chinese CpGV isolates, termed CpGV-ZY, -JQ, -ALE, -KS1, -KS2, -ZY2 and -WW, the re-sequenced isolates CpGV-M, -S, -E2, -I12 and the Iranian isolate CpGV-I0X, as well as the active ingredients of commercial virus selections from MadexPlus, MadexMAX, MadexTOP (V15), V14, V34, V45 and Carpovirusine EVO2. First, resistance testing or full range bioassays were conducted to determine the resistance-breaking capacity or the median lethal concentration (LC50) of the Chinese CpGV isolates against susceptible and three resistant CM strains, representing type I to III resistance (Chapter 2). The isolates were further screened for the presence of the additional 2×12 bp repeat insertion in CpGV gene pe38 (ORF24), which had been proposed to be the target of type I resistance in the Mexican isolate CpGV-M. It was found that the isolates CpGV-JQ, -KS1 and -ZY2 could break type I resistance, though a distinct delay was observed in the infection process. The isolates followed the previously established “pe38 model” of resistance-breaking, except CpGV-WW, which lacked the 2×12 bp repeat involved in resistance-breaking but failed to overcome type I resistance. However, CpGV-WW was able to overcome type II and type III resistance. Correlation of bioassay results and the isolates’ pe38 repeat structure were in agreement with the potential role of pe38 as the major target for resistance in CpRR1, except for CpGV-WW. Second, resistance tests with CpGV-M revealed a certain decline of the resistance level of CM strain CpRR1, expressing type I resistance, after it had been reared for several years without virus pressure (Chapter 3). Therefore, two newly selected lines, CpRR1_F5 and CpRR1_F7, were established by mass crossing experiments combined with virus selection on CpGV-M. Resistance level of the newly selected lines was determined by full range bioassays. The successful selection process resulted in a 15- to 160-fold increase of the LC50 of CpRR1_F5 resistance compared to CpRR1, suggesting that the rearing in absence of virus selection was most likely the main factor involved the observed resistance decline of CpRR1. Additionally, some fitness costs of fecundity were recorded in the re-selected CpRR1_F5. Single-pair crossing of CpRR1_F5 and CpRR1-F7 with susceptible CM, followed by a resistance testing with a discriminating concentration of CpGV-M occlusion bodies, revealed a dominant but not fully sex-linked inheritance arguing for a partial change of previous genetic traits in CpRR1. Third, in Chapter 4 the genomic difference among seven new Chinese CpGV isolates could provide some answers for the virulence difference observed in bioassays. After Illumina NGS sequencing, the genome annotation and phylogenetic analyses of these isolates indicated that the genomes were highly conserved and related to known CpGV isolates, despite a considerable geographic distance. However, two new phylogenetic lineages, termed genome groups F (CpGV-JQ and -ZY2) and G (CpGV-ALE), were proposed in addition to previous phylogenetic genome groups A to E. The genetic composition of the isolates was further quantified on the basis of previously identified genome group specific single nucleotide polymorphisms (SNPs). In addition of 223 new SNP positions out of total 563 SNPs were detected against CpGV-M reference sequence, which represented virus characteristics of Chinese isolates. Whereas CpGV-WW was proposed to be genetically highly homogeneous, belonging to genome group E, the other six isolates were mixtures of at least two genotypes. Thereof CpGV-ZY, -KS1 and -KS2 were highly similar and were composed of variable ratios of genome group A (CpGV-M) and genome group E (CpGV-WW). Detailed quantification of the 12 bp repeat unit of pe38 corresponded to the results obtained from PCR and Sanger sequence analyses (Chapter 2). Fourth, to achieve a fully comprehensive perspective of CpGVs of different origin, 20 CpGV isolates, including twelve natural isolates from different geographic locations and eight selected CpGV strains, were analyzed together for the distribution and frequency of single nucleotide polymorphisms (SNPs) in NGS genome data and for the abundance of the 12 bp repeat unit in pe38 (Chapter 5). The results indicated that CpGV-M, -WW, -S and MadexPlus were genetically highly homogenous isolates with a low rate of polymorphisms, while other isolates were composed of two or more genome groups at different ratios. Based on hierarchical clustering on principal components (HCPC) analysis, six distinct clusters were proposed, which represents the previously proposed main phylogenetic lineages, though the insertions and deletions were not included in cluster analysis. Relative location of different isolates in HCPC further reflected the ratio of variable compositions of different genome groups. For the quantification of the proportions of 1-5×12 bp repeat units in the different CpGV isolates a “read counting” method was developed and showed a high diversity and less conserved characteristics in pe38 than literature reported before. The established methods for SNP quantification and HCPC analysis provide novel tools to decipher the molecular complexity of genome mixtures in virus isolates, thus depicting the population structure of baculovirus isolates in a more adequate form than genome consensus based analyses. In summary, the results in this thesis showed that resistance loss in CpRR1 is developing in laboratory under continuous rearing without virus pressure. Newly discovered CpGV isolates exhibited high potential for control of known types of field resistance of CM. The established methods to determine positional SNP distribution can be easily extended to other (baculo)viruses to assess isolate composition and genetic diversity and to study quality and stability of virus mixtures during propagation. It can be further applied to determine its potential for control of resistant CM on molecular level, since CpGV isolates with the similar virulence patterns were found to be grouped together considering their spatial location in factor map of HCPC. Understanding CpGV population structure and the genetic adaption between baculovirus and host insect give a crucial blueprint to improve current strategies of CpGV resistance management in the field.

Alternatives oder übersetztes Abstract:
Alternatives AbstractSprache

Das Cydia pomonella granulovirus (CpGV) ist ein hoch virulentes Pathogen der Larven des Apfelwicklers (= Obstmade) (CM, Cydia pomonella L.) und ist eines der erfolgreichsten kommerziellen Baculovirus-basierten biologischen Pflanzenschutzmittel; es wird weltweit auf mehreren hunderttausend Hektar im Kernobstanbau eingesetzt. In den letzten Jahren wurden drei Resistenztypen (I bis III) in Freilandpopulationen des Apfelwicklers gegenüber CpGV beobachtet, andererseits wurden aber auch Resistenz-brechende CpGV-Isolate entdeckt. Das System CpGV-Apfelwickler stellt somit ein ideales Model dar, die Interaktion und genetische Adaptation von Baculoviren und ihren Wirten zu untersuchen. Das Ziel dieser Dissertation ist die Evaluierung des Potentials kürzlich entdeckter CpGV-Isolate aus dem Nordwesten Chinas anfällige und resistente Apfelwicklerlinien zu infizieren, und die Stabilität und Wiederherstellung des Reistenzttyp I des Apfelwicklerstammes CpRR1 mittels Massenkreuzungen und viraler Selektion zu untersuchen. Um die genotypischen und biologischen Unterschiede des CpGV näher zu bestimmen, wurde die Populationsstruktur von 20 CpGV-Isolaten mittels Illumina next generation sequenzierung (NGS) charakterisiert. Diese umfassen sieben neue chinesische CpGV-Isolate, die als CpGV-ZY, -JQ, -ALE, -KS1, -KS2, -ZY2 und -WW bezeichnet wurden, die re-sequenzierten Isolate CpGV-M, -S, -E2, -I12 und das Iranische Isolate CpGV-I0X, sowie die Wirkstoffe der kommerziellen Selektionen MadexPlus, MadexMAX, MadexTOP (V15), V14, V34, V45 und Carpovirusine EVO2. Zunächst wurden Resistenztests oder Bioassays durchgeführt, um die Resistenz-brechenden Eigenschaftenoder die mittlere letale Konzentration (LC50) der sieben chinesischen CpGV-Isolate gegenüber anfälligen und resistenten Apfelwickler-Stämmen des Resistenztyps I-III zu bestimmen (Kapitel 2). Die Isolate wurden weiterhin auf das Vorhandensein der zusätzlichen 2×12 bp-Wiederholungsinsertion in CpGV-Gen pe38 (ORF24), das als Zielort des Resistenztyps I in CpGV-M gilt, mittels PCR und Sanger-Sequenzierung überprüft. Es wurde festgestellt, dass die Isolate CpGV-JQ, -KS1 und -ZY2 den Resistenztyp I brechen, obgleich eine deutliche Verzögerung im Infektionsverlauf zu beobachten war. Alle Isolate folgten dem früher etablierten „pe38-Modell“ der Resistenzbrechung, mit Ausnahme von CpGV-WW. Dieses Isolat beherbergte zwar den genetischen Faktor zur Resistenzbrechung, zeigte aber eine geringe Virulenz gegenüber CpRR1 (Resistenztyp I), andererseits jedoch eine hohe Aktivität gegenüber Apfelwicklerstämmen des Resistenztyps II und III. Der Zusammenhang der Ergebnisse aus den Infektionsversuchen und die Kartierung der 12 bp-Wiederholungen in den einzelnen Isolaten stützen ganz überwiegend die frühere Hypothese, dass pe38 das Hauptziel des Resistenztyps I ist. Zweitens, Resistenztests mit CpGV-M zeigten eine gewisse Abnahme des Resistenzniveaus des Apfelwickler-Stammes CpRR1 (Resistenztyps I), nachdem dieser Stamm mehrere Jahre ohne Virusdruck gehalten worden war (Kapitel 3). Daher wurden zwei neu selektierte Apfelwicklerlinien, CpRR1_F5 und CpRR1_F7, durch Massenkreuzungen in Verbindung mit einer Selektion durch CpGV-M etabliert. Das Resistenzniveau der neu ausgewählten Linien wurde mittels Bestimmung der mittleren letalen Konzentration (LC50) ermittelt. Das erfolgreiche Selektionsverfahren führte zu einem 15- bis 160-fachen Anstieg des LC50-Wertes von CpRR1_F5 gegenüber CpRR1, was darauf hindeutete, dass die mehrjährige Zucht ohne Virusselektion die Hauptursache gewesen sein könnte, die zu dem beobachteten Resistenzverlust von CpRR1 geführt hatte. Zudem wurden Fitnesskosten in Bezug aud die Fertilität der Linie CpRR1_F5 erfasst. Einzelpaarkreuzungen von CpRR1_F5 und CpRR1_F7 mit einer anfälligem Apfelwicklerlinie, gefolgt von einem Resistenztest mit einer diskriminierenden Konzentration von CpGV-M Einschlusskörpern, ergab eine dominante, aber nicht vollständig geschlechtsgebundene Vererbung der Resistenz, die auf eine partielle Veränderung des ursprünglichen genetischen Merkmals von CpRR1 hinweist. Da die genomischen Unterschiede zwischen den sieben Chinesischen CpGV-Isolaten mit ihrer biologischen Aktivitäten korreliert sein könnten, wurden deren Genome mittels Illumina NGS sequenziert (Kapitel 4). Die Genomannotation und die phylogenetischen Untersuchungen zeigten, dass deren Genome trotz der beträchtlichen geographischen Entfernung zu anderen Herkunftsorten des CpGV stark konserviert waren und Verwandtschaften mit anderen bekannten CpGV-Isolaten aufwiesen. Zusätzlich zu den bereits früher definierten phylogenetischen CpGV-Genomgruppen A bis E wurden zwei weitere Genomgruppen F (CpGV-JQ und -ZY2) und G (CpGV-ALE) gefunden. Die genetische Zusammensetzung der sieben CpGV-Isolate wurde anhand früher identifizierter Genomgruppen-spezifischer Einzelnukleotidpolymorphismen (single nucleotide polymorphisms, SNPs) quantifiziert. Im Vergleich zum bisherigen Kenntnisstand der genetischen Diversität des CpGV wurden in den neuen CpGV-Isolaten 223 neue SNP-Positionen von insgesamt 563 SNPs gegenüber der Referenzsequenz des CpGV-M nachgewiesen, die Sequenzsignaturen chinesischer CpGV-Isolate darstellten. Basierend auf der SNP-Verteilung wurde das Isolat CpGV-WW als ein sehr homogenes Isolat der Genomgruppe E klassifiziert, während die sechs anderen Isolate Mischungen von mindestens zwei Genotypen darstellten: die Isolate CpGV-ZY, -KS1 und -KS2 waren sehr ähnlich zu einander und bestanden aus einem variablen Verhältnis von Isolaten der Genomgruppe A (CpGV-M) und der Genomgruppe E (CpGV-WW). Eine detaillierte Quantifizierung der 12-bp-Wiederholungseinheit im Gen pe38 entsprach den mittels PCR und Sanger-Sequenzierung erhaltenen Ergebnissen aus Kapitel 2. Um einen umfassenden Blick auf die genetische Diversität von 20 CpGV-Isolaten verschiedener Herkünfte, einschließlich zwölf geografischer Isolate und acht selektierten CpGV-Stämmen, zu werfen, wurden die Verteilung und die Häufigkeit von SNPs und das Vorkommen der 12 bp-Wiederholung im Gen pe38 untersucht (Kapitel 5). Die Ergebnisse zeigten, dass CpGV-M, -WW, -S und MadexPlus genetisch sehr homogene Isolate mit einer sehr niedrigen Rate an Polymorphismen waren, während andere Isolate Mischungen aus zwei oder mehr Genomgruppen mit unterschiedlichen Verhältnissen zusammengeordnet werden konnten. Basierend auf einer Hauptkomponentenanalyse und hierarchischen Clusterung (HCPC) der Häufigkeitsverteilungen aller SNPs wurden die 20 CpGV-Genome in sechs verschiedene Cluster eingeordnet, die den früher vorgeschlagenen phylogenetischen Hauptlinien des CpGV entsprechen. Insertionen und Deletionen wurden bei der Clusterung nicht berücksichtigt. Die relative Lage des verschiedenen Isolate innerhalb der HCPC-Analyse spiegelte ferner das Verhältnis der variablen Zusammensetzungen verschiedener Genomgruppen wider. Die Messung des Anteils der 1-5×12 bp-Wiederholungseinheiten des pe38 in den verschiedenen Isolaten wurde unter Verwendung einer „Read-Counting“-Methode optimiert und zeigte eine sehr hohe Variabilität dieser Wiederholungsstruktur innerhalb der einzelnen CpGV-Isolate. Die etablierten Methoden der SNP-Quantifizierung und HCPC-Analyse bieten neuartige Werkzeuge zur Entschlüsselung der molekularen Komplexität von Genomgemischen in Virusisolaten, wodurch die Populationsstruktur von Baculovirus-Isolaten in einer angemesseneren Form als durch Analysen, die auf Konsensussequenzen der Genome beruhen, dargestellt werden kann. Zusammenfassend haben die Ergebnisse dieser Arbeit gezeigt, dass sich der Resistenzverlust von CpRR1 im Labor durch dauerhafte Zucht ohne Virusdruck entwickelte und nur teilweise re-selektiert werden konnte. Neu entdeckte CpGV-Isolate aus China sind potenziell für die Bekämpfung von Apfelwicklerpopulationen mit CpGV-Resistenz geeignet. Die Untersuchung der genetischen Diversität und der Populationsstruktur CpGV-Isolaten mit unterschiedlicher Herkunft bieten nicht nur einen vertieften und detaillierten Einblick in die molekular Diversität des CpGV in Korrelation mit seinen Virulenzeigenschaften, sowie einen wichtigen Beitrag zum Verständnis der gegenseitigen Anpassung zwischen Baculovirus und ihren Wirtsinsekten, sondern liefern auch entsprechende genetische Informationen um die derzeitigen Strategien des Resistenzmanagements bei CpGV weiterzuentwickeln.

Deutsch
URN: urn:nbn:de:tuda-tuprints-88643
Sachgruppe der Dewey Dezimalklassifikatin (DDC): 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
Fachbereich(e)/-gebiet(e): 10 Fachbereich Biologie
10 Fachbereich Biologie > Microbial Control / Insect Virology and Molecular Insect Pathology
Hinterlegungsdatum: 18 Jun 2020 09:45
Letzte Änderung: 23 Jun 2020 05:13
PPN:
Referenten: Jehle, Prof. Dr. Johannes ; Thiel, Prof. Dr. Gerhard
Datum der mündlichen Prüfung / Verteidigung / mdl. Prüfung: 8 Mai 2019
Export:
Suche nach Titel in: TUfind oder in Google
Frage zum Eintrag Frage zum Eintrag

Optionen (nur für Redakteure)
Redaktionelle Details anzeigen Redaktionelle Details anzeigen