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Grapevine leafroll-associated virus type 3 (GLRaV-3) is the major causative agent of grapevine leafroll disease. The disease has a major negative impact on grape production for wineries, and can cause up to 62.8% loss in production. Despite the negative impact of GLRaV-3 on the grapevine industry worldwide, knowledge on the variability of the virus, which is essential for developing effective control measure of the virus in vineyards, is surprisingly scarce. To test this, six primers sets used in a one tube, one step polymerase chain reaction (PCR) protocol, together with ELISA were used to detect GLRaV-3 virus in 135 plant samples collected from a single vineyard. As expected the more sensitive PCR detected more infected samples than ELISA. However, some samples yielded positive results with the ELISA, but negative results using PCR. This might suggest that strain variants exist. Amongst PCR results of the different primer sets, anomalous results occurred, as often a plant will yield an amplicon with one primer set, but not with another primer set. Using the entire set of 7 PCR results per sample, each plant was assigned a PCR ‘fingerprint’. This yielded 24 different fingerprints in the vineyard. Mapping the spatial distribution of given fingerprints supported the possibility that strain variants exist. However, sequencing areas incorporating the primer binding sites showed no nucleotide sequence differences, indicating that the anomalous PCR results were not due to variants, but rather to protocol error. The PCR protocol used initially was adapted to obtain more optimal detection of virus. Different extraction methods and PCR protocols were tested. It was found that using the two step RT-PCR and using a less dilute plant macerate in ELISA extraction buffer (1:5), yielded amplicon of the expected size from all known infected plant samples. The protocol was further optimized with regards the RT step and subsequent PCR. Since the modified protocol did detect all known infected plant samples it can be concluded that in the 135 plant samples tested no significant sequence variation in strains at the primer binding sites occurred and that the anomalous PCR results initially obtained were due to a sub-optimal extraction method. / Dissertation (MSc (Microbiology))--University of Pretoria, 2008. / Microbiology and Plant Pathology / unrestricted

O vírus da tristeza dos citros (CTV) é uma das maiores ameaças à citricultura mundial. No Brasil, mesmo com a pré-imunização e com a substituição de porta-enxertos, estirpes fortes de CTV ainda causam prejuízos consideráveis. Com o aparecimento da Morte Súbita dos Citros em 1999 e a possível relação desta doença com o CTV, este vírus voltou a figurar como patógeno de importância no cenário da citricultura brasileira. Uma das possíveis soluções para o controle de viroses em fruteiras é a obtenção de plantas transgênicas resistentes ou imunes. O objetivo deste trabalho foi avaliar a resistência ao CTV de plantas transgênicas de laranja \'Hamlin\' contendo três construções gênicas oriundas de seqüências do genoma do CTV. Estas construções gênicas visaram ativar rotas de RNAi (hairpin da capa protéica e seqüência conservada antisenso do CTV) e mecanismos de defesa relacionados à expressão da capa protéica do CTV. As plantas transgênicas foram desafiadas com uma estirpe fraca de CTV (CTV-IAC) por meio de borbulhas e pulgões pretos (Toxoptera citricida Kirkaldy) contendo o vírus. A avaliação da resistênica à replicação viral foi feita por análises de ELISA. As plantas transgênicas foram consideradas não resistentes à infecção e translocação viral quando inoculadas com borbulhas. Entretanto algumas plantas mostraram retardamento da infecção. Não foi possível determinar se houve resistência à transmissão de CTV por pulgões já que a técnica utilizada não foi capaz de infectar os controles de maneira uniforme. / The Citrus tristeza virus (CTV) is one of the greatest threats to the citrus industry worldwide. In Brazil, CTV continues to cause damage through strong strains despite the use of techniques like cross-protection and substitution of intolerant rootstocks. With the appearance and spread of the Citrus Sudden Death disease in 1999 and its possible relation to CTV, this virus was again among important pathogens within the Brazilian citrus industry. One of the possible solutions for controlling virus diseases in fruit crops is the development of immune or resistant transgenic plants. The objective of this work was to evaluate the resistance to CTV of transgenic \'Hamlin\' sweet orange plants containing three transgenic constructs obtained from CTV genomic sequences. The genetic constructs used aimed to activate RNAi defense routes (coat protein hairpin and a conserved sequence from CTV) and resistance mechanisms related to the coat protein expression. The transgenic plants were challenged with a weak strain of CTV, CTV-IAC, by bud and aphid (Toxoptera citricida Kirkaldy) inoculation. The evaluation of viral replication was done by ELISA analysis. The transgenic plants were considered susceptible to viral replication and translocation when bud inoculated. However, a few plants showed retardation of infection. It was not possible to determine resistance in the aphid transmission assay since the controls were not uniformly inoculated.

O vírus da tristeza dos citros (CTV) é uma das maiores ameaças à citricultura mundial. No Brasil, mesmo com a pré-imunização e com a substituição de porta-enxertos, estirpes fortes de CTV ainda causam prejuízos consideráveis. Com o aparecimento da Morte Súbita dos Citros em 1999 e a possível relação desta doença com o CTV, este vírus voltou a figurar como patógeno de importância no cenário da citricultura brasileira. Uma das possíveis soluções para o controle de viroses em fruteiras é a obtenção de plantas transgênicas resistentes ou imunes. O objetivo deste trabalho foi avaliar a resistência ao CTV de plantas transgênicas de laranja \'Hamlin\' contendo três construções gênicas oriundas de seqüências do genoma do CTV. Estas construções gênicas visaram ativar rotas de RNAi (hairpin da capa protéica e seqüência conservada antisenso do CTV) e mecanismos de defesa relacionados à expressão da capa protéica do CTV. As plantas transgênicas foram desafiadas com uma estirpe fraca de CTV (CTV-IAC) por meio de borbulhas e pulgões pretos (Toxoptera citricida Kirkaldy) contendo o vírus. A avaliação da resistênica à replicação viral foi feita por análises de ELISA. As plantas transgênicas foram consideradas não resistentes à infecção e translocação viral quando inoculadas com borbulhas. Entretanto algumas plantas mostraram retardamento da infecção. Não foi possível determinar se houve resistência à transmissão de CTV por pulgões já que a técnica utilizada não foi capaz de infectar os controles de maneira uniforme. / The Citrus tristeza virus (CTV) is one of the greatest threats to the citrus industry worldwide. In Brazil, CTV continues to cause damage through strong strains despite the use of techniques like cross-protection and substitution of intolerant rootstocks. With the appearance and spread of the Citrus Sudden Death disease in 1999 and its possible relation to CTV, this virus was again among important pathogens within the Brazilian citrus industry. One of the possible solutions for controlling virus diseases in fruit crops is the development of immune or resistant transgenic plants. The objective of this work was to evaluate the resistance to CTV of transgenic \'Hamlin\' sweet orange plants containing three transgenic constructs obtained from CTV genomic sequences. The genetic constructs used aimed to activate RNAi defense routes (coat protein hairpin and a conserved sequence from CTV) and resistance mechanisms related to the coat protein expression. The transgenic plants were challenged with a weak strain of CTV, CTV-IAC, by bud and aphid (Toxoptera citricida Kirkaldy) inoculation. The evaluation of viral replication was done by ELISA analysis. The transgenic plants were considered susceptible to viral replication and translocation when bud inoculated. However, a few plants showed retardation of infection. It was not possible to determine resistance in the aphid transmission assay since the controls were not uniformly inoculated.

Thesis (PhD (Genetics))--University of Stellenbosch, 2011. / Includes bibliography / ENGLISH ABSTRACT: Grapevine diseases, in particular virus and virus-like diseases, are threatening grapevine industries worldwide; also in South Africa. Grapevine leafroll (GLR) is one of the most important diseases of grapevines, occurring in all grape-producing countries worldwide. Grapevine leafroll-associated virus 3 (GLRaV-3) is known to be closely associated with GLR disease and occurs commonly in South African vineyards. In this study three genetic variants of GLRaV-3 were identified in vineyards of the Western Cape, South Africaby single strand conformation polymorphism (SSCP) profiles generated from a region amplified in ORF5. A specific SSCP profile could be assigned to each variant group and these wereconfirmed by sequencing of the ORF5 regions.These results demonstrated that SSCP analysis on this region in ORF5 provides a fast and reliable indication of the GLRaV-3 variant status of a plant, which in many instances showed mixed infections. The full genome sequence of one representative of each variant group i.e. isolates 621 (group I), 623 (group II) and PL-20 (group III), was determined by sequencing overlapping cloned fragments of these isolates. The sequences of genomic 5’ ends of these isolates were determined by RLM-RACE. Sequence alignment of the 5’UTRs indicated significant sequence and length variation in this region, between the three South African variant groups. Nucleotide sequence alignment of the Hsp70h and CP gene regions of these isolates with those of isolates from elsewhere in the world, followed by phylogenetic analysis, further supported the presence of three GLRaV-3 variants in South Africa, and that two or three additional variant groups occurs elsewhere in the world. We further investigated the prevalence of these three GLRaV-3 variants in mother blocksof different cultivars and from different vine growing regions, using SSCP analysis. The majority of the plants studied, were infected with the group II variant, similar to isolates 623 and GP18. The distribution of the three GLRaV-3 variants within a spatio-temporally recorded cluster of diseased plants was studied by means of SSCP profile analysis. We showed that different GLRaV-3 variants are transmitted to adjacent plants in an infection cluster. Results showed that, in some leafroll disease clusters, the variant that was present in the original GLRaV-3 infected plant of a cluster was transmitted to adjacent plants in a row and across rows. Some plants in the cluster were also infected with variants not present in the original plant. These infections could have been caused by mealybug vectors feeding on plants from surrounding areas and then infecting these plants. The scientific information generated on GLRaV-3 variants in this project contributed to the advancement of our knowledge of genetic variability and provides a basis of further epidemiology and vector-virus studies. The study showed for the first time that different GLRaV-3 variants were transmitted to adjacent plants in a row and across rows in a GLR disease cluster. The diversity detected in the 5’UTR between variants from the three genetic groups provides a platform for the further study of the biological characteristics of GLRaV-3 variants. / AFRIKAANSE OPSOMMING: Wingerdsiektes, veral virus siektes, bedreig wingerd industrieë wêreldwyd, asook die Suid Afrikaanse wingerdbedryf. Rolbladsiekte is een van die belangrikste siektes op wingerd en kom wêreldwyd voor. Die virus, grapevine leafroll-associated virus 3 (GLRaV-3), word sterk geassosieer met Rolbladsiekte en kom wydverspreid voor in Suid Afrikaanse wingerde. Tydens hierdie studie is drie genetiese variante van GLRaV-3 geïdentifiseer in wingerd moederblokke in die Wes-Kaap. Die GLRaV-3 variante is geïdentifiseer met ‘n tegniek wat ‘single-strand conformation polymorphism (SSCP)’ genoem word. Die SSCP profiele was gegenereer vanaf PKR produkte van die ORF5 area op die genoom van GLRaV-3. Die geamplifiseerde produk van die ORF5 gebied is gebruik om die SSCP profiele te verkry en DNA-volgorde data in die gebied het die drie SSCP profiele gestaaf. Hierdie metode om virus variasie te bestudeer in plante is vinnig en betroubare resultate is verkry. Gemengde infeksies, wat gereeld in wingerd voorkom, kon ook met die tegniek opgespoor word. Die volledige nukleotied-volgorde van elkeen van die drie GLRaV-3 genome is volledig bepaal. Die isolate wat die drie variant groepe verteenwoordig is isolaat 621 (groep I), 623 (groep II) en PL-20 (groep III). Die nukleotiedvolgorde in die 5’UTR is bepaal met die RLM-RACE tegniek. Wanneer die 5’UTRs van die drie variante vergelyk is, het dit getoon dat daar verskille is in die volgordes en lengtes voorgekom het. Ander dele van die genoom, o.a. die dopproteïen (CP) en Hsp70 areas, is filogeneties vergelyk met isolate van regoor die wêreld. In die filogenetiese analise is bevind dat die drie GLRaV-3 variante saamgegroepeer het met ander isolate in die wêreld en dat daar elders ook twee to drie addisionele variant groepe van GLRaV-3 voorkom. Die verspreiding van die drie GLRaV-3 variante in wingerde is bestudeer in verskillende kultivars en in verskillende verbouingsgebiede. Die meerderheid van die plante in die studie was geïnfekteer met die groep II variant wat dieselfde is as isolate 623 en GP18. Die voorkoms van die drie variante in ‘n siekte cluster is bestudeer d.m.v SSCP. Die studie het gewys dat verskillende GLRaV-3 variante versprei word na aangrensende plante in ‘n ry en tussen rye. In sommige gevalle is die variant wat in die oorspronklik geïnfekteerde plant voorkom, oorgedra na naasliggende plante. Sommige van die plante in the infeksie area was ook met ander GLRaV-3 variante geïnfekteer wat moontlik deur wolluise oorgedra is vanaf naburige geïnfekteerde plante. Die wetenskaplike inligting wat tydens hierdie studie beskryf word aangaande die identifikasie van GLRaV-3 variante, dra by tot die molekulêre kennis van GLRaV-3 en verskaf ‘n basis vir verdure epidemiologiese -en insek oordragingstudies. Die studie het vir die eerste keer bewys dat verskillende GLRaV-3 variante na aanliggende plante in ‘n ry asook oor rye oorgedra word. Die diversiteit tussen die GLRaV-3 variant groepe in die 5’UTR moet verder ondersoek word en die deel van die genoom kan ‘n belangrike rol speel in die biologiese eienskappe van die variante.

El virus de la tristeza de los cítricos (Citrus tristeza virus; CTV) es el agente causal de unas de las enfermedades virales de los árboles cítricos más devastadoras en el mundo. CTV está restringido al floema en su huésped cítrico natural, y ha desarrollado tres proteínas supresoras de silenciamiento que actúan a nivel intra-(p23 y p20) e intercelular (p20 y p25) para superar la fuerte defensa antiviral del huésped. La interferencia de RNA, una aproximación basada en el uso de dsRNA para desencadenar el silenciamiento de RNA, ha sido utilizada ampliamente para generar plantas transgénicas resistentes a virus. Considerando el importante papel de p23, p20 y p25 en la patogénesis de CTV, hemos transformado plantas de lima Mexicana con un vector intrón-horquilla que porta la secuencia completa en versión no traducible de los genes p25, p20, p23 y el extremo 3¿-UTR de la cepa T36 de CTV, para intentar silenciar su expresión en células infectadas. Se ha observado resistencia completa a la infección viral en tres líneas transgénicas, manteniéndose todas sus propagaciones asintomáticas y libres de virus tras ser inoculadas mediante injerto con CTV-T36, tanto en el portainjertos no transgénico como directamente sobre la variedad transgénica. La acumulación de siRNA derivados del transgén fue necesaria pero no suficiente para lograr resistencia frente a CTV en las plantas. Al inocular propagaciones de las líneas transgénicas inmunes con una cepa de CTV divergente, la resistencia fue parcialmente superada, destacando la importancia de la identidad de secuencia en el mecanismo subyacente a la interferencia de RNA. Este trabajo es el primero en que se consigue resistencia completa a CTV en un huésped cítrico muy sensible, actuando simultáneamente sobre los tres supresores virales de silenciamiento mediante interferencia de RNA. La proteína p23 codificada por el virus es además un importante factor de patogenicidad. La expresión ectópica de p23 en plantas de cítricos induce aberraciones fenológicas semejantes a síntomas de CTV. Para estudiar en más detalle el papel de p23 en la patogénesis de CTV, se ha sobre-expresado en lima Mexicana el gen p23 de CTV T36 y tres versiones truncadas del mismo bajo el control del promotor 35S del virus del mosaico de la coliflor (Cauliflower mosaic virus). Solo la versión truncada, que expresa los aminoácidos del 1 al 157 (p23-¿157) indujo síntomas similares a los producidos por CTV, aunque más suaves que los inducidos por la expresión de la proteína p23 entera (209 aminoácidos), permitiendo delimitar la región responsable de la patogénesis de p23 en cítricos a un fragmento de 157 aminoácidos que incluye el dedo de zinc y los motivos básicos flanqueantes de la proteína. La actividad de p23 como supresor de silenciamiento de RNA en N. benthamiana se perdía en todos los mutantes de p23 probados, lo cual indica que la supresión de silenciamiento implica a la mayoría de las regiones de la proteína. Para profundizar más en el papel de p23 en la patogénesis, en un siguiente paso hemos restringido la expresión de transgenes derivados de p23 a células asociadas al floema de lima Mexicana mediante el uso del promotor especifico de floema del virus del moteado amarillo de la comelina (Commelina yellow mottle virus, CoYMV). Se transformó lima Mexicana con construcciones que portaban el gen p23 completo, ya sea de la cepa agresiva de CTV T36 o de la suave T317, o con un fragmento que comprende el dedo de zinc y los motivos básicos flanqueantes de la primera, todas ellas bajo el control bien del promotor de CoYMV o bien del promotor constitutivo 35S. La expresión de estas construcciones en el floema dio lugar a aberraciones semejantes a los síntomas específicos de CTV, pero no a los síntomas inespecíficos observados cuando se expresaba p23 de forma constitutiva. Por otra parte, la apariencia e intensidad de las aberraciones fenotípicas más notorias similares a síntomas inducidos por CTV generadas por la expresión específica en floema del gen p23 se relacionó positivamente con la agresividad de la cepa origen utilizada. Además, la expresión en tejidos floemáticos del fragmento de p23 que comprende el dominio de dedo de zinc y los motivos básicos flanqueantes fue suficiente para inducir síntomas semejantes a los producidos por la infección con CTV, confirmando así que la región N-terminal delimitada por los aminoácidos 1 y 157 podría determinar, al menos en parte, la patogénesis de CTV en lima Mexicana. / Citrus tristeza virus (CTV) is the causal agent of one of the most devastating viral diseases of citrus trees in the world. CTV is phloem-restricted in natural citrus hosts, and has evolved three silencing suppressor proteins acting at intra- (p23 and p20) and inter-cellular level (p20 and p25) to overcome strong host antiviral defense in citrus. RNA interference (RNAi), an approach based on using dsRNA to trigger RNA silencing, has been widely used for generating transgenic plants resistant against viruses. Considering the important role of p23, p20 and p25 in CTV pathogenesis, we have transformed Mexican lime plants with an intron-hairpin vector carrying full untranslatable versions of genes p25, p20, p23 and the 3¿-UTR from the CTV strain T36, to attempt silencing their expression in CTV-infected cells. Complete resistance to viral infection was observed in three transgenic lines, with all their propagations remaining symptomless and virus-free after graft-inoculation with CTV-T36, either in the non-transgenic rootstock or directly in the transgenic scion. Accumulation of transgene-derived siRNAs was necessary but not sufficient for CTV resistance. Challenging immune transformants with a divergent CTV strain resulted in partial breakage of the resistance, stressing the importance of sequence identity in the underlying RNAi mechanism. This is the first evidence that it is possible to achieve full resistance to CTV in a highly sensitive citrus host by targeting simultaneously its three viral silencing suppressors through RNAi. The p23 protein encoded by the virus is additionally an important pathogenicity factor. Ectopic expression of p23 in transgenic citrus plants induces developmental aberrations resembling CTV symptoms. To explore in more detail the role of p23 in CTV pathogenesis, the p23 gene from CTV T36 and three truncated versions thereof under the control of the Cauliflower mosaic virus 35S promoter were used to transform Mexican lime. Only the truncated version expressing amino acids 1 to 157 (p23¿158-209) elicited CTV-like symptoms, similar to, albeit milder than, those incited by expressing the whole p23 protein (209 amino acids), thus delimiting the region responsible for p23 pathogenesis in citrus to a 157 amino acid fragment including the Zn finger and flanking basic motifs of the protein. RNA silencing suppressor activity of p23 in N. benthamiana was abolished by all mutants tested, indicating that silencing suppression involves most p23 regions. To better define the role of p23 in CTV pathogenesis, we next restricted the expression of p23-derived transgenes to phloem-associated cells in Mexican lime plants by means of using the phloem-specific promoter from Commelina yellow mottle virus (CoYMV). Constructions carrying the complete gene p23 from either the severe T36 or the mild T317 CTV strains, or a fragment comprising the zinc-finger and flanking basic motifs from the former, either under the control of the CoYMV promoter or the constitutive 35S promoter were used for genetic transformation of Mexican lime. Expression of these constructs in the phloem incited aberrations resembling CTV-specific symptoms, but not the unspecific symptoms observed when p23 was constitutively expressed. Moreover, appearance and intensity of the most notorious CTV-like phenotypic aberrations induced by the phloem-specific expression of the p23 gene were positively related with the aggressiveness of the source CTV strain used. Additionally, expression in phloem-tissues of the p23 fragment comprising the zinc-finger domain and flanking basic motifs was sufficient to induce CTV-like symptoms, corroborating that the N-terminal region (delimited by amino acids 1 and 157) determines, at least in part, CTV pathogenesis in Mexican lime. / Soler Calvo, N. (2013). Transgenic resistance against Citrus tristeza virus (CTV) and analysis of the viral p23 protein as pathogenicity determinant in citrus [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/31631 / TESIS