A molecular, morphological and biological characterisation of the genus Globodera (Nematoda: Heteroderidae) in South Africa

Knoetze, Rinus (2014-03)

Thesis (PhD)--Stellenbosch University, 2014.

Thesis

ENGLISH ABSTRACT: A molecular, morphological and biological characterisation of the genus Globodera (Nematoda: Heteroderidae) in South Africa is presented. The aims of the study were to determine the spread of the genus in South Africa; to study the systematics and describe the characteristics of the group and to gain a more complete understanding of the biology of the group as agricultural pests. Surveys were conducted in the Cape Floristic Region and in all the potato-producing areas of South Africa. The surveys unearthed new species of cyst nematodes and determined the spread of Globodera rostochiensis in the country. Phylogenetic analysis of sequences from ITS-rDNA was used to infer phylogenetic relationships among cyst nematodes from South Africa. The analyses established the distinct phylogenetic positions of cyst nematode populations from South Africa relative to an array of other cyst nematode species and indicated the existence of four new species of cyst nematodes. Analysis of random amplified polymorphic DNA (RAPD) banding patterns revealed intraspecific genetic variation amongst populations of Globodera rostochiensis. In order to provide molecular protocols for the accurate identification of South African cyst nematodes, species-specific primers and restriction enzymes were tested for their ability to discriminate between local Globodera spp. A combination of the molecular, morphological and morphometric characteristics of these populations were used to describe three new species of cyst nematodes. Experiments to determine the effect of storage temperature on the viability and hatching of South African populations of G. rostochiensis, showed differences in the responses of different populations to different storage temperatures. Experiments to determine the effect of field conditions on the viability and hatching of South African populations of G. rostochiensis, indicated that a decline in viable eggs in cysts from different populations occur, but suggests that the cysts will be able to survive for much longer in these soils than was expected. Spontaneous hatch was the main contributor to the decline of viability of cysts in the soil. Recording of soil temperatures in different locations indicated that the average temperature at 20 cm depth was approximately 20°C, the optimum temperature for the reproduction of G. rostochiensis, as confirmed by in vitro reproduction tests, which also showed that multiplication and survival is influenced negatively when the temperatures rise above 25°C. Reproduction on differential potato clones confirmed the pathotype of all the South African populations of G. rostochiensis as Ro1. After assessing the reproduction of G. rostochiensis on indigenous solanaceous plants, it was concluded that none of these plants induce substantial hatch in G. rostochiensis, nor do they support multiplication of the nematode. The results of this project have an impact on inquiries at all taxonomic levels, while also having an essential practical application in nematology. Knowledge of the distribution, pathogenicity, survival potential and reproduction capacity of Globodera species in South African soils are valuable for the design of effective management strategies as well as regulatory measures.

AFRIKAANSE OPSOMMING: ‘n Molekulêre, morfologiese en biologiese karakterisering van die genus Globodera (Nematoda: Heteroderidae) in Suid-Afrika word aangebied. Die doelwitte van die studieprojek was om die verspreiding van die genus in Suid-Afrika vas te stel, om die sistematiek van die groep te bestudeer en om ‘n meer volledige begrip van die biologie van die groep te bekom. Opnames is in die Kaapse Floristiese streek en in al die aartappelproduserende gebiede in die land gedoen. Tydens die opnames is nuwe sist nematode spesies gevind en die verspreiding van Globodera rostochiensis in Suid-Afrika is vasgestel. Filogenetiese analises van die basispaar opeenvolgings van ITS-rDNS is gebruik om die filogenetiese verwantskappe tussen die sist nematodes van Suid-Afrika vas te stel. Die spesifieke filogenetiese posisies van die nematodes, relatief tot ander spesies het gedui op die teenwoordigheid van 4 nuwe spesies. ‘n Analise van “random amplified polymorphic DNA” (RAPD) bandpatrone het intraspesifieke variasie tussen populasies van G. rostochiensis uitgewys. Diagnostiese tegnieke, aan die hand van spesies-spesifieke inleiers en restriksie-ensieme, is geevalueer vir hul vermoë om Globodera spesies van mekaar te onderskei. ‘n Kombinasie van molekulére, morfologiese en morfometriese karaktertrekke is gebruik vir die beskrywing van drie nuwe Globodera spesies. Eksperimente om die effek van verskillende temperature op die lewenskragtigheid en uitbroei van Suid-Afrikaanse populasies van G. rostochiensis vas te stel, het verskille in die reaksies van die poulasies uitgewys. Eksperimente om die effek van veldtoestande op die lewenskragtigheid en uitbroei van Suid-Afrikaanse populasies van G. rostochiensis vas te stel, het gewys dat alhoewel ‘n afname in die lewenskragtigheid van eiers plaasvind, sal die siste nog steeds langer in die grond oorleef as wat verwag is. Spontane uitbroei van eiers was die grootste oorsaak van die afname in lewenskragtigheid van siste in die grond. Die monitoring van grondtemperature in verskillende lokaliteite, het gewys dat die gemiddelde temperatuur, 20 cm onder die grond, nagenoeg 20°C was. Die optimum temperatuur vir die aanteling van G. rostochiensis, soos gewys deur in vitro toetse is ook 20°C, maar ‘n skerp daling vind plaas by temperature hoer as 25°C. Aanteling op verskillende aartappel cultivars, het gewys dat die patotipe van plaaslike populasies van G. rostochiensis, Ro1 is. Toetse op inheemse Solanum plante het gewys dat die plante nie goeie gashere vir G. rostochiensis is nie. Die bevindings van hierdie studieprojek het ‘n impak op die taksonomie van die groep en kennis van die verspreiding, patogenisiteit en oorlewing van die nematodes onder Suid-Afrikaanse toestande is van waarde vir die daarstelling van effektiewe beheerstrategiee en wetstoepaslike regulasies.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/86734
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