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Using large-scale genomics to improve grain yield in bread wheat forming part of a MS-MARS pre-breeding scheme
Thesis (MScAgric)--Stellenbosch University, 2021.
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| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2021
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| _version_ | 1867614063699165184 |
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| access_status_str | Open Access |
| author | Mulweli Judy, Mudau |
| author2 | Botes, Willem |
| author_browse | Botes, Willem Mulweli Judy, Mudau |
| author_facet | Botes, Willem Mulweli Judy, Mudau |
| author_sort | Mulweli Judy, Mudau |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2021. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/123947 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:46:04.365Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/123947 Using large-scale genomics to improve grain yield in bread wheat forming part of a MS-MARS pre-breeding scheme Mulweli Judy, Mudau Botes, Willem Visser, Marike Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. Genomics Marker assisted selection Male sterility in plants -- Genetic aspects Wheat (Triticum spp.) -- Grain yield UCTD Thesis (MScAgric)--Stellenbosch University, 2021. ENGLISH ABSTRACT: The wheat crop (Triticum spp.) is cultivated worldwide for various uses. Contributing to the world’s diet about a fifth of the calories and more than half of carbohydrates consumed by humans. With the growing population, reduced production area and various biotic and abiotic stresses, there is a concern amongst plant breeders that with the current wheat varieties, food security will be severely compromised. To gain higher yields, new approaches need to be developed and implemented that will ensure stable and sustainable increases in crop production. One of the approaches is high throughput genotyping which provides information and access to genome-wide molecular markers. This can be done using SNP and SNP marker technology. This is ideal since SNPs are the most abundant source of variation in the wheat genome. Another approach is using recurrent mass selection, which makes use of genetic male sterility and optimises gene pyramiding. The aim of this study was to identify crossing parents as part of the MS-MARS pre-breeding scheme and to use large-scale genomics to attribute molecular markers to high yielding traits. For the MS-MARS pre-breeding scheme, Welgevallen lines were used. The female lines were from the MS-MARS cycle and since MS-MARS pre-breeding scheme is continuous and multi- year, this population is vastly diverse and segregates for various genes. The donor population was also derived from the MS-MARS pre-breeding scheme. The standard panel of markers, used within the Stellenbosch University Plant Breeding Laboratory (SU-PBL), were used in the screening of female and donor population. The standard panel of markers consisted of molecular markers for rust resistance genes, height genes and baking quality genes. Using the data from molecular and phenotypic screening, crossing parents were identified. A successful MS-MARS cycle was completed and crossing seed was produced. For the second aim, data from molecular screening using a single nucleotide polymorphism (SNP) microarray known as the Wheat Breeder’s Array (high-density Affymetrix Axiom® genotyping array) was obtained from the John Inness Centre. This data described the INEW population. Yield determining traits were identified from literature and extensive phenotyping was done on this population. From this data, genome-wide association studies were done and significant SNP markers were identified. Although nine significant SNP markers were identified, only two had a BLAST annotation for T. aestivum, AX-94467554 and AX-94781089. These two SNP markers were linked to V-SNARE domain-containing protein and an uncharacterised hypothetical protein, respectively. Using the phenotypic data, five crossing parents from the INEW population were identified to be used in MS-MARS pre-breeding scheme. Future studies will include the testing of the efficacy of the identified SNP markers in the selection of genotypes, using marker assisted selection and phenotyping to potentially be added to the standard panel of molecular markers at SU-PBL. Secondly, the continuation of the MS-MARS pre-breeding scheme as well as the screening and use of the identified crossing parents in MS-MARS. AFRIKAANSE OPSOMMING: Die koringgewas (Triticum spp.) word wêreldwyd vir verskeie gebruike verbou. Dit dra by tot ongeveer 'n vyfde van die kalorieë en meer as die helfte van koolhidrate wat deur mense in hulle dieet verbruik word. Met die groeiende bevolking, verminderde produksiegebied en verskeie biotiese en abiotiese stresfaktore, is daar kommer onder planttelers dat met die huidige koringvariëteite, voedselsekuriteit ernstig bedreig sal word. Om hoër oesopbrengste te verkry, moet nuwe benaderings ontwikkel en geïmplementeer word wat stabiele toenames in gewasproduksie sal verseker. Een van die nuwe biotegnologiebenaderings is hoë deurset enkelnukleotied-polimorfisme (ENP) genotipering wat inligting en toegang tot genoomwye molekulêremerkers verskaf. Dit is ideaal aangesien ENP's die volopste bron van genetiese variasie in die koringgenoom is. Nog 'n teelbenadering is die gebruik van herhalende massaseleksie, wat gebruik maak van genetiese manlike steriliteit en geoptimaliseerde geenpiramidering. Die doel van hierdie studie was om kruisingsouers te identifiseer wat deel moet word van die MS-MARS voorteelingsskema en tweedens om grootskaalse genomiese instrumente te gebruik om molekulêremerkers aan hoë-opbrengseienskappe toe te skryf. Vir die MS-MARS voortelingsskema is Welgevallen-lyne gebruik. Die vroulike lyne was afkomstig vanaf die MS- MARS wat aaneenlopend en meerjarig is, daarom is hierdie populasie baie geneties divers en segregeer vir verskeie gene. Die skenkerpopulasie is ook afkomstig vanaf die MS-MARS voorteelskema. ʼn Standaard paneel van merkers is gebruik in die sifting van vroulike en skenker populasies, wat bestaan het uit molekulêre merkers vir roes weerstands-, hoogte- en bakkwaliteitsgene. Deur die data van molekulêre en fenotipiese sifting te gebruik, is kruisingsouers geïdentifiseer. ’n Suksesvolle MS-MARS siklus is voltooi en saad is geproduseer. Vir die genomiese studies is data van molekulêre sifting met behulp van 'n ENP- mikromatriks bekend as die Wheat Breeder's Array (Affymetrix Axiom®) verkry vanaf die John Innes Center. Hierdie data het die INEW-bevolking omskryf. Opbrengs-bepalende eienskappe is uit literatuur geïdentifiseer en uitgebreide fenotipering is op hierdie populasie gedoen. Uit hierdie data is ʼn genoomwye-assosiasiestudies gedoen en betekenisvolle ENP-merkers is geïdentifiseer. Alhoewel nege betekenisvolle ENP-merkers geïdentifiseer is, het slegs twee 'n BLAST annotasie vir T. aestivum gehad, nl. AX-94467554 en AX-94781089. Hierdie twee ENP-merkers is onderskeidelik aan ‘n V-SNARE-domeinbevattende proteïen en 'n ongekarakteriseerde hipotetiese proteïen gekoppel. Deur die fenotipiese data te gebruik, is vyf kruisingsouers uit die INEW-populasie geïdentifiseer om in die MS-MARS voortelingsskema gebruik te word. Toekomstige studies sal die bevestiging van die geïdentifiseerde ENP-merkers insluit om sodoende moontlik by die standaardpaneel van molekulêremerkers by die SU-PBL gevoeg te word. Tweedens, die voortsetting van die MS-MARS voortelingsskema sowel as die sifting en gebruik van die geïdentifiseerde kruisingsouers in MS-MARS sal ook by toekomstige studies ingesluit word. Masters 2021-12-06T14:17:46Z 2021-12-22T14:30:48Z 2021-12-06T14:17:46Z 2021-12-22T14:30:48Z 2021-12 Thesis http://hdl.handle.net/10019.1/123947 en_ZA Stellenbosch University xvi, 80 pages : illustrations (some color), maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Genomics Marker assisted selection Male sterility in plants -- Genetic aspects Wheat (Triticum spp.) -- Grain yield UCTD Mulweli Judy, Mudau Using large-scale genomics to improve grain yield in bread wheat forming part of a MS-MARS pre-breeding scheme |
| title | Using large-scale genomics to improve grain yield in bread wheat forming part of a MS-MARS pre-breeding scheme |
| title_full | Using large-scale genomics to improve grain yield in bread wheat forming part of a MS-MARS pre-breeding scheme |
| title_fullStr | Using large-scale genomics to improve grain yield in bread wheat forming part of a MS-MARS pre-breeding scheme |
| title_full_unstemmed | Using large-scale genomics to improve grain yield in bread wheat forming part of a MS-MARS pre-breeding scheme |
| title_short | Using large-scale genomics to improve grain yield in bread wheat forming part of a MS-MARS pre-breeding scheme |
| title_sort | using large scale genomics to improve grain yield in bread wheat forming part of a ms mars pre breeding scheme |
| topic | Genomics Marker assisted selection Male sterility in plants -- Genetic aspects Wheat (Triticum spp.) -- Grain yield UCTD |
| url | http://hdl.handle.net/10019.1/123947 |
| work_keys_str_mv | AT mulwelijudymudau usinglargescalegenomicstoimprovegrainyieldinbreadwheatformingpartofamsmarsprebreedingscheme |