Evaluation of East African bananas for resistance to Fusarium Oxysporum f. Sp. cubense race 1

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dc.contributor.advisorViljoen, Altusen_ZA
dc.contributor.advisorMostert, Dianeen_ZA
dc.contributor.advisorMahuku, Georgeen_ZA
dc.contributor.authorNdayihanzamaso, Privaten_ZA
dc.contributor.otherStellenbosch University. Faculty of AgriSciences. Dept. of Plant Pathology.en_ZA
dc.date.accessioned2020-02-18T16:18:40Z
dc.date.accessioned2020-04-28T15:10:42Z
dc.date.available2020-02-18T16:18:40Z
dc.date.available2020-04-28T15:10:42Z
dc.date.issued2020-03
dc.descriptionThesis (PhDAgric)--Stellenbosch University, 2020. en_ZA
dc.description.abstractENGLISH ABSTRACT: Banana is a staple food and source of income for millions of smallholder farmers in East and Central Africa (ECA). Consumption per capita in countries such as Burundi, Rwanda and Uganda ranges from 120 kg to more than 400 kg per year, which is six to 20 times the global average consumption per capita. Bananas cultivated in ECA consist of cooking varieties, such as East African Highland bananas (EAHB), Bluggoe, and juice/sweet dessert varieties such as Pisang Awak, Sukari Ndizi, Gros Michel and Cavendish bananas. EAHB include diploid bananas such Mchare, Muraru, Mlali and Paka (mostly cooking types), whereas EAHB triploids include Matooke (a cooking type) and Mbidde (a juice/beer type). Fusarium wilt of banana, caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), is present in most banana-growing regions of ECA. Foc comprises three races based on their pathogenicity to a group of differential cultivars, with Foc race 1, race 2 and race 4 causing disease to Gros Michel, Bluggoe and Cavendish bananas, respectively. All three races are present in Africa, but only Foc races 1 and 2 occur in ECA. Foc races 1 and 2 strains in ECA group consist of six vegetative compatibility groups, which cluster together as Foc Lineage VI. In this study, molecular markers specific to Foc Lineage VI were developed from the DNA-directed RNA polymerase III subunit (RPC2) gene region. The primer set was combined in a multiplex PCR assay with the primer set FocLin6bF/R, which was developed from the translation elongation factor-1 alpha (TEF-1α) gene. The multiplex PCR assay was validated on a worldwide population of 623 known Foc isolates, other formae speciales and non-pathogenic isolates of Fusarium oxysporum. The multiplex PCR can be used as an accurate diagnostic tool for Foc Lineage VI strains. Effective management of banana Fusarium wilt can be achieved by planting banana varieties resistant to Foc. Resistant bananas, however, require many years of breeding and field-testing under multiple geographical conditions. Field evaluation is reliable but time consuming and expensive, and not feasible for quarantine strains. Small plant screening methods are, therefore, needed to speed up the evaluation of banana varieties for Foc resistance. To this end, a small plant screening method for resistance to banana Fusarium wilt was optimized by investigating the effect of inoculum concentration, inoculation method and plant age on disease development, and the value of phenolic compounds and Foc DNA as indicators of disease resistance. The method, which consisted of planting 2- to 3-month-old banana plants in soil amended with 2-10 g Foc-colonised millet seeds per kg of potting soil, was reliable, and qPCR and rhizome discoloration were suitable for evaluating and ranking the disease response of banana varieties. Phenolic compounds were, however, not consistent in differentiating cultivars’ resistance when the same genotypes were inoculated with Foc race 1 and subtropical race 4 (STR4), and cannot be considered a reliable indicator of resistance. The optimized millet seed technique is useful in mass screening of newly developed genotypes for resistance to Foc, and can be used in the screening for Fusarium wilt resistance against quarantine variants of Foc in quarantine facilities. EAHB triploid banana cultivars are resistant to Foc race 1 and 2 in ECA, but dessert varieties in the region are susceptible. Resistance of diploid Mchare, Muraru and Mlali bananas, as well as newly developed diploid and triploid EAHB hybrids, is largely unknown. Therefore, in this study eight Mchare cultivars and 19 NARITA hybrids were evaluated for resistance to Foc race 1 in the field and screen house in Tanzania and in Uganda. Eight Muraru cultivars, 23 Mchare hybrids and 60 Matooke hybrids were also screened in pot trials in a screen house. Mchare and Muraru cultivars were all susceptible to Foc race 1, whereas the response of Mchare, NARITA and Matooke hybrids ranged from susceptible to resistant. Triploid hybrids were not expected to be susceptible as their parents were resistant to Foc race 1. This suggest that resistance in banana is multi-gene controlled and heterozygous, and that the genes segregated during meiosis into gamete cells leading to a loss of resistance. This study generated valuable information towards the management of Fusarium wilt in the ECA region. Molecular markers that were developed are reliable and affordable to research centres and extension services in the region, and can speed up the diagnosis of Foc Lineage VI strains. The screening method developed in this study will improve the reliability of small plant testing, and will reduce time and cost associated with field evaluation of new varieties.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Piesang is ʼn stapelvoedsel en bron van inkomste vir miljoene kleinboere in Oos- en Sentraal- Afrika (OSA). Verbruik per kapita in lande soos Burundi, Rwanda en Uganda wissel van 120 kg tot meer as 400 kg per jaar, wat ses tot 20 keer die wêreld se gemiddelde verbruik per kapita is. Piesangs wat in OSA verbou word bestaan uit variëteite wat gekook moet word voor dit geëet word, soos Oos-Afrikaanse Hoogland Piesangs (OAHP), Bluggoe, en variëteite wat gebruik word vir hul sap en vir vars eet soos Pisang Awak, Sukari Ndizi, Gros Michel en Cavendish. OAHP sluit diploïede piesangs in soos Mchare, Muraru, Mlali en Paka (meesal kook tipes) sowel as OAHP triploïede piesangs soos Matooke (ʼn kook tipe) en Mbidde (ʼn sap/bier tipe). Fusarium verwelk van piesangs, veroorsaak deur die grondgedraagde swam Fusarium oxysporum f. sp. cubense (Foc), word in die meeste piesang-produserende areas van OSA gevind. Foc bestaan uit drie rasse, gebaseer op hul patogenisiteit teenoor ʼn groep van verskillende kultivars, met Foc rasse 1, 2 en 4 wat onderskeidelik siekte van Gros Michel, Bluggoe en Cavendish piesangs veroorsaak. Al drie die rasse is in Afrika teenwoordig, maar slegs Foc rasse 1 en 2 isolate kom in OSA voor. Die twee rasse bestaan verder uit ses vegetatiewe verenigbaarheidsgroepe, wat saam as Foc Stamlyn VI groepeer. In hierdie studie is ‘n molekulêre merker spesifiek tot Foc Stamlyn VI vanaf die DNS-gerigte RNS polimerase III sub-eenheid (RPC2) geen-area ontwikkel. Die merker is in ʼn multipleks PKR toets saam met ʼn merker vir FocLin6bF/R gekombineer wat vanaf die translasie verlengingsfaktor-1 alfa (TEF-1α) geen ontwikkel is. Die PKR toets is daarna op ʼn wêreldwye populasie van 623 bekende Foc isolate, ander formae speciales en nie-patogene isolate van F. oxysporum uitgevoer, en as ʼn akkurate diagnostiese toets vir Foc Stamlyn VI isolate bewys. Piesang Fusarium verwelksiekte kan effektief bestuur word deur weerstandbiedende piesangvariëteite te plant. Die ontwikkeling van weerstandbiedende piesangs vereis egter baie jare van teling en veld-evaluasie onder verskillende geografiese toestande. Veld-evaluasie is betroubaar maar tydrowend en duur, en is nie moontlik met kwarantyn-isolate nie. Kleinplant evaluasiemetodes word dus benodig om die evaluasie van piesangvariëteite vir Foc weerstand te versnel. Daarom was ʼn kleinplant evaluasiemetode vir weerstand teen piesang Fusarium verwelksiekte ge-optimiseer deur die effek van inokulum konsentrasie, inokulasie metode en plant-ouderdom, sowel as die waarde van fenoliese verbindings en Foc DNS as indikators van siekteweerstand te ondersoek. Die infeksie van 2- tot 3-maand-oue piesangplante met 2-10 g Foc-gekoloniseerde milletsaad per kg potgrond het betroubare resultate gelewer, met ʼn goeie korrelasie tussen kwantitatiewe PKR resultate en risoom verkleuring ten opsigte van die siektereaksie van variëteite. Die produksie van fenoliese verbindings deur piesangvariëteite na infeksie met Foc ras 1 en subtropiese ras 4 (STR4) het egter nie konsekwente resultate gelewer nie, en kan dus nie as ʼn betroubare indikator van weerstand beskou word nie. Die milletsaad tegniek kan in kwarantynfasiliteite gebruik word vir die massa-evaluasie van nuut-ontwikkelde genotipes vir weerstand teen Foc. OAHP triploïede piesangkultivars is weerstandbiedend teen Foc rasse 1 en 2 in OSA, maar soet variëteite is vatbaar. Weerstand van diploïede Mchare, Muraru en Mlali piesangs, asook nuut-ontwikkelde diploïed en triploïed OAHP basters is grootliks onbekend. In die studie was agt Mchare kultivars en 19 NARITA basters gevolglik vir weerstand teen Foc ras 1 in die veld en in ʼn nethuis in Tanzanië en Uganda geëvalueer. Agt Muraru kultivars, 23 Mchare basters en 60 Matooke basters is ook in potproewe in die nethuis geëvalueer. Mchare en Muraru kultivars was almal vatbaar vir Foc ras 1, terwyl die reaksie van Mchare, NARITA en Matooke basters gewissel het van vatbaar tot weerstandbiedend. Daar is nie verwag dat triploïede basters vatbaar sou wees nie aangesien hul stamlyne weerstandbiedend teen Foc ras 1 was. Dit dui aan dat weerstand in piesangs deur verskeie gene beheer word en heterosigoties mag wees, en dat gene wat tydens meiose in gameetselle skei tot ʼn verlies in weerstand kan lei. Hierdie studie het waardevolle inligting ingesamel vir die bestuur van Fusarium verwelk in OSA. Molekulêre merkers wat ontwikkel is, is betroubaar en bekostigbaar, en kan die diagnose van Foc Stamlyn VI isolate by navorsingsentrums en by voorligtingsdiensareas versnel. Die evaluasiemetode wat in hierdie studie ontwikkel is, sal die betroubaarheid van kleinplant toetsing verbeter, en sal die tyd en koste geassosieer met veld-evaluasie van nuwe variëteite, verminder.af_ZA
dc.description.versionDoctorateen_ZA
dc.embargo.terms2023-03-01
dc.format.extentx, 159 pages : illustrations (some color), mapsen_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/108354
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshBananas -- Africa, Easten_ZA
dc.subject.lcshBananas -- Diseases and pests -- Africa, Easten_ZA
dc.subject.lcshFusarium wilt of banana -- Africa, East -- Managementen_ZA
dc.subject.lcshFusarium oxysporum -- Controlen_ZA
dc.subject.lcshBananas -- Disease and pest resistance -- Genetic aspectsen_ZA
dc.subject.lcshFarms, Small -- Africa, Easten_ZA
dc.subject.nameUCTDen_ZA
dc.titleEvaluation of East African bananas for resistance to Fusarium Oxysporum f. Sp. cubense race 1en_ZA
dc.typeThesisen_ZA
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