Determining the phenotypic and molecular diversity within a collection of wheat wild relatives

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dc.contributor.advisorBotes, Willemen_ZA
dc.contributor.advisorLe Maitre, Nicholasen_ZA
dc.contributor.authorBester, Cecileen_ZA
dc.contributor.otherStellenbosch University. Faculty of Agrisciences. Dept. of Genetics.eZA
dc.date.accessioned2023-03-05T09:19:04Z
dc.date.accessioned2023-05-18T07:06:31Z
dc.date.available2023-03-05T09:19:04Z
dc.date.available2023-05-18T07:06:31Z
dc.date.issued2023-03
dc.descriptionThesis (MScAgric)--Stellenbosch University, 2023. en_ZA
dc.description.abstractENGLISH ABSTRACT: Common bread wheat, Triticum aestivum L., is the third most important staple crop, after rice and maize. Wheat provides 20% of the globally consumed calories, and is cultivated on 242 389 108 ha globally. In South Africa, wheat was planted on 523 500 ha with a total production of 2 285 000 tonnes in the 2021/2022 season. The continuous improvement of wheat is important for global and local food security. Crop wild relatives are rich sources of genetic diversity that have been used in 4 157 documented cases of plant improvement by 2022. Wheat wild relatives, like Triticum and Aegilops spp. have been employed 333 times for wheat improvement by 2022. The Stellenbosch University Plant Breeding Laboratory has a collection of 1246 different wheat wild relatives belonging to the genera Triticum and Aegilops. There is limited information on the accessions from this collection, and the diversity present within, restricting the use of these plant genetic resources in wheat improvement. Obtaining more information that can assist when planning introductions, selections, renewal, description, and characterisation of the material is therefore vital. The development of digital phenotyping and characterisation methods can aid in the determination of morphological diversity and species identification. Chloroplast DNA is universal in plants and allows for the assessment of molecular diversity between species with different genomic combinations. From the Stellenbosch University Plant Breeding Laboratory crop wild relative collection, 92 entries were renewed, identified, characterised, and described. The collection showed a high level of morphological diversity in grain yield, flag leaf area and awn types. To improve phenotyping, a digital method of spike length estimation, using ImageJ, was compared to actual physical measurements. There was no significant difference between values obtained by these two methods, verifying the technique. Transfer Learning was applied to train pre-trained MobileNet Convolutional Neural Network models to distinguish between genus, species, subspecies and variety, with accuracies of 0.8750, 0.923, 0.742 and 0.600, respectively. These models can be applied to increase the accuracy of plant identification. Twelve chloroplast simple sequence repeats in four multiplex reactions were used to determine the genetic diversity within the wheat wild relative collection. Polymorphic information content ranged from 0.615 to 0.972 and gene diversity from 0.663 to 0.9724. These values indicate that there is a high level of diversity present within the wheat wild relative collection. Due to the high morphological, and molecular diversity within the ex situ species material collection, the plant genetic resources have a good potential for use in wheat breeding for crop improvement. The information can assist breeders to select the best wild relatives to be used in interspecies crosses to improve common bread wheat.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Brood koring, Triticum aestivum L., is die derde belangrikste stapel voedsel, naas rys en mielies. Koring voorsien 20% van die kaloriee wereldwyd en word op 242 389 108 ha verbou. Tydens die 2021/2022 seisoen was koring op 523 500 ha in Suid Africa geplant met 'n totale produksie van 2 285 00 ton. Wilde koring-verwante plante, insluitend Triticum en Aegilops spesies, is teen 2022 in 333 gevalle van koring verbetering gebruik. 'n Versameling van 1246 wilde koring spesies, vanuit die Triticum en Aegilops genera, word by die Stellenbosch Universiteit Plantteelt Laboratorium gehuisves. Die gebruik van hierdie plant genetiese hulpbronne vir koring verbetering word beperk deur die beperkte data beskikbaar oor die inskrywings en die diversiteit wat hulle huisves. Dit is belangrik om meer inligting oor die inskrywings te bekom, wat die seleksie, hernuwing, beskrywing en karakterisering van die materiaal kan verbeter. Die ontwikkeling van digitale fenotipering en karakterisering metodes kan plant spesies identifikasie en die assessering van morfologiese diversiteit verbeter. Chloroplast DNA is universeel in plante en laat die vergelyking van molekulere diversiteit tussen spesies met verskillende genoom kombinasies toe. Uit die Stellenbosch Universiteit Plantteelt Laboratorium is 92 inskrywings hernu, identifiseer, gekarakteriseer en beskryf. Die versameling het 'n hoe vlak van morfologiese diversiteit in graan gewig, baard en vlagblaar area. 'n Digitale metode wat aar lengte bepaal deur die gebruik van lmageJ, is vergelyk met die fisiese metings in 'n poging om fenotipering te verbeter. Die tegniek is geverifieer aangesien daar geen beduidende verskil tussen die waardes van die twee verskillende metodes was nie. Oordrag leer was toegepas op 'n vooraf geleerde MobileNet Convolutional Neural Netwerk om tussen genus, spesies, subspesies en variteit te onderskei, met akkuraatheid van 0.8750, 0.923, 0.742 en 0.600 onderskeidelik. Hierdie modelle kan toegepas word om die akkuraatheid van plant identifikasie te verbeter. Twaalf chloroplast eenvoudige volgorde herhalings is in vier multipleks reaksies gebruik om die genetiese diversiteit van die wilde koring versameling te bepaal. Die polimorfiese inligting inhoud het gestrek van 0.615 tot 0.972, en geen diversiteit van 0.663 tot 0.9724. Hierdie waardes is 'n aanduiding dat daar 'n hoe vlak van diversiteit in die versameling wilde koring voorkom. Die plant genetiese hulpbronne het 'n groot potensiaal vir gebruik in 'n koring teel program vir gewas verbetering, oor die hoe vlak van morfologiese en molekulere diversiteit. Die inligting behaal uit die studie kan plant telers assisteer om die beste koring-verwante spesies te selekteer vir inter-spesies kruisings, met die oog om brood koring te verbeter.af_ZA
dc.description.versionMastersen_ZA
dc.format.extentxvi, 180 pages : illustrations (some color), mapsen_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/127142
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshPlant breeding -- Genetic aspectsen_ZA
dc.subject.lcshWheat (Triticum aestivum L.) -- South Africa -- Geneticsen_ZA
dc.subject.lcshGenotype-environment interaction -- South Africaen_ZA
dc.subject.lcshWheat -- Varietiesen_ZA
dc.subject.nameUCTDen_ZA
dc.titleDetermining the phenotypic and molecular diversity within a collection of wheat wild relativesen_ZA
dc.typeThesisen_ZA
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