Assessing Phytophthora cinnamomi seasonal root colonisation patterns and pathogen response to management practices (phosphonates and rootstock tolerance) in South African avocado orchards
| dc.contributor.advisor | McLeod, Adele | en_ZA |
| dc.contributor.advisor | Dann, Elizabeth | en_ZA |
| dc.contributor.author | Jolliffe, Jenna Bryanne | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of AgriSciences. Dept. of Plant Pathology. | en_ZA |
| dc.date.accessioned | 2019-02-22T10:55:21Z | |
| dc.date.accessioned | 2019-04-17T08:09:00Z | |
| dc.date.available | 2021-12-01T03:00:11Z | |
| dc.date.issued | 2019-04 | |
| dc.description | Thesis (MScAgric)--Stellenbosch University, 2019. | en_ZA |
| dc.description.abstract | ENGLISH ABSTRACT: Phytophthora root rot (PRR), caused by Phytophthora cinnamomi (Pc), is a destructive soilborne disease that can cause major economic losses in commercial avocado orchards. Despite this, there is limited information on the pathogen’s seasonal colonisation patterns, as well as which sampling strategy and quantification method would be best for assessing it. Current limitations in Pc quantification methods can lead to inaccurate assessments of PRR management strategies including phosphonate fungicides and PRR-tolerant rootstocks. The current study was able to identify a peak in seasonal Pc root colonisation in late autumn (May) in mature avocado orchards situated in two main production regions (Mooketsi and Letaba) in the Limpopo province of South Africa. During two investigated growing seasons (2017 and 2018), Pc root quantities were significantly higher in May 2018 than in March (early autumn), August (late winter) and October/November (late spring) of the same season (2018). In 2017, colonisation trends were less evident, which is likely due to the less conducive PRR conditions that prevailed, especially in the Mooketsi region. In Letaba (2017), August and May yielded the highest Pc root quantities in most orchards, but these did not differ significantly from the other months (March and October/November). In May, Pc root quantities were furthermore significantly positively correlated with the number of hours at soil temperatures of 15-19°C, but negatively with 20-24°C. Soil moisture fluctuations were not associated with Pc root quantities. Evaluation of two sampling strategies consisting of four tree groups (each containing five trees) and one tree group (20 trees), showed that both approaches are suitable for investigating Pc colonisation patterns. A traditional root baiting method, where leaf baits were plated onto selective media, was as effective in identifying colonisation trends as a molecular approach using small-scale root DNA extractions and quantitative real-time PCR (qPCR) analysis. A large-scale root DNA extraction and qPCR analysis method was deemed less effective. A molecular quantification (qPCR) approach was shown to be ineffective for evaluating two management strategies (phosphonate treatments and rootstock tolerance) in avocado orchards showing no obvious aboveground symptoms of PRR decline. Although root phosphite (breakdown product of phosphonates) concentrations of a 2x trunk injection treatment applied at the preventative dosage (0.3 g a.i./m2) were significantly higher than the untreated control, the Pc root and soil DNA concentrations were not significantly reduced by the phosphite, relative to the untreated control. This was for quantifications conducted in either May or October 2018 and using the best of three evaluated Pc-specific qPCR assays. The potentially more PRR-tolerant R0.06 rootstock yielded higher Pc root DNA concentrations than the Dusa® rootstock in November 2017, but not in the other two sampling months (March and May 2018). The identification of effective sampling strategies, Pc root quantification methods and the Pc root colonisation patterns in avocado orchards in the current study is important. Since May had the highest root colonisation levels, PRR management practices should be put in place to achieve optimal root protection during, or just prior to, this period (late autumn). The effective sampling and quantification methods that were identified for studying seasonal root colonisation patterns in avocado, will be useful for other studies that are conducted on the over 5000 host plant species of Pc. Alternative quantification methods to qPCR for assessing management strategies must be investigated. However, it is possible that qPCR analysis may be successful for evaluating management strategies if improvements are made to the trial design, and if analyses are conducted in diseased rather than asymptomatic orchards. | en_ZA |
| dc.description.abstract | AFRIKAANSE OPSOMMING: Phytophthora wortelvrot (PW) wat deur Phytophthora cinnamomi (Pc) veroorsaak word, is ‘n vernietigende grondgedraagde siekte wat grootskaalse ekonomiese verliese in kommersiële avokado-boorde veroorsaak. Ten spyte hiervan, is daar ‘n gebrek aan kennis oor die patogeen se seisoenale kolonisasie patrone, asook watter monsternemingstrategie en kwantifiseringsmetode die beste sou wees om dit te bepaal. Huidige tekortkominge in Pc kwantifiseringsmetodes kan tot onakkurate toepassing van PW bestuurstrategie lei, insluitende fosfonaat swamdoders en PW-bestande onderstamme. Die huidige studie kon ‘n piek in seisoenale Pc wortelkolonisasie identifiseer, naamlik láát herfs (Mei) in volwasse avokado-boorde, wat in twee hoof produksiestreke geleë is (Mooketsi en Letaba) in die Limpopo provinsie van Suid-Afrika. Gedurende twee groeiseisoene (2017 en 2018) wat ondersoek is, was Pc wortelhoeveelhede betekenisvol hoër in Mei 2018 as in Maart (vroeë herfs), Augustus (láát winter) en Oktober/November (láát lente) van dieselfde seisoen (2018). In 2017 was kolonisasie-neigings minder opmerklik, wat moontlik ‘n gevolg was van minder gunstige toestande vir PW wat geheers het, veral in die Mooketsi-streek. In Letaba (2017), het Augustus en Maart die hoogste Pc wortelhoeveelhede in die meeste boorde opgelewer, maar dit het nie betekenisvol van die ander maande (Maart en Oktober/November) verskil nie. In Mei was Pc wortelhoeveelhede verder betekenisvol positief gekorreleer met die hoeveelheid ure by grondtemperature van 15-19°C, maar negatief gekorreleer met 20-24°C. Grondvog fluktuasies het nie met Pc wortelhoeveelhede verband gehou nie. Evaluasie van twee monsternemingstrategieë wat uit vier groepe bome (elke groep bestaande uit vyf bome) en een groep met twintig bome bestaan het, het getoon dat beide benaderings geskik is om Pc kolonisasie patrone te ondersoek. ‘n Tradisionele wortellokaasmetode, waar blaarlokaas op selektiewe media geplaas is, was net so effektief om kolonisasie neigings te identifiseer as ‘n molekulêre benadering waar kleinskaal wortel DNS ekstraksies en kwantitatiewe real-time PKR (qPKR) analise gebruik is. ‘n Grootskaalse wortel DNS ekstraksie en kwantitatiewe polimerase kettingreaksie (qPKR) analisemetode was minder effektief geag. Dit het geblyk dat ‘n molekulêre kwantifiserings (qPKR) benadering oneffektief was om twee bestuurstrategieë te evalueer (fosfonaatbehandelings en onderstam bestandheid) in avokado-boorde wat geen duidelike bogrondse simptome van PW-agteruitgang getoon het nie. Hoewel wortelfosfiet (afbraakproduk van fosfonate) konsentrasies van ‘n 2x staminspuitingbehandeling wat teen die voorkomende dosis (0.3 g a.i./m2) toegedien is, betekenisvol hoër was as die onbehandelde kontrole, was die Pc wortel- en grond DNS- konsentrasies nie betekenisvol deur die fosfiet verminder, relatief tot die onbehandelde kontrole nie. Dit was vir kwantifikasies wat óf in Mei óf in Oktober 2018 gedoen is, en deur die gebruik van die beste van die drie geëvalueerde Pc-spesifiek qPKR toetse. Die potensieel meer PW-bestande R0.06 onderstam het hoër Pc wortel DNS konsentrasies gelewer as die Dusa® onderstam in November 2017, maar nie in die ander twee monsterneming maande (Maart en Mei 2018) nie. Die identifikasie van effektiewe monsternemingstrategieë, Pc wortelkwantifiseringsmetodes en Pc wortelkolonisasie patrone in avokado-boorde in die huidige studie is belangrik. Aangesien Mei die hoogste wortelkolonisasievlakke gehad het, behoort PW bestuurspraktyke in plek gestel te word om die optimale wortelbeskerming gedurende, of net voor, hierdie periode (láát herfs) te verkry. Die effektiewe monsterneming- en kwantifikasie-metodes wat geïdentifiseer is vir die bestudering van seisoenale wortelkolonisasie patrone in avokado, sal nuttig wees vir verdere studies wat op 5000 gasheerplantspesies van Pc uitgevoer word. Alternatiewe kwantifikasiemetodes as qPKR om bestuurstrategieë te evalueer, moet ondersoek word. Dit is egter moontlik dat qPKR ontleding suksesvol kan wees vir die evaluering van bestuurstrategieë indien daar verbeterings gemaak word aan die proef–ontwerp, en indien ontledings uitgevoer word in siek eerder as asimptomatiese boorde. | af_ZA |
| dc.description.version | Masters | en_ZA |
| dc.embargo.terms | 2021-12-01 | |
| dc.format.extent | xi, 144 pages | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/105699 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch : Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject | Phytophthora cinnamomi -- Genetics | en_ZA |
| dc.subject | Avocado orchards -- South Africa | en_ZA |
| dc.subject | Phytophthora cinnamomi -- Seasonal variations | en_ZA |
| dc.subject | Phytophthora root rot -- Colonisation | en_ZA |
| dc.subject | Efficacy | en_ZA |
| dc.subject | Avocado industry -- Management -- South Africa | en_ZA |
| dc.subject | Avocado -- Postharvest losses -- Control | en_ZA |
| dc.subject | Avocado -- Rootstocks | en_ZA |
| dc.subject | Avocado -- Effect of chemicals on | en_ZA |
| dc.subject | UCTD | en_ZA |
| dc.title | Assessing Phytophthora cinnamomi seasonal root colonisation patterns and pathogen response to management practices (phosphonates and rootstock tolerance) in South African avocado orchards | en_ZA |
| dc.type | Thesis | en_ZA |