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Molecular characterisation and pathogenicity of the South African venturia inaequalis (apple scab) population
Thesis (PhD)--Stellenbosch University, 2016.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2016
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| _version_ | 1867614139056128000 |
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| access_status_str | Open Access |
| author | Koopman, Trevor Ashley |
| author2 | Lennox, Cheryl L. |
| author_browse | Koopman, Trevor Ashley Lennox, Cheryl L. |
| author_facet | Lennox, Cheryl L. Koopman, Trevor Ashley |
| author_sort | Koopman, Trevor Ashley |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhD)--Stellenbosch University, 2016. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/100082 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:47:17.083Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/100082 Molecular characterisation and pathogenicity of the South African venturia inaequalis (apple scab) population Koopman, Trevor Ashley Lennox, Cheryl L. Tobutt, K. R. Bester, Cecilia Meitz-Hopkins, Julia C. Stellenbosch University. Faculty of AgriSciences. Department of Plant Pathology. Venturia inaequalis (apple scab) Venturia inaequalis (apple scab) -- Molecular characterisation Apples -- Diseases and pests Apples -- Molecular genetics UCTD Thesis (PhD)--Stellenbosch University, 2016. ENGLISH ABSTRACT: Venturia inaequalis, the causal agent of apple scab, is one of the most important fungal diseases on apple, causing major economic crop losses in almost all the apple growing regions world-wide. The disease is mainly controlled by fungicides and requires between 6 and 15 applications, depending on the weather conditions, to effectively control the disease in South Africa. In this study, V. inaequalis samples were collected over two seasons from symptomatic leaves and fruit from the four principal apple growing regions of South Africa namely the Koue Bokkeveld, Elgin and the Upper and Lower Langkloof areas. This was to assess the genetic diversity, pathogenicity, virulence and determination of races occurring in these four South African V. inaequalis populations. A subset (129 and 139 isolates) of different apple scab isolates from the four apple growing regions were sequenced for specific gene areas of V. inaequalis including polymorphic virulence factors. Nucleotide variation was found within the ITS (four haplotypes) and ABC2-NB2 (six haplotypes) gene regions for the South African population. Four non-synonymous polymorphisms were detected in the ABC-NB2 gene region. Another subset of the ABC-NB2 gene region samples (20) was used to sequence two candidate effector genes (THN- and Vice16 genes) and polymorphism of between two to five nucleotide changes were found. The population structure of V. inaequalis from four South African apple growing regions was determined for the first time. Two sub-populations were found, with the Elgin population different from the others, when V. inaequalis isolates were genotyped with seven SSR- markers. Due to sexual outcrossing most of the genetic differences in the V. inaequalis population were found within the populations. High gene flow was observed due to the many migration events that had occurred between the regions. On the other hand, identical genotypes (clones) were found from two seasons in two regions, indicating overwintering asexual inoculum (conidia). In this study the V. inaequalis races occurring in South Africa were determined for the first time. The accessions ‘Royal Gala’ (0), ‘Golden Delicious’ (Rvi1), A723 (Rvi10) and ‘Hansen’s Baccata#2’ (Rvi12) were found to be susceptible with abundant sporulation on the leaves 14 days after inoculation. Single spore V. inaequalis isolates were used to inoculate different apple cultivars without dominant resistance genes. The single spore isolates differed with respect to their ability to infect and sporulate on these different cultivars. A qPCR method was also used to determine the infection level of the single spore isolates, and the results of the visual scoring and qPCR were comparable. The qPCR method seems to be reliable in detecting fungal DNA in asymptomatic host tissue and is useful for testing virulence between apple scab isolates. AFRIKAANS OPSOMMING: Venturia inaequalis wat appelskurf veroorsaak, is een die belangrikste swamsiektes op appels en veroorsaak wêreldwyd groot ekonomiesie oesverliese in byna alle appel-verbouingsgebiede. Die siekte word hoofsaaklik deur swamdoders beheer en afhangende van die weerstoestande, tussen 6 en 15 spuitebehandelings word vir effektiewe beheer vereis in Suid Afrika. In die studie was simptomatiese letsels op blare en vrugte van V. inaequalis vanaf vier verskillende appelverbouingsgebiede in Suid-Afrika naamlik, Koue Bokkeveld, Laer en Hoër Langkloof en die Elgin streek versamel. Die doel was om die populasie genetikastruktuur, virulensie en die veskillende appleskurfswamrasse te bepaal. ‘n Subgroep van verskillende appelskurfsiekte isolate uit die vier appelverbouings-gebiede, was vir variasie in spesifieke geengebiede van V. Inaequalis, waaronder ‘n hoogs polimorfiese virulensie faktor, ondersoek. Nukleotied variasie is in die ITS- (vier moontlike haplotipes) en ABC2-NB2 (ses moontlike haplotipes) geengebiede vir die Suid-Afrikaanse populasie gevind. Die nukleotied veranderinge in die ABC-NB2 geengebied is deur aminosuur veranderinge veroorsaak, met 'n hoë voorkoms van aantal sinoniem veranderinge. 'n Subgroep van die ABC-NB2 geengebied isolate (20) is gebruik om twee kandidaat effektor gene (THN- en Vice16 gene) te ondersoek en polimorfisme van tussen twee en vyf nukleotied veranderinge is gevind. Die populasie genetiese struktuur van V. inaequalis in verskillende appelverbouings-gebiede van Suid-Afrika is vir die eerste keer bepaal. Twee subpopulasies, met die Elgin streek verskillend van die ander drie streke, is deur van sewe SSR merkers te gebruik, gevind. Die meeste van die genetiese varaisie wat in die populasies gevind is, is a.g.v. die seksuele rekombinasie van V. inaequalis. Hoë geen-vloei, met migrasie tussen die vier verbouings-gebiede het voorgekom. Oorwintering van konidia kon tot die bevinding van dieselfde genotiepes (klone) oor twee seisoene bygedra het. Die V. inaequalis rasse is vir die eerste keer in Suid-Afrika bepaal. Die appelplante ‘Royal Gala’ (0), ‘Golden Delicious’ (Rvi1), A723 (Rvi10) en ‘Hansens baccata # 2’ (Rvi12) was vatbaar met baie sporulasie op die blare, 14 dae na inokulasie. Enkelspoor V. inaequalis isolate is gebruik om verskillende appelkultivars sonder dominante weerstandsgene te inokuleer. Die enkelspoor isolate verskil met betrekking tot hul vermoë om suksesvol te inokuleer en te sporuleer op verskillende kultivars. ‘n qPCR metode is ook gebruik om die infeksievlak van die enkelspoor isolate te bepaal en die resultate van die visuele simptoom evaluasie en qPCR was vergelykbaar. Die qPCR metode blyk betroubaar te wees in die opspoor van die swam DNA in asimptomatiese gasheerweefsel en is dus nuttig vir die toets van virulensie tussen appleskurf isolate. Doctoral 2016-12-22T13:13:10Z 2019-03-31T03:00:17Z 2016-12 Thesis http://hdl.handle.net/10019.1/100082 en_ZA Stellenbosch University 149 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Venturia inaequalis (apple scab) Venturia inaequalis (apple scab) -- Molecular characterisation Apples -- Diseases and pests Apples -- Molecular genetics UCTD Koopman, Trevor Ashley Molecular characterisation and pathogenicity of the South African venturia inaequalis (apple scab) population |
| title | Molecular characterisation and pathogenicity of the South African venturia inaequalis (apple scab) population |
| title_full | Molecular characterisation and pathogenicity of the South African venturia inaequalis (apple scab) population |
| title_fullStr | Molecular characterisation and pathogenicity of the South African venturia inaequalis (apple scab) population |
| title_full_unstemmed | Molecular characterisation and pathogenicity of the South African venturia inaequalis (apple scab) population |
| title_short | Molecular characterisation and pathogenicity of the South African venturia inaequalis (apple scab) population |
| title_sort | molecular characterisation and pathogenicity of the south african venturia inaequalis apple scab population |
| topic | Venturia inaequalis (apple scab) Venturia inaequalis (apple scab) -- Molecular characterisation Apples -- Diseases and pests Apples -- Molecular genetics UCTD |
| url | http://hdl.handle.net/10019.1/100082 |
| work_keys_str_mv | AT koopmantrevorashley molecularcharacterisationandpathogenicityofthesouthafricanventuriainaequalisapplescabpopulation |