Dissertations / Theses on the topic 'Wheat – Disease and pest resistance – Testing'

Doctor of Philosophy
The responses of 92 barley genotypes to selected P. hordei pathotypes was assessed in greenhouse tests at seedling growth stages and in the field at adult plant growth stages to determine known or unknown resistances. On the basis of multipathotype tests, 35 genotypes were postulated to carry Rph2, Rph4, Rph5, Rph12, RphCantala alone or combinations of Rph2 + Rph4 and Rph1 + Rph2, whereas 52 genotypes lacked detectable seedling resistance to P. hordei. Five genotypes carried seedling resistance that was effective to all pathotypes tested, of which four were believed to carry uncharacterised resistance based on pedigree information. Field tests at adult plant growth stages indicated that while 28 genotypes were susceptible, 57 carried uncharacterised APR to P. hordei. Pedigree analysis indicated that APR in the test genotypes could have been derived from three different sources. The resistant responses of seven cultivars at adult plant growth stages were believed to be due to the presence of seedling resistance effective against the field pathotypes. Genetic studies conducted on 10 barley genotypes suggested that ‘Vada’, ‘Nagrad’, ‘Gilbert’, ‘Ulandra (NT)’ and ‘WI3407’ each carry one gene providing adult plant resistance to P. hordei. Genotypes ‘Patty’, ‘Pompadour’ ‘Athos’, ‘Dash’ and ‘RAH1995’ showed digenic inheritance of APR at one field site and monogenic inheritance at a second. One of the genes identified in each of these cultivars provided high levels of APR and was effective at both field sites. The second APR gene was effective only at one field site, and it conferred low levels of APR. Tests of allelism between resistant genotypes confirmed a common APR gene in all genotypes with the exception of ‘WI3407’, which based on pedigree information was genetically distinct from the gene common in ‘Vada’, ‘Nagrad’, ‘Patty’, ‘RAH1995’ and ‘Pompadour’. An incompletely dominant gene, Rph14, identified previously in an accession of Hordeum vulgare confers resistance to all known pathotypes of P. hordei in Australia. The inheritance of Rph14 was confirmed using 146 and 106 F3 lines derived from the crosses ‘Baudin’/ ‘PI 584760’ (Rph14) and ‘Ricardo’/‘PI 584760’ (Rph14), respectively. Bulk segregant analysis on DNA from the parental genotypes and resistant and susceptible DNA bulks from F3 lines using diversity array technology (DArT) markers located Rph14 to the short arm of chromosome 2H. Polymerase chain reaction (PCR) based marker analysis identified a single simple sequence repeat (SSR) marker, Bmag692, linked closely to Rph14 at a map distance of 2.1 and 3.8 cM in the populations ‘Baudin’/ ‘PI 584760’and ‘Ricardo’/‘PI 584760’, respectively. Seedlings of 62 Australian and two exotic barley cultivars were assessed for resistance to a variant of Puccinia striiformis, referred to as BGYR, which causes stripe rust on several wild Hordeum species and some genotypes of cultivated barley. With the exception of six Australian barley cultivars and an exotic cultivar, all displayed resistance to the pathogen. Genetic analyses of six Australian barley cultivars and the Algerian barley ‘Sahara 3771’, suggested that they carried either one or two major seedling resistance genes to the pathogen. A single recessive seedling resistance gene, Bgyr1, identified in ‘Sahara 3771’ was located on the long arm of chromosome 7H and flanked by restriction fragment length polymorphism (RFLP) markers wg420 and cdo347 at genetic distances of 12.8 and 21.9 cM, respectively. Mapping resistance to BGYR at adult plant growth stages using a doubled haploid population derived from the cross ‘Clipper’/‘Sahara 3771’ identified two major QTLs on the long arms of chromosomes 3H and 7H that explained 26 and 18% of total phenotypic variation, respectively. The QTL located on chromosome 7HL corresponded to the seedling resistance gene Bgyr1. The second QTL was concluded to correspond to a single adult plant resistance gene designated Bgyr2, originating from cultivar ‘Clipper’.

Thesis (MSc.) -- Stellenbosch University, 1997.
ENGLISH ABSTRACT: An octoploid triticale was derived from the F1 of a Russian wheat aphid resistant rye, 'Turkey 77', and 'Chinese Spring' wheat. The alloploid was crossed (a) to common wheat, and (b) to the 'Imperial' rye to 'Chinese Spring' disomic addition lines. F2 progeny from these crosses were tested for Russian wheat aphid resistance and C-banded. Resistance was found to be associated with chromosome arm 1RS of the 'Turkey 77' rye genome. This initial work was done by MARAIS (1991) who made a RWA resistant, monotelosomic 1RS ('Turkey 77') addition plant available for the study. The F3 progeny of this monotelosomic addition plant was used to confirm the RWA resistance on chromosome 1RS. The monotelosomic addition plant was then crossed with the wheat cultivar 'Gamtoos', which has the 1BL.1 RS 'Veery' translocation. Unlike the 1RS segment in 'Gamtoos', the 'Turkey 77'- derived 1RS telosome did not express the rust resistance genes 5r31 and Lr26 which could then be used as markers. From the F1 a monotelosomic 1RS addition plant that was also heterozygous for the 1BL.1 RS translocation, was selected and testcrossed with an aphid susceptible common wheat, 'Inia 66'. Meiotic pairing between the .rye arms resulted in the recovery of five euploid, Russian wheat aphid resistant plants out of a progeny of 99 euploids. One recombinant also retained 5r31 and Lr26 and was allowed to self pollinate. With the aid of SOS-PAGE profiles, Russian wheat aphid resistant 1BL.1 RS translocation homozygotes were identified and it was possible to confirm that the Russian wheat aphid resistance gene was in fact transferred to the 1BL.1RS ('Veery') translocation. Two attempts were made to map the Russiar, wheat aphid locus or loci. (1) Telosomic mapping was attempted. For this purpose a plant with 2n = 40 + 1BL.1 RS + 1RS was obtained, and testcrossed with a Russian wheat aphid susceptible wheat. (2) A disomic, recombined 1BL.1 RS translocation line with Russian wheat aphid resistance but lacking the Lr26 and Sr31 alleles was crossed with 'Gamtoos' and the F1 testcrossed. The testcross in both strategies were done with 'Chinese Spring'. In the first experiment the Sr31 locus was located 10.42 map units from the Lr26 locus. The rust resistance data implied that the genetic distance estimates may be unreliable and therefore the laborious Russian wheat aphid resistance tests were not done. In the second experiment a Russian wheat aphid resistance gene was located 14.5 map units from the Lr26 locus. In the latter cross nonmendel ian segregation of the Russian wheat aphid resistance evidently occurred which implied that the estimated map distance may be inaccurate. It was also not possible to determine the number of genes involved from the data.
Digitized at 300 dpi Colour & b/W PDF format (OCR), using ,KODAK i 1220 PLUS scanner. Digitised, Ricardo Davids on request from ILL 25 April 2013
AFRIKAANSE OPSOMMING: 'n Oktaplo"lede triticale is gemaak vanaf die F1 van 'n kruising tussen 'n Russiese koringluis-weerstandbiedende rog, 'Turkey 77', en die koringkultivar 'Chinese Spring'. Die alloplo"led is gekruis met gewone broodkoring en met 'Imperial' rog/'Chinese Spring' disomiese addissielyne. Die F2 nageslag vanaf hierdie kruisings is getoets vir Russiese koringluisweerstandbiedendheid en C-bande is ook gedoen. Weerstand is gevind wat geassosieer is met die 1RS chromosoomarm van 'Turkey 77'. Hierdie oorspronklike werk is deur MARAIS (1991) gedoen en uit sy materiaal is 'n monotelosomiese 1RS ('Turkey 77') addissieplant beskikbaar gestel vir die huidige studie. Die F3 nageslag van hierdie monotelosomiese addissieplant is gebruik om die weerstand teen die Russiese koringluis op chromosoom 1RS te bevestig. Die monotelosomiese addissieplant is ook gekruis met die koringkultivar 'Gamtoos' wat die 1BL.1 RS-translokasie dra. Hoewel die 1RS segment van 'Gamtoos' die roesweerstandsgene, Sr31 en Lr26 uitdruk, is dit nie die geval met die 'Turkey 77' 1RS telosoom nie. Hierdie gene kon dus as merkergene gebruik word. Vanuit die F1 is 'n monotelosomiese 1RS addissieplant geselekteer wat ook heterosigoties was vir die 1BL.1 RStranslokasie. Hierdie plant is getoetskruis met 'n luisvatbare gewone broodkoring, 'Inia 66'. Meiotiese paring tussen die rogarms het daartoe gelei dat vyf euplo"lede Russiese koringluis-weerstandbiedende nageslag uit 99 euplo"lede nageslag geselekteer kon word. Een rekombinant het ook Sr31 en Lr26 behou en is toegelaat om self te bestuif. Met behulp van SDSPAGE profiele is Russiese koringluis-weerstandbiedende 1BL.1 RStranslokasie homosigote ge"ldentifiseer en kon bevestig word dat die weerstandsgeen vir die Russiese koringluis oorgedra is na die 1BL.1 RS ('Veery') -translokasie. Twee strategies is gevolg om die Russiese koringluislokus of -loci te karteer: (1) 'n Telosomiese analise is gedoen. 'n Plant met 2n = 40 + 1BL.1 RS + 1RS is verkry en met 'n luisvatbare koring bestuif. (2) 'n Gerekombineerde, disomiese plant met Russiese koringluis-weerstandbiedendheid maar sonder die Lr26 en Sr31 allele is gekruis met 'Gamtoos' en die F1 getoetskruis. Die toetskruisouer in beide die strategiee was 'Chinese Spring'. In die eerste eksperiment is die Sr31-lokus 10.42 kaarteenhede vanaf die Lr26-lokus gelokaliseer. Die raesdata het ge"impliseer dat onbetraubare genetiese kaarteenhede geskat sou word en daarom is die omslagtige Russiese koringluis weerstandsbepalings nie gedoen nie. In die tweede eksperiment is die Russiese koringluis-weerstandsgeen op 14.5 kaarteenhede vanaf die Lr26-lokus gelokaliseer. Nie-Mendeliese segregasie van die Russiese koringluis-weerstand in hierdie karteringseksperiment het ge'impliseer dat die berekende kaartafstand onakkuraat mag wees. Dit was ook nie moontlik om op grand van die data die aantal gene betrakke af te lei nie.

Tan spot, caused by Pyrenophora tritici-repentis (Ptr), is a major foliar disease on wheat. The pathosystem involves three pairs of necrotrophic effector (NE) and host sensitivity (S) gene interactions, namely Ptr ToxA-Tsn1, Ptr ToxB-Tsc2 and Ptr ToxC-Tsc1. Additionally, genetic factors conferring race-nonspecific resistance have been identified. The objectives of this study were to map tan spot resistance QTL and investigate the role of NE-S interactions in disease in durum using association and bi-parental mapping. Evaluation of a worldwide collection of durum accessions allowed identifying highly resistant nineteen lines to multiple Ptr races. Association mapping revealed genomic regions on chromosomes 1A, 2B and 3B significantly associated with resistance to tan spot, which likely correspond to Tsc1, Tsc2 and racenonspecific resistance. Using a bi-parental population derived from Ben and PI 41025, we found that ToxA-Tsn1 interaction plays no significant role in disease, instead a major race-nonspecific QTL on chromosome 5A was identified.

Bibliography: leaves 137-163. his is a comprehensive study of induced homoeologous recombination along most of the complete genetic length of two homoeologous chromosomes in the Triticeae (7A of common wheat and 7Ai of Agropyron intermedium), using co-dominant DNA markers. Chromosome 7Ai was chosen as a model alien chromosome because is has been reported to carry agronomically important genes conferring resistance to stem rust and barley yellow dwarf virus on its short and long arms, respectively.

Several potential pathways exist for significant nitrogen loss from nitrogen fertilizer applied to winter wheat in Virginia. A number of materials have been previously identified which inhibit steps in one or more of these loss pathways. Ammonium polyphosphate, ammonium thiosulfate, dicyandiamide, potassium chloride, and monoammonium phosphate were chosen for use in the present study. They were mixed, singly and in combinations, with UAN solution or urea solution and spring top-dressed on soft red winter wheat. Experiments were conducted over two growing seasons at two locations each season. Nitrogen uptake was measured in mid-season and yield measured at harvest. In the second season, field measurement of ammonia volatilization was performed in the experiment utilizing urea solution. Addition of monoammonium phosphate significantly reduced volatilization from urea solution applied to winter wheat at both locations; however, weather conditions were such that total volatilization was low in this season, and the reduced losses were not reflected in increased nitrogen uptake or yield. None of the treatments significantly increased yield in any experiment, nor consistently increased mid-season nitrogen uptake.
Master of Science

Wheat (Triticum aestivum and T. Durum) is an extremely important agronomic crop produced worldwide. Wheat consumption has doubled in the last 30 years with approximately 600 million tons consumed per annum. According to the International Maize and Wheat Improvement Center, worldwide wheat demand will increase over 40 percent by 2020, while land as well as resources available for the production will decrease significantly if the current trend prevails. The wheat industry is challenged with abiotic and biotic stressors that lead to reduction in crop yields. Increase knowledge of wheat’s biochemical constitution and functional biology is of paramount importance to improve wheat so as to meet with this demand. Pesticides and fungicides are being used to control biotic stress imposed by insect pest and fungi pathogens but these chemicals pose a risk to the environment and human health. To this effect, there is re-evaluation of pesticides currently in use by the Environmental Protection Agency, via mandates of the 1996 Food Quality Protection Act and those with higher perceived risks are banned. Genetic resistance is now a more environmental friendly and effective method of controlling insect pest and rust diseases of wheat than the costly spraying with pesticides and fungicides. Although, resistant cultivars effectively prevent current prevailing pathotypes of leaf rust and biotypes of Russian wheat aphid from attacking wheat, new pathotypes and biotypes of the pathogen/pest may develop and infect resistant cultivars. Therefore, breeders are continually searching for new sources of resistance. Proteomic approaches can be utilised to ascertain target enzymes and proteins from resistant lines that could be utilised to augment the natural tolerance of agronomically favourable varieties of wheat. With this ultimate goal in mind, the aim of this study was to elucidate the mechanism and synchronicity of wheat resistance to leaf rust (Puccinia triticina) and Russian wheat aphid (Duiraphis noxia) SA1. To determine the resistance mechanism of the wheat cultivars to leaf rust infection and Russian wheat aphid infestation, a proteomics approach using two-dimensional gel electrophoresis was used in order to determine the effect of RWA SA1 on the wheat cultivars proteome. Differentially expressed proteins that were up or down regulated (appearing or disappearing) were identified using PDQuestTM Basic 2-DE Gel analysis software. Proteins bands of interest were in-gel trypsin digested as per the protocol described in Schevchenko et al. (2007) and analysed using a Dionex Ultimate 3000 RSLC system coupled to an AB Sciex 6600 TripleTOF mass spectrometer. Protein pilot v5 using Paragon search engine (AB Sciex) was used for comparison of the obtained MS/MS spectra with a custom database containing sequences of Puccinia triticina (Uniprot Swissprot), Triticum aestivum (Uniprot TrEMBL) and Russian wheat aphid (Uniprot TrEMBL) as well as a list of sequences from common contaminating proteins. Proteins with a threshold of ≥99.9 percent confidence were reported. A total of 72 proteins were putatively identified from the 37 protein spots excised originating from either leaf rust or Russian wheat aphid experiments. Sixty-three of these proteins were associated with wheat response to stress imposed by RWA SA1 feeding while 39 were associated with infection by Puccinia triticina. Several enzymes involved in the Calvin cycle, electron transport and ATP synthesis were observed to be differentially regulated suggesting greater metabolic requirements in the wheat plants following aphid infestation and leaf rust infection. Proteins directly associated with photosynthesis were also differentially regulated following RWA SA1 infestation and P.

Thesis ( MScAgric) -- Stellenbosch University, 1997.
ENGLISH ABSTRACT: Stem rust is considered the most damaging of the wheat rusts causing yield losses of more than 50% in epidemic years. Similarly, Russian wheat aphids (RWA) can be regarded as one ofthe most devastating insect pests of wheat. Yield losses due to R W A primarily result from a reduction in plant resources (sucking plant sap). Secondary losses are incurred by viruses transmitted during feeding. Mapping disease and insect resistance genes that are effective against prevailing pathotypes and biotypes of South Africa will optimize their utilization in breeding programmes. The wheat line, 87M66-2-l, is homozygous for a single dominant stem rust resistance gene located on chromosome lD. This stem rust resistance gene has been derived from Triticum tauschii accession RL5289 and is here referred to as Srtau. The aim of this study was to determine the chromosome arm involved. Following the chromosome arm allocation of Srtau, its possible linkage with the genes Rg2, Lr 21 , Sr X and Sr 33 was studied. A telosomic analysis has shown that Srtau is located on chromosome arm 1 DS and is linked to the centromere with a recombination frequency of 21 ± 3 .40%. Glume blotch and a heavy mildew infection of segregating families planted in the field in 1996 made the linkage study between Lr 21 (leaf rust resistance) and Rg2 (glume colour) impossible. However, estimated linkages of 9 ± 1.9 map units between Sr33 (stem rust resistance) and Srtau, ± 6 map units between Sr X (stem rust resistance) and Sr 3 3 and ± 1 0 map units between Sr X and Srtau suggested that SrX, Sr33 and Srtau are closely linked on I DS. Taking existing map data into consideration, it seems that the most likely order of the genes is: centromere - Srtau - Sr 3 3 - Sr X. A single dominant R W A resistance gene, Dn5, was identified in the T aestivum accession 'SA 463' and is located on chromosome 7D. The aim ofthis study was to determine the chromosome arm involved. The possible linkage of Dn5 with the endopeptidase locus, Ep-D1 b. and chlorina mutant gene, cn-D1, was then studied. Endopeptidase zymograms of 'SA 463' revealed two unknown polymorphisms. F 2 monosomic analyses involving the chromosomes 7 A, 7B and 7D were performed in an attempt to identify the loci associated with these polymorphisms. Dn5 was mapped on chromosome arm 7DL. A recombination frequency of60 ± 4.53% between Dn5 and the centromere suggested the absence of linkage. Linkage between Ep-Dl and cn-Dl could not be calculated as a result of similar isoelectric points of the 7DL encoded endopeptidases of the parental material studied. Recombination frequencies of32 ± 4.97% between Dn5 and EpDl and 37 ± 6.30% between Dn5 and cn-Dl were, however, encountered. The two novel endopeptidase alleles encountered in 'SA 463' were designated as Ep-Dle and Ep-Ald. A RWA resistance gene was transferred from the rye accession ' Turkey 77' to wheat and in the process the RWA resistant wheat lines 91M37-7 and 91M37-51 were derived. No rye chromatin could be detected in these plants following C-banding. The aim of this study was to determine (i) on which chromosome the gene(s) is located, and (ii) whether the resistance can be the result of a small intercalary translocation of rye chromatin. A monosomic analysis of the RWA resistance gene in 91M37-51 has shown that a single dominant resistance gene occurs on chromosome 7D. The use of rye-specific dispersed probes did not reveal any polymorphisms between the negative controls and RW A resistant lines 91M3 7- 7 and 91M37-51 which would suggest that it is unlikely that the resistance was derived from rye.
AFRIKAANSE OPSOMMING: Stamroes word as die mees vemietigende graanroessiekte beskou en het in epidemiese jare oesverliese van meer as 50% tot gevolg. Russiese koringluise is eweneens een van die emstigste insekplae van koring. Russiese koringluise veroorsaak oesverliese deurdat dit plantsap uitsuig en die plant van voedingstowwe beroof. Dit tree egter ook as 'n virusvektor op en kan so indirekte oesverliese veroorsaak. Kartering van siekte- en insekweerstandsgene wat effektief is teen die Suid-Afrikaanse patotipes en biotipes, sal hulle gebruik in teelprogramme optimiseer. Die koringlyn, 87M66-2-l , is homosigoties vir 'n dominante stamroes-weerstandsgeen wat op chromosoom ID voorkom. Hierdie weerstandsgeen is uit die Triticum tauschii aanwins, RL5289, afkomstig en word hiema verwys as Srtau. Daar is gepoog om te bepaal op watter chromosoomarm Srtau voorkom, waama sy koppeling met betrekking tot die gene Rg2, Lr21 , SrX en Sr33 bepaal is. 'n Telosoomanalise het getoon dat Srtau op chromosoom-arm 1 DS voorkom en gekoppel is aan die sentromeer met 'n rekombinasie-frekwensie van 21 ± 3.40%. Segregerende populasies wat in 1996 in die land geplant is, is hewig deur aarvlek en poeieragtige meeldou besmet en dit het die moontlike bepaling van koppeling tussen Lr21 (blaarroesweerstand) en Rg2 (aarkaffie kleur) belemmer. Koppelingsafstande van 9 ± 1. 9 kaart-eenhede tussen Sr 33 (stamroesweerstand) en Srt au, ± 6 kaart -eenhede tussen Sr X ( stamroesweerstand) en Sr 3 3 en ± 1 0 kaart -eenhede tussen SrX en Srtau is geraam en toon dat SrX, Sr33 en Srtau nou gekoppel is. Die waarskynlikste volgorde van die gene op lDS is: sentromeer- Srtau- Sr33- SrX. 'n Enkele dominante Russiese koringluis-weerstandsgeen, Dn5, is in dieT aestivum aanwins 'SA 463 ' ge"identifiseer en kom op chromosoom 7D voor. Die studie het ten doel gehad om te bepaal op watter chromosoom-arm Dn5 voorkom, asook wat die koppeling van Dn5 met die endopeptidase lokus, Ep-Dl, en die chlorina mutante geen, cn-Dl , is. Endopeptidase simograrnme van 'SA 463' het twee onbekende polimorfismes getoon. Die gene wat kodeer vir hierdie twee polimorfismes is met behulp van F2 monosoom-analises wat die chromosome 7 A, 7B en 7D betrek, gei:dentifiseer. Dn5 is op chromosoom 7DL gekarteer. 'n Rekombinasie-frekwensie van 60 ± 4.53% is gevind vir die sentromeer en Dn5 en dui op die afwesigheid van koppeling. Koppeling tussen Ep-Dl en cn-Dl kon nie bepaal word nie omdat die endopeptidase bande geproduseer deur die ouerlike materiaal wat in die studie gebruik is, nie met sekerheid in die nageslag onderskei kon word nie. Rekombinasie-frekwensies van 32 ± 4.97% tussen Dn5 en Ep-Dl en 37 ± 6.30% tussen Dn5 en cn-Dl is egter bereken. Dit word voorgestel dat daar na die twee onbekende endopeptidase-allele wat in 'SA 463 ' voorkom, verwys word as Ep-Dle en Ep-Ald. 'n Russiese koringluis-weerstandsgeen is uit die rog-aanwins, 'Turkey 77', oorgedra na koring en in die proses is die Russies koringluis weerstandbiedende lyne, 91M37-7 en 91M37-51 , geproduseer. Geen rog-chromatien kon egter met behulp van C-bande in hierdie lyne waargeneem word nie. Die doel van die studie was om te bepaal (i) op watter chromosoom die geen(e) voorkom, en (ii), of die Russiese koringluis weerstandsgeen die gevolg kan wees van 'n klein interkalere translokasie van rog- chromatien. 'n Monosoom-analise van die Russiese koringluis-weerstandsgeen in 91M37-51 het getoon dat 'n enkele dominante weerstandsgeen op chromosoom 7D voorkom. Rog-spesifieke herhalende peilers het geen polimorfismes tussen negatiewe kontroles en die Russiese koringluis weerstandbiedende lyne 91M37-7 en 91M37-51 getoon nie. Dit is dus onwaarskynlik dat die weerstand in die lyne uit rog verhaal is.

Most breeding programs aim at developing superior germplasm and better cultivars that combine high yield, disease and pest resistance, and end-use quality to satisfy the requirements of the growers as well as industry. A population, consisting of 138 F2-8 recombinant inbred lines (RILs) derived from a cross between ‘Steele-ND’ and ND 735, was evaluated to study the inheritance pattern of the septoria tritici blotch (STB)-resistant genes, agronomic and quality traits. The framework map made of 392 markers, including 28 simple sequence repeat (SSR) markers and 364 DArT markers, spanned a total distance of 1789.3 cM and consisted of 17 linkage groups. The map position of quantitative trait loci (QTL) found in this study coincided with the map position of durable STB resistance genes, Stb1. Thirteen QTL were detected for agronomic and quality traits. More saturation of the current map is needed to explore more QTL for this population.

Thesis (MSc)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: Wheat rust, caused by the Puccinia spp., is a global biotic cause of wheat yield losses. This disease can effectively be combatted by implementing rust resistant wheat cultivars. The release of new resistant wheat cultivars is however prolonged due to the time needed to fix resistance genes in a good quality background and develop pure breeding wheat lines. The aim of this study was the pyramiding of novel species derived leaf and stripe rust resistance genes in bread wheat lines through the utilization of high throughput marker assisted selection and microspore derived doubled haploid technology.
AFRIKAANSE OPSOMMING: Koringroes het wêreldwyd verliese in koringopbrengste tot gevolg. Dit word veroorsaak deur die Puccinia fungi. Hierdie siekte kan effektief beveg word deur die verbouing van roesbestande kultivars. Die vrystel van nuwe weerstandbiedende kultivars is egter ‘n langdurige proses weens die tyd verbonde daaraan om weerstandsgene te fikseer in ‘n genetiese agtergrond met ‘n goeie kwaliteit en om dan suiwertelende lyne te ontwikkel. Die doelwit van hierdie studie was om nuwe spesie-verhaalde blaar- en streeproes weestandsgene in koringlyne te stapel met behulp van merker bemiddelde seleksie en mikrospoor geassosieerde verdubbelde haploïede tegnologie.

Thesis (PhD (Genetics))--University of Stellenbosch, 2010.
Includes bibliography.
ENGLISH ABSTRACT: The wild relatives are an important source of new genes for the genetic improvement of wheat. At Stellenbosch University the leaf and stripe rust resistance genes Lr54 and Yr37 were transferred from Aegilops kotschyi to chromosome 2DL of wheat. In an attempt to reduce the size of the whole-arm translocation on which the resistance genes occur, homoeologous pairing was induced between the wheat and corresponding Ae. kotschyi chromatin. The purpose of this study was to: (i) Evaluate the testcross progeny thus obtained; identify translocation recombinants that retained Lr54/Yr37 and to characterize these using molecular markers (ii) Test for the presence of genes for photoperiod insensitivity (Ppd) and reduced height (Rht) believed to be associated with the translocation (iii) Develop a SCAR marker for the most useful recombinant that could be recovered. Ten putative translocation recombinants were identified following the screening of 159 hemizygous testcross F1 plants with three microsatellite markers specific for chromosome arm 2DL. The recombinants were then characterized with another five microsatellite markers. Using the eight microsatellite markers the recombinants were ordered in two size categories with recombinant #74 being the shortest and having retained only proximal alien chromatin on 2DL. In addition to microsatellite markers, RAPDs, RGAs, AFLPs and SCAR markers were genetically mapped to the translocation and further resolved the recombinants into three size categories. In an attempt to find suitable markers linked to the shortest recombinant (#74) a polymorphic 410 bp AFLP fragment produced with the enzyme/selective nucleotide combination EcoRI – AAC/MseI – CAT, was converted into a dominant SCAR marker. In addition three microsatellite markers that mapped to recombinant #74 provided a useful recessive molecular marker system to detect Lr54/Yr37. Evaluation of the 10 recombinants with four 2DS-specific microsatellite markers revealed a large deletion of this chromosome arm in recombinant #74. This deletion may affect plant phenotypic characteristics and a strategy to replace the deleted region in recombinant #74 is proposed. To test for the presence of a gene for photoperiod insensitivity on the translocation, translocation-carriers plus controls were subjected to long and short day treatments, and the effect on time to flowering was studied. However, no evidence was found for the presence of such a gene. A height experiment to test for the presence of an Rht gene on the translocation confirmed its presence. This gene (designated H) appeared to be different from Rht8 on chromosome 2DS and was mapped on 2DL. While H does not occur in a chromosome region that corresponds with the location of Rht8, it does not rule out the possibility that they could be orthologous loci. Plant height data obtained for recombinant #74 suggested that H was lost through recombination in this particular recombinant. A greenhouse experiment suggested that the full-length translocation increased 100 kernel mass but had a detrimental effect on overall plant yield. Since a much shorter recombinant (#74) has been obtained, this will also have to be evaluated for associated effects. Such an evaluation needs to be done under commercial growing conditions and should involve the comparison of near-isogenic bulks with and without recombinant chromosome #74. The stripe rust resistance gene (Yr37) was mapped by screening hemizygous TF2 progeny of the 10 recombinants with Puccinia striiformis pathotype 6E22A+. Recombinant #74 retained both Lr54 and Yr37 and the two genes therefore occur towards the centromere.
AFRIKAANSE OPSOMMING: Wilde verwante spesies is ‘n belangrike bron van nuwe gene vir die genetiese verbetering van koring. By die Universiteit van Stellenbosch is die blaar-roes en streep-roes weerstandsgene Lr54 en Yr37 vanaf Aegilops kotschyi na chromosoom 2DL van koring oorgedra. ‘n Poging is vervolgens aangewend om die vol-armtranslokasie waarop die weerstandsgene voorkom te verklein deur homoeoloë paring tussen die koring en ooreenstemmende Ae. kotschyi chromatien te induseer. Die doelstelling van hierdie studie was daarom as volg: (a) Evaluering van die verkreë toetskruis-nageslag asook die identifisering en karakterisering van translokasie rekombinante wat Lr54/Yr37 behou het. (b) Toetsing vir fotoperiode onsensitiwiteits- (Ppd) en verkorte plant-hoogte (Rht) gene wat moontlik op die translokasie kon voorkom. (c) Die ontwikkeling van ‘n volgorde-spesifieke polimerase kettingreaksie (PKR) vir die mees bruikbare rekombinant. Tien translokasie rekombinante is geïdentifiseer nadat 159 hemisigotiese toetskruis F1-plante met drie mikrosatelliet-merkers, spesifiek vir chromosoom-arm 2DL, ge-evalueer is. Die rekombinante is hierna met vyf verdere mikrosatellietmerkers getoets. Die data van die agt mikrosatelliet-loci het die rekombinante in twee grootte-kategorieë geplaas waarvan rekombinant #74 die kortste was met slegs die proksimale gedeelte van 2DL wat uit vreemde chromatien bestaan. Behalwe mikrosatellite-merkers is toevallig-geamplifiseerde polimorfiese DNS (RAPD), weerstandsgeen-analoog (RGA), geamplifiseerde volgordelengte polimorfisme (AFLP) en volgorde-gekarakteriseerde geamplifiseerde-streke (SCAR) merkers ook geneties op die translokasie gekarteer. Data van die addisionele merkers het dit moontlik gemaak om die rekombinante in drie grootte-kategorieë te skei. Pogings om ‘n merker vir die kortse rekombinant (#74) te vind, het gelei tot die omskakeling van ‘n 410 bp polimorfiese AFLP-fragment (geproduseer met die ensiem/selektiewenukleotied kombinasie EcoRI - AAC/MseI - CAT), na ‘n dominante, volgordespesifieke PKR-merker. Hierbenewens kan drie mikrosatelliet-merkers wat op rekombinant #74 karteer as resessiewe merkers vir die identifisering van Lr54/Yr37 gebruik word. Die evaluering van die 10 rekombinante met vier chromosoom 2DSspesifieke mikrosatelliet-merkers het ‘n groot delesie van chromosoom-arm 2DS in rekombinant #74 uitgewys. Die delesie mag plant fenotipiese kenmerke beïnvloed en daarom is ‘n strategie vir die vervanging daarvan in rekombinant #74 voorgestel. Ten einde te toets of ‘n geen vir fotoperiode-onsensitiwiteit op die translokaie voorkom is translokasie-draers en kontroles aan lang- en kortdag-behandelings onderwerp en is die effek hiervan op dae-tot-blom gemeet. Geen bewyse vir so ‘n geen kon gevind word nie. ‘n Hoogte-eksperiment om te toets vir die teenwoordigheid van ‘n Rht-geen op die translokasie, het bevestig dat so ‘n geen wel voorkom. Die geen (voorgestelde simbool H) is gekarteer op 2DL en verskil oënskynlik van Rht8 op chromosoom 2DS. Die verskillende chromosoom-ligging van H en Rht8 skakel egter nie die moontlikheid dat hulle ortoloë loci mag wees uit nie. Plant-hoogte data vir rekombinant #74 het daarop gedui dat H nie meer in hierdie rekombinant voorkom nie. Data van ‘n glashuis-eksperiment het daarop gedui dat die vollengte-translokasie 100-korrel-massa verhoog maar dat dit plant-opbrengs verlaag. Aangesien ‘n aansienlike korter rekombinant (#74) verkry is, sal dit ook vir gekoppelde effekte getoets moet word. So ‘n evaluering moet egter onder kommersiële toestande gedoen word met gebruik van naby isogeniese-lyne met en sonder rekombinante chromosoom #74. Die streep-roes weerstandgeen (Yr37) is gekarteer deur hemisigotiese TF2- nageslag van die 10 rekombinante te toets vir weerstand teen Puccinia striiformis patotipe 6E22A+. Rekombinant #74 het beide Lr54 en Yr37 behou en die twee gene karteer dus naby die sentromeer.

Thesis (MSc)--Stellenbosch University, 2014.
ENGLISH ABSTRACT: Wheat production is globally affected by several different wheat rust diseases. The rust diseases can effectively be controlled by the deployment of multiple resistance genes that confer durable resistance. One of the most effective strategies to incorporate resistance genes is by the implementation of recurrent mass selection as it maximizes opportunities for gene pyramiding. The implementation of a recurrent mass selection program in wheat can effectively be enhanced with the use of genetic male sterility and the incorporation of maker assisted-selection (MAS). The aim of the study was to pyramid wheat rust resistance genes in wheat lines by utilizing a male sterile mediated marker-assisted recurrent selection breeding (MS-MARS) scheme. An existing segregating MS-MARS base population and resistance donor lines carrying genes of interest (Sr26, Sr35 and Sr45) were used as female and male crossing parents. Potential markers for the genes of interest were first identified and validated on the male population. PCR based markers tested for Sr26 and Sr45 easily distinguished between resistant and non-resistant plants in the study, while markers tested for the detection of Sr35 and Sr45 in most instances failed to do so. The identified Sr26 marker (Sr26#43) was successfully added to the SU-PBL’s standardized marker set in a multiplex reaction. The standardized marker set and the co-dominant PCR marker for Sr45 were used to screen male and female populations before and after cross-pollination. Several wheat rust resistance genes were present in various frequencies in both male and female populations prior to the first crossing cycle, except Sr26 and Sr45. Increases in gene frequencies and combinations were obtained after the first crossing cycle, highlighting the effectiveness of the MS-MARS breeding strategy to improve gene frequencies of desirable genes. Two MS-MARS crossing cycles were successfully completed and large numbers of hybrid seeds were produced in a short period of time by selecting male sterile plants based on distinct characteristics induced by the dominant male sterility gene. Future studies will include the wide deployment of Sr26 and Sr45 in the MS-MARS breeding program as markers are now available and can be included in the SU-PBL’s standardized marker set for the effective detection of these genes, the development of gene-specific markers for Sr35 to ascertain the presence of the gene in the MS-MARS population and the specific selection of male sterile plants with wide open glumes to maximize outcrossing rates.
AFRIKAANSE OPSOMMING: Koring produksie word wêreldwyd aansienlik deur koringroes siektes geaffekteer. Die siektes kan doeltreffend beheer word deur die ontplooing van veelvuldige weerstandsgene, wat langdurige weerstand tot gevolg het. Een van die mees doeltreffendste strategieë om weerstandsgene in n koring plant te inkorporeer is deur die implementering van herhalende massa seleksie (HMS), siende dat dit geleenthede vir geen stapeling maksimaliseer. Die implementering van 'n HMS program in koring kan effektief aangewend word met behulp van genetiese manlike steriliteit en merker bemiddelde seleksie (MBS). Die doelwit van hierdie studie was om veelvuldige koringroes weerstandsgene in koring lyne te stapel met behulp van die manlik steriliteits merker bemiddelde herhalende seleksie (MS-MBHS)-telingsskema. ‘n Gevestigde segregerende MS-MARS basis populasie en donor lyne, wat die gene (Sr26, Sr35 en Sr45) van belang dra, was onderskeidelik as vroulike en manlike kruisingsouers gebruik. Potensiële molekulêre merkers vir die gene van belang was eers geidentifiseer in literatuur en op die donor lyne getoets, voordat dit vir die opsporing van die gene in die nageslag gebruik was. Polimerase ketting reaksie (PKR)-gebaseerde merkers wat getoets was vir Sr26 en Sr45, kon maklik tussen weerstand en nie-weerstandbiedende plante in die studie onderskei, terwyl ander merkers vir die opsporing van Sr35 en Sr45 nie so doeltreffend was nie. Die geidentifiseerde Sr26 merker was suksesvol bygevoeg tot die SU-PBL se gestandardiseerde merkerpaneel, in ‘n multipleks reaksie. Die gestandardiseerde merkerpaneel en die ko-dominante PKR merker vir Sr45 was gebruik om die manlike en vroulike populasie te analiseer vir die teenwoordigheid van verskeie weerstandsgene voor en na kruisbestuiwing. Merker analise het die teenwoordigheid van verskeie koringroes weerstandsgene in verskillende frekwensies in beide die manlike en vroulike populasie voor die eerste kruising siklus aangedui. Sr26 en Sr45 was egter afwesig in beide populasies. ‘n Toename in geen frekwensies en kombinasies was waargeneem na die eerste kruising siklus. Dit het gevolglik die doeltreffendheid van die MS-MARS teling strategie beklemtoon. Twee herhalende kruising siklusse was suksesvol voltooi en groot hoeveelhede bastersaad was verkry vanaf steriele plante wat geselekteer was op grond van unieke eienskappe wat hulle vertoon as gevolg van die manlike steriliteits geen. Toekomstige studies sluit in, die groot skaalse gebruik van Sr26 en Sr45 in die MS-MARS teelprogram aangesien merkers nou beskikbaar is en gebruik kan word in die MS-MARS teelprogram vir die doeltreffende opsporing van hierdie gene, die ontwikkeling van ‘n geen-spesifieke merker vir Sr35 om die teenwoordigheid van die geen in die MS-MARS populasie vas te stel, en die selektering van manlike steriele plante met wyd oop kaffies om kruisbestuiwing te verhoog.

Take - all disease ( caused by Gaeumannomyces graminis var tritici, Ggt ) can be suppressed by soil microorganisms after continuous monoculture of wheat ( take - all decline, TAD ). Fluorescent pseudomonads have been implicated in this suppression. Two strategies for controlling take - ail are the in situ development of disease suppressive soil, and / or the application of a biocontrol agent. However, TAD takes up to 10 years to develop after initially high levels of disease, and the performance of bacterial biocontrol agents has been inconsistent. It is not known what environmental factors select for disease antagonists. In this work the role of diseased root lesions in directing the evolution of a native pseudomonad community, and a model disease antagonist, Pseudomonas corrugate strain 2140 ( Pc2140 ) for increased disease suppression was investigated. This work shows that root lesions are a distinct niche, supporting increased populations of total aerobic bacteria ( TAB ), pseudomonads and Pc2140 ( compared to non - lesioned sections of diseased roots and healthy roots ). Lesions selected for fluorescent pseudomonads and pseudomonads which increase take - all severity. In. contrast, lesions selected for non - pseudomonads which decrease take - all, and healthy roots selected for non - fluorescent pseudomonads which decrease take - all. It was concluded that non - fluorescent pseudomonads and non - pseudomonads were important in reducing take - all, but not fluorescent pseudomonads. Pc2140 produced multiple variant phenotypes in vitro and on wheat roots which were altered in ( 1 ) their ability to inhibit pathogens in vitro and control take - all, and ( 2 ) GC - FAME and BIOLOG profiles to the extent that some variants were identified as different species. Different sets of phenotypes were produced in vitro and on roots. After 108 weeks culture of Pc2140 on root lesions and healthy wheat roots, variant colony types were generally slightly decreased in ability to reduce take - all, and reisolates with the wild type colony morphology were generally slightly increased in ability to reduce take - all compared to the ancestral Pc2140. This is the first report on the diversification of a pseudomonad biocontrol agent on roots, and has implications for the taxonomic identification and grouping of isolates based on phenotypic characteristics.
Thesis (Ph.D.)--Department of Crop Protection, 1998.

Thesis (PhD (Agric)) -- Stellenbosch University, 2003.
ENGLISH ABSTRACT: Stripe (yellow) rust of wheat, caused by Puccinia striiformis f.sp. tritici, was first detected as a single introduction into South Africa in 1996. Two additional pathotypes have since been identified. Control of the disease may be achieved by use of genetic adult plant resistance (APR) as is present in the local cultivar 'Kariega'. The aim of this project was to understand the genetic basis of the APR in 'Kariega' to facilitate breeding of new varieties with genetic resistance to stripe rust. A partial linkage map of a 'Kariega X Avocet S' doubled haploid population covering all 21 wheat chromosomes was generated using 208 DNA markers, viz, 62 SSR, 133 AFLP, 3 RGA and 10 SRAP markers, and 4 alternative loci. The different marker techniques detected varying polymorphism, viz, overall SSR: 46%, AFLP: 7%, SRAP: 6% and RGA: 9%, and the markers produced low levels of missing data (4%) and segregation distortion (5%). A significant feature of the linkage map was the low polymorphism found in the D genome, viz, 19% of all mapped DNA markers, 11% of all AFLP markers and 30% of the total genome map distance. A region exhibiting significant segregation distortion was mapped to chromosome 4A and a seedling resistance gene for stem rust (Puccinia graminis f.sp . tritici), Sr26, mapped to chromosome 6A close to three SSR markers. The leaf tip necrosis gene, Ltn, which was also segregating in the population, mapped to chromosome 7D. Protocols for SRAP and RGA were optimised, and SRAP marker use in wheat genetic linkage studies is reported for the first time. The linkage map was used together with growth chamber and replicated field disease scores for QTL mapping. Chromosomes showing statistically significant QTL effects were then targeted with supplementary SSR markers for higher resolution mapping. The quality of disease resistance phenotypic data was confirmed by correlation analysis between the different scorers for reaction type (0.799±0.023) and for transformed percentage leaf area infected (0.942±0.007). Major QTL were consistently identified on chromosome 7D (explaining some 25-48% of the variation) and on chromosome 2B (21-46%) using transformed percentage leaf area infected and transformed reaction type scores (early and final) with interval mapping and modified interval mapping techniques. Both chromosomal regions have previously been identified in other studies and the 7D QTL is thought likely to be the previously mapped APR gene Yr 18. Minor QTL were identified on chromosomes lA and 4A with the QTL on 4A being more prominent at the early field scoring for both score types. A QTL evidently originating from 'Avocet S' was detected under growth chamber conditions but was not detected in the field, suggesting genotype-environment interaction and highlighting the need for modifications of growth chamber conditions to better simulate conditions in the field. The genetic basis of the APR to stripe rust exhibited by 'Kariega' was established by mapping of QTL controlling this trait. The linkage map constructed will be a valuable resource for future genetic studies and provides a facility for mapping other polymorphic traits in the parents of this population with a considerable saving in costs.
AFRIKAANSE OPSOMMING: Streep of geelroes van koring word veroorsaak deur Puccinia striiformis f. sp tritici, en is die eerste keer in 1996 in Suid-Afrika na introduksie van 'n enkele patotipe waargeneem. Twee verdere patotipes is sedertdien in Suid-Afrika gei"dentifiseer. Beheer van die siekte word veral moontlik gemaak deur die gebruik van genetiese volwasseplantweerstand soos gei"dentifiseer in die plaaslike kultivar 'Kariega'. Die doel van hierdie studie was om die genetiese grondslag van die streeproesweerstand te ontrafel ten einde die teling van nuwe bestande kultivars moontlik te maak. 'n Verdubbelde haplo1ede populasie uit die kruising 'Kariega X Avocet S' is aangewend om 'n gedeeltelike koppelingskaart vir die volle stel van 21 koring chromosome saam te stel. Die kaart het uit 208 DNA merkers, nl., 62 SSR, 133 AFLP, 3 RGA, 10 SRAP merkers en 4 ander lokusse bestaan. Totale polimorfisme wat deur die verskillende merkersisteme opgespoor is, was as volg: SSR: 46%, RGA: 9%, AFLP: 7% en SRAP: 6%. Die mate van ontbrekende data was gering (4%) asook die mate van segregasie distorsie (5%) van 'n enkele geval wat op chromosoom 4A gekarteer is. 'n Prominente kenmerk van die koppelingskaart is die relatiewe gebrek aan polimorfiese merkers op die D-genoom, nl., slegs 19% van alle DNA merkers en 11% van alle AFLP merkers wat slegs 30% van die totale genoom kaartafstand bestaan het. Die stamroes (Puccinia graminis f. sp. tritici) saailingweerstandsgeen, Sr26, karteer op chromosoom 6A naby drie SSR merkers. Die geen vir blaartipnekrose, Ltn, karteer op chromosoom 7D. Protokolle vir SRAP en RGA merkers is ge-optimiseer en gebruik van SRAP merkers in koppelings-analise word vir die eerste keer in koring gerapporteer. Die koppelingskaart is in kombinasie met groeikamerdata en gerepliseerde veldproefdata gebruik om die gene (QTL) vir volwasseplant streeproesweerstand te karteer. Chromosome met statisties betekenisvolle QTL is met aanvullende SSR merkers geteiken om die resolusie van kartering verder te verhoog. Die kwaliteit van fenotipiese data, soos in die proewe aangeteken, is bevestig deur korrelasies te bereken tussen lesings geneem deur onafhanklike plantpataloe (0.799 ± 0.023 vir reaksietipe en 0.942 ± 0.007 vir getransformeerde persentasie blaaroppervlakte besmet). Hoofeffek QTL vir die twee maatstawwe van weerstand is deur middel van die metodes van interval QTL kartering en gemodifiseerde interval QTL kartering konsekwent op chromosome 7D (25-48% van variasie verklaar) en 2B (21-46% van variasie verklaar) ge"identifiseer. In vorige studies is aangetoon dat beide chromosome 7D en 2B QTL vir volwasseplant streeproesweerstand dra. Die 7D QTL is waarskynlik die weerstandsgeen, Yr 18. QTL met klein effekte op weerstand is op chromosome lA en 4A ge"identifiseer. Die effek van laasgenoemde geen was meer prominent in die velddata in die vroee datum van weerstandsbeoordeling. Een QTL, afkomstig van 'Avocet S', is slegs onder groeikamertoestande identifiseerbaar. Dit dui op moontlike genotipe-omgewing wisselwerking en beklemtoon die noodsaaklikheid om aanpassings te maak in groeikamertoestande vir beter simulasie van veldproeftoestande. Die genetiese grondslag van volwasseplantweerstand teen streeproes in die kultivar 'Kariega' is deur QTL kartering bepaal. Die 'Kariega X Avocet S' koppelingskaart kan as 'n waardevolle basis dien vir toekomstige genetiese ontledings van ander polimorfiese kenmerke in die populasie.

T. aestivum ssp. spelta Iranian type has long been thought to potentially be the direct non-free threshing hexaploid progenitor. I evaluated a RIL population derived from a cross between CS and Iranian spelta accession P503 to identify loci suppressing free-threshabilty in P503. Identification of QTL associated with threshability in region known to harbor the Tg2A gene, and an inactive tg2D allele supported the hypothesis of Iranian spelta being derived from a more recent hybridization between free-threshing hexaploid and emmer wheat. Parastagonospora nodorum is an important fungal pathogen and secretes necrotrophic effectors that evoke cell death. In this research, a DH population segregating for Snn5 was used to saturate Snn5 region of chromosome 4B with molecular markers. The physical distance between Snn5 flanking markers was narrowed to 1.38 Mb with genetic distance of 2.8 cM. The markers developed in this study will provide a strong foundation for map-based cloning of Snn5.

Thesis (PhD)--Stellenbosch University, 2015
ENGLISH ABSTRACT : Diuraphis noxia Kurdjumov (Russian Wheat Aphid; RWA) is a pest of wheat and barley that has spread from its home range in the fertile crescent to most wheat producing countries except Australia. Since its first introduction to South Africa and the USA in the late 20th century, breeding programs for wheat phenotypes resistant to the aphid were put in place. Conventional breeding practices rely on phenotypic screening to verify traits carried by offspring and genetic tools such as marker assisted selection (MAS) have greatly aided this process in speed and accuracy. The size and complexity of the wheat genome, its allopolyploid nature and repetitive elements have, however, posed a challenge to studies on the genetics of this cereal crop. Many studies have focused on chromosome 3B which is the largest of the wheat chromosomes and easily separated from the redundant genomic background by techniques such as flow cytometry. The similarity in size of the remaining chromosomes however, limits the application of flow cytometry to their isolation. Databases such as Grain-Genes (http://wheat.pw.usda.gov/GG2/index.shtml) house marker data from various mapping studies for all wheat chromosomes and in 2014 the International Wheat Genome Sequencing Consortium (IWGSC) completed the draft genome sequence of wheat categorized by chromosome. Sources of resistance (Dn resistance genes) against RWA are located on chromosome 7D. but despite the marker and sequence data available currently, mapping studies specific for the Dn resistance genes are few. Additionally, sequence data available is derived from cultivars susceptible to RWA and is not comprehensively annotated and assembled in many cases. In this study, we demonstrate a novel, combined approach to isolate and characterize the Dn resistance genes through the use of a genetic map constructed from Amplified Fragment Length Polymorphism (AFLP), Expressed Sequence Tag (EST) and microsatellite markers and a physical map constructed from Next Generation Sequencing (NGS) data of ditelosomic chromosomes (7DS and 7DL) isolated by microdissection on the PALM microbeam system. A 122.8 cM genetic map was produced from 38 polymorphic AFLP markers and two ESTs with the microsatellite Xgwm111 as anchor to related genetic maps. Through comparison to maps available on GrainGenes the location of the Dn1 resistance gene was narrowed down to a deletion bin (7DS5-0.36-0.62) on the short arm of chromosome 7D with an AFLP marker (E-ACT/M-CTG_0270.84) mapping closely at 3.5 cM and two ESTs mapping at 15.3 cM and 15.9 cM from Dn1. Isolation of individual chromosome arms 7DS and 7DL using the PALM Microbeam system allowed sequencing of the chromosome without the redundancy of the remainder of the hexaploid genome. Through isolating the chromosome arms in this way, a >80-fold reduction in genome size was achieved as well as a major reduction in repetitive elements. Analysis of the sequencing data confirmed that 7DL is the physically shorter arm of the chromosome though it contains the majority of protein coding sequences.
AFRIKAANSE OPSOMMING : Diuraphis noxia Kurdjumov (Russiese koring-luis; RWA) is « pes wat op koring en gars voorkom. Die pes het vanaf sy tuiste in die midde Ooste na meeste koringproduserende lande behalwe Australië versprei. Sedert die eerste bekendstelling van RWA in Suid Afrika en die VSA in die vroeë 20ste eeu is teelprogramme ten gunste van koring lyne met weerstand teen RWA begin. Tradisionele teelprogramme maak op fisieise observasie van die fenotipe staat om te verifieer of plante in die nageslag die gewenste eienskap dra. Genetiese metodes soos merkerondersteunde seleksie (MAS) versnel hierdie selekteringsproses grootliks. Die grootte en kompleksiteit van die koring genoom asook die polyploïde en herhalende natuur daarvan is « groot hindernis vir genetiese studies van hierdie graangewas. Baie studies het op chromosoom 3B gefokus wat die grootste van die koring chromosome is en dus maklik vanaf die res van die oorbodige genomiese agtergond deur tegnieke soos vloeisitometrie geskei word. Die ooreenkoms in grootte tussen die res van die chromosome bemoeilik die toepassing van vloeisitometrie om hulle te isoleer. Databasisse soos GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml) bevat merker data vanaf verskeie karterings-studies vir al die chromosome en in 2014 het die "International Wheat Genome Sequencing Consortium"(IWGSC) die voorlopige basispaarvolgorde van die koring genoom bekendgestel, gekategoriseer volgens chromosoom. Weerstandsbronne (Dn weerstandsgene) teen RWA kom meestal op chromosoom 7D voor. Ten spyte van merker en basispaarvolgorde data tans beskikbaar is karterings-studies spesifiek tot die Dn gene skaars en basispaarvolgorde data is vanaf kultivars afkomstig wat nie weerstandbiedend teen RWA is nie en waarvan die annotasie en samestelling baie keer nie goed is nie. In hierdie studie demonstreer ons « nuwe, gekombineerde aanslag om die Dn weerstandsgene te isoleer en karakteriseer deur van « genetiese kaart opgestel met "Amplified Fragment Length Polymorphism"(AFLP), "Expressed Sequence Tag"(EST) en mikrosatelliet merkers asook « fisiese kaart saamgestel deur die volgende-generasiebasispaarvolgordebepaling van ditelosomiese chromosome (7DS en 7DL) geïsoleer deur mikrodisseksie met die "PALM Microbeam"sisteem gebruik te maak. « Genetiese kaart van 122.8 cM was met 38 polimorfiese AFLP merkers en twee EST merkers geskep. Die mikrosatelliet, Xgwm111, is ook ingesluit en het as anker vir verwante genetiese-kaarte gedien. Deur vergelyking met genetiese-kaarte op GrainGenes is die posisie van die Dn1 weerstandsgeen vernou na « delesie bin (7DS5-0.36-0.62) op die kort arm van chromosoom 7D met « AFLP merker (EACT/ M-CTG_0270.84) wat ongeveer 3.5 cM vanaf die geen karteer. Die twee EST merkers is 15.3 cM en 15.9 cM vanaf die geen gekarteer. Isolering van die individuele chromosoom arms, 7DS en 7DL, deur van die "PALM Microbeam"sisteem gebruik te maak het basispaarvolgordebepaling van die chromosoom toegelaat sonder die oortolligheid van die res van die hexaploïde genoom. Deur die chromosoom so te isoleer is « >80-maal verkleining in genoom grootte bereik insluitend « groot reduksie in herhalende elemente. Analise van die data vanaf basispaarvolgordebepaling het bevestig dat chromosoom 7D die fisiese kleiner chromosoom is maar dat dit die meerderheid van proteïn koderende basispaarvolgordes bevat.

Thesis (PhD (Agric)) -- Stellenbosch University, 2001.
ENGLISH ABSTRACT: Chromosome arm 7DL of common wheat carries genes for agronomically important traits such as leaf rust, stem rust, Russian wheat aphid and eye spot resistance. Some of these genes occur on introgressed foreign chromatin, which restricts their utility in breeding. The 7DL genetic maps are poorly resolved, which seriously hampers attempts to manipulate the genes and introgressed regions in breeding. This dissertation represents an attempt to improve our knowledge of the relative map positions of three resistance genes that have significant potential for use in local breeding programmes. The leaf rust resistance gene, Lr19, is located on a Thinopyrum ponticum-derived translocation which occupies a large part of the terminal end of 7DL. The translocation also carries genes for less favourable traits such as yellow flour colour. Attempts have been made to reduce the size of the translocation through allosyndetic pairing induction; the primary aims being to remove deleterious genes and to minimise the amount of foreign chromatin associated with Lr19 so it can be recombined with other useful 7DL genes. Twenty-nine 'Indis'-derived Lr 19 deletion mutants were previously produced by gamma irradiation and a physical map was constructed. In this study, the set of mutant lines were further analysed using 144 Sse8387I/Msei and 32 EcoRI/Msel amplified fragment length polymorphism (AFLP) primer combinations. The previous physical map, which was based on five restriction fragment length polymorphism (RFLP) markers and five structural gene loci, was extended and now includes 95 novel AFLP markers (86 Sse8387I/Msei and 9EcoRI!Msel markers), of which seven map close to Lr 19. Most of the deletions could be ordered according to size and the improved map has already been used to characterise shortened recombinant forms of the Lr 19 translocation. An unsuccessful attempt was made to convert one of the seven markers closest to Lr 19 into a sequence-specific marker. However, an AFLP marker located distally from Lr 19 was successfully converted into a sequence-specific marker in collaboration with other researchers. An attempt was also made to map and tag the Russian wheat aphid (RWA) resistance gene, Dn5. A doubled haploid mapping population consisting of 94 lines was created and typed for Dn5, four microsatellite loci and the endopeptidase locus, Ep-Dl. The Dn5 locus mapped 25.4 cM and 28.6 cM distally from Xg.vm111 and Xg.vm437, respectively, but was not linked to Xgwm428, Xgwm3 7 or Ep-Dl. Tagging of Dn5 was attempted by screening twelve homozygous resistant and seven homozygous susceptible F2 lines from a cross between 'Chinese Spring' and 'PI 294994' with 70 Sse8387IIi\1sei AFLP primer combinations. Only two potentially useful polymorphisms (one in coupling and one in repulsion phase) were identified. Conversion of the coupling phase marker to a sequence-specific marker was not successful. The eyespot resistance gene, Pchl , was derived from Triticum ventricosum and is present in the wheat VPM-1. Close association between Pchl and the endopeptidase Ep-Dlb allele has been reported previously. Pchl/Ep-Dl was tagged by screening ten wheat genotypes (each homozygous for the confirmed presence or absence of Pchl and/or Ep-Dl b) with 36 Sse83 87I/ Msei AFLP primer combinations. Three AFLP markers were closely associated with Pchl I Ep-D 1, one of which was targeted for conversion into a sequence-specific marker. The sequence-specific marker contained a microsatellite core motif and was found to be useful for tagging Pchl!Ep-Dl. A genetic distance of 2 cM was calculated between the novel microsatellite marker and Ep-Dl. The microsatellite marker was also polymorphic for the Lr 19 translocation and it was possible to map it between the Wsp-Dl and Sr25 loci. In this dissertation, mapping and/or tagging of three important resistance genes were achieved. Due to the fact that all markers used in these studies were not polymorphic between all of the targeted regions, it was not possible to fully integrate the data obtained for the three regions.
AFRIKAANSE OPSOMMING: Chromosoom arm 7DL van broodkoring dra gene vir agronomies-belangrike kenrnerke soos blaarroes, stamroes, Russiese koringluis en oogvlek weerstand. Sommige van hierdie gene kom voor in blokke spesie-verhaalde chromatien wat hul bruikbaarheid in teling beperk. Die genetiese kaarte van 7DL is swak ontwikkel en dit maak dit baie moeilik om hierdie gene en spesie-verhaalde streke tydens teling te manipuleer. Hierdie proefskrif verteenwoordig 'n paging om kennis van die relatiewe kaart liggings van drie weerstandsgene, met betekenisvolle potensiaal in plaaslike tee! programme, te verbreed. Die blaarroes weerstandsgeen, Lr 19, kom voor op 'n Thinopyrum ponticum-verhaalde translokasie wat 'n groot terminale gedeelte van 7DL beslaan. Die translokasie dra ook gene vir minder gewensde kenrnerke soos gee! meelkleur. Pogings is aangewend om die translokasie deur homoeoloe parings-induksie te verkort. Die doe! was om nadelige gene te verplaas en die hoeveelheid vreemde chromatien geassosieer met Lr 19 te minimiseer sodat dit met ander nuttige gene op 7DL gerekombineer kan word. Nege-en-twintig 'Indis'-verhaalde Lr 19 delesie mutante is vroeer met gamma bestraling geproduseer en gebruik om 'n fisiese kaart op te stel. Teenswoordig is die stel mutante verder ontleed met behulp van 144 Sse8387I!Msei en 32 EcoRII Msel amplifikasie-fragment-lengte-polimorfisme (AFLP) inleier kombinasies. Die bestaande fisiese kaart, wat gebaseer was op vyf restriksie-fragment-lengte-polimorfisme (RFLP) merkers en vyf strukturele geen loki, is uitgebrei en sluit nou 95 unieke AFLP merkers (86 Sse8387I/Msel en 9EcoRI/Msel merkers) in, waarvan sewe naby aan Lr19 karteer. Die meeste van die delesies kon op grond van hulle grootte gegroepeer word en die verbeterde fisiese kaart is alreeds gebruik om verkorte rekombinante vorms van die Lr 19 translokasie te karakteriseer. 'n Onsuksesvolle paging is aangewend om een van die sewe merkers naaste aan Lr 19 om te skakel na 'n volgorde-spesifieke merker. 'n AFLP merker wat distaal van Lr 19 karteer is egter wel suksesvol in samewerking met ander navorsers omgeskakel na 'n volgordespesifieke merker. 'n Paging is ook aangewend om die Russiese koringluis (RKL) weerstandsgeen, Dn5, te karteer en merkers gekoppel aan die geen te identifiseer. 'n Verdubbelde-haplo!ede karteringspopulasie van 94 lyne is geskep en getipeer vir Dn5, vier mikrosatelliet loki en die endopeptidase lokus, Ep-D1. Die Dn5 lokus karteer 25.4 cM en 28.6 cM distaal van Xgwml11 en Xgwm437, respektiewelik, maar was me gekoppel met Xgwm428, Xgwm37 of Ep-D1 me. Twaalf homosigoties weerstandbiedende en sewe homosigoties vatbare F2 lyne uit die kruising: 'Chinese Spring' I 'PI 294994' is met 70 Sse8387VMsel AFLP inleier kombinasies getoets in 'n poging om merkers vir Dn5 te identifiseer. Slegs twee moontlik bruikbare polimorfismes (een in koppelings- en een in repulsie fase ), is ge'identifiseer. Omskakeling van die koppelingsfase merker na 'n volgorde-spesifieke merker was onsuksesvol. Die oogvlek weerstandsgeen, Pch1, is uit Triticum ventricosum oorgedra en kom voor in die koringlyn, VPM-1. Noue koppeling van Pch1 en die endopeptidase alleel, Ep-D1 b, is vantevore gerapporteer. Merkers is vir P chl I Ep-D 1 gevind deur tien koring genoti pes ( elkeen homosigoties vir die bevestigde teenwoordigheid of afwesigheid van Pch1 en/of Ep-D1 b) te toets met 36 Sse83871/kfsel AFLP inleier kombinasies. Drie AFLP merkers is gevind wat nou koppel met Pchl!Ep-D1 , waarvan een gekies is vir omskakeling na 'n volgorde-spesifieke merker. Die volgorde-spesifieke merker het 'n mikrosatelliet kernmotief bevat en was nuttig as merker vir Pch1/Ep-D1. 'n Genetiese afstand van 2 cM is tussen die unieke mikrosatelliet merker en Ep-D1 bereken. Die mikrosatelliet merker was ook polimorfies vir die Lr 19 translokasie en dit is tussen die Wsp-D1 en Sr25 loki gekarteer. Kartering en/of identifikasie van merkers vir drie belangrike weerstandsgene was suksesvol in hierdie studie. Omdat al die merkers wat gebruik is, nie polimorf was tussen al die streke van belang nie, was dit nie moontlik om die data vir elk van die drie streke ten volle te integreer nie.

Thesis (MSc (Genetics))--University of Stellenbosch, 2005.
The Russian wheat aphid, Diuraphis noxia (Mordvilko), is a serious insect pest of wheat and barley. It affects the quality and yield of grain by sucking plant sap from the newest growth whilst toxic substances are injected that destroy plant tissue. The Russian wheat aphid also acts as a vector of plant viruses. The cultivation of aphid resistant cultivars is the preferred control strategy and nine resistance genes, designated Dn1 to Dn9, have been identified. Another undesignated gene, Dnx, was found in the wheat accession PI220127. Mapping of the resistance genes relative to known markers will improve their use in breeding programs. The dominant RWA resistance gene, Dn5, was identified in the accession PI294994 and mapped to chromosome arm 7DL. However, recent reports have placed Dn5 on ...

The Russian wheat aphid (RWA) (Diuraphis noxia Kurdjumov) is a major pest of cultivated small grains. It is particularly devastating because of is high reproductive rate which results in the growth of large populations which become damaging to its host plants. Development of resistant barley (Hordeum vulgare L.) cultivars is complicated as resistance is polygenic. As a result, the industry remains at risk now that the RWA has spread throughout South Africa. It has, as recently as, 2013, been identified in the SW Cape, which was previously geographically isolated. This is South Africa‟s principle barley growing region. Now a potentially huge problem exists. Therefore, it is imperative that an alternative to pesticide use is found. Testing potential innate resistance in barley cultivars is thus, critical. In this thesis, I present data on four barely cultivars where I have examined their resistance/ lack of resistance to three known RWA biotypes, RWASA1, RWASA2 and RWASA3. The barley varieties used were two economically important South African malt barley cultivars (S5 and SSG 564) along with two potentially RWA resistant Afghan accessions (CIho 4125 and CIho 4159). The RWA biotype population growth rates on each of the plants were determined over a 14 day period. The aim was to establish baseline data of the effects of RWA population growth on the host plants under ambient CO2 (380 – 400 ppm) conditions. The extent of RWA feeding damage was investigated at the cell level by examining saliva deposition and cell disruption using Transmission Electron Microscopy; at the tissue/vascular level using fluorescence microscopy, to determine the extent of callose formation; at a whole leaf level by recording percent chlorosis and leaf roll; and finally, at a whole plant level by measuring biomass loss.The experiments were repeated under elevated CO2 (450 ppm) to model any changes in RWA/plant interaction with respect to future climate change. The effects of an elevated CO2 environment and RWA feeding on host plant foliar N and C:N ratio were compared to ambient CO2 conditions, to provide a clearer picture of the potential nutrient drain that a feeding RWA colony exacts on its host. Of the varieties tested, the CIho accessions performed better than the two SA barley cultivars as the CIho accessions appeared to express a mild antibiosis resistance response as RWA populations, particularly those of RWASA1, were smaller than those observed on either S5 or SSG 564. In addition, less damage was evident in the two CIho accessions due to RWA feeding. II RWASA2 was the most virulent of the three RWA biotypes tested, followed by RWASA3 while RWASA1 was the least virulent. Under elevated CO2 conditions, RWA feeding damage was exacerbated but the trend of biotype virulence remained the same. Higher aphid population sizes were recorded under elevated CO2, meant that even the more resistant CIho accessions were overcome by the increased demand made by the larger aphid colonies on the host plants. The % foliar N data showed that under elevated CO2 aphid-free control plants had increased N levels in their leaves. Increased “food” supply (as shown by the increased N levels) therefore allowed significantly larger aphid populations to develop on the plants exposed to elevated CO2, due to improved nutrient status of the phloem sap taken up by RWA. The knock-on effect of a higher aphid population was increased cell disruption as a result of extensive probing, extensive formations of wound callose, with the result that phloem damage impeded nutrient flow through the vascular tissues which contributed to chlorosis and (eventually plant) death. The major conclusion from this study is that even a mild CO2 elevation resulted in an increase aphid population which may pose a severe and very real threat to a barley crop. Therefore, without effort to identify and deploy resistant barley cultivars, it could well be possible that future barley cultivation in South Africa may no longer be viable.

Includes bibliographical references (leaves 265-296). Pathogens associated with root damage were investigated in the Murray Mallee region of South Australia over the 1987-1989 growing seasons. Occurence of fungal species and the root lesion nematode (Pratylenchus neglectus) was assessed, and related to the appearance and severity of symptoms on the roots. Field experiments were supplemented with innoculation tests in the glasshouse and laboratory.

Thesis (MSc (Genetics))--University of Stellenbosch, 2009.
Worldwide, the rust diseases cause significant annual wheat yield losses (Wallwork 1992; Chrispeels & Sadava 1994). The utilization of host plant resistance to reduce such losses is of great importance particularly because biological control avoids the negative environmental impact of agricultural chemicals (Dedryver et al. 1996). The wild relatives of wheat are a ready source of genes for resistance to disease and insect pests. A large degree of gene synteny still exists among wheat and its wild relatives (Newbury & Paterson 2003). It is therefore possible to transfer a chromosome segment containing useful genes to a homologous region in the recipient genome without serious disruption of genetic information. Special cytogenetic techniques are employed to transfer genes from the wild relatives to the wheat genomes (Knott 1989). Unfortunately the transfer of useful genes may be accompanied by the simultaneous transfer of undesirable genes or redundant species chromatin which has to be mapped and removed (Feuillet et al. 2007). DNA markers are extremely useful for the characterisation and shortening of introgressed regions containing genes of interest (Ranade et al. 2001), and may also be used for marker aided selection of the resistance when the genes are employed commercially. Eight wheat lines containing translocations/introgressions of wild species-derived resistance genes were developed by the Department of Genetics (SU). These lines are presently being characterized and mapped and attempts are also being made to shorten the respective translocations. This study aimed to find DNA markers for the various translocations and to convert these into more reliable SCAR markers that can be used in continued attempts to characterize and improve the respective resistance sources. A total of 260 RAPD and 21 RGAP primers were used to screen the eight translocations and, with the exception of Lr19, it was possible to identify polymorpic bands associated with each translocation. However, it was not possible to convert all of these into more reliable SCAR markers. The primary reason for this was the low repeatability of most of the bands. Certain marker fragments turned out to be repeatable but could not be converted successfully. Some of the latter can, however, be used directly (in RAPD or RGAP reactions) as markers. The Lr19 translocation used in the study (Lr19-149-299) is a significantly reduced version of the original translocation and failure to identify polymorphisms associated with it can probably be ascribed to its small size. The following numbers of markers (direct and converted into SCARs) were Worldwide, the rust diseases cause significant annual wheat yield losses (Wallwork 1992; Chrispeels & Sadava 1994). The utilization of host plant resistance to reduce such losses is of great importance particularly because biological control avoids the negative environmental impact of agricultural chemicals (Dedryver et al. 1996). The wild relatives of wheat are a ready source of genes for resistance to disease and insect pests. A large degree of gene synteny still exists among wheat and its wild relatives (Newbury & Paterson 2003). It is therefore possible to transfer a chromosome segment containing useful genes to a homologous region in the recipient genome without serious disruption of genetic information. Special cytogenetic techniques are employed to transfer genes from the wild relatives to the wheat genomes (Knott 1989). Unfortunately the transfer of useful genes may be accompanied by the simultaneous transfer of undesirable genes or redundant species chromatin which has to be mapped and removed (Feuillet et al. 2007). DNA markers are extremely useful for the characterisation and shortening of introgressed regions containing genes of interest (Ranade et al. 2001), and may also be used for marker aided selection of the resistance when the genes are employed commercially. Eight wheat lines containing translocations/introgressions of wild species-derived resistance genes were developed by the Department of Genetics (SU). These lines are presently being characterized and mapped and attempts are also being made to shorten the respective translocations. This study aimed to find DNA markers for the various translocations and to convert these into more reliable SCAR markers that can be used in continued attempts to characterize and improve the respective resistance sources. A total of 260 RAPD and 21 RGAP primers were used to screen the eight translocations and, with the exception of Lr19, it was possible to identify polymorpic bands associated with each translocation. However, it was not possible to convert all of these into more reliable SCAR markers. The primary reason for this was the low repeatability of most of the bands. Certain marker fragments turned out to be repeatable but could not be converted successfully. Some of the latter can, however, be used directly (in RAPD or RGAP reactions) as markers. The Lr19 translocation used in the study (Lr19-149-299) is a significantly reduced version of the original translocation and failure to identify polymorphisms associated with it can probably be ascribed to its small size. The following numbers of markers (direct and converted into SCARs) were v identified: S8-introgression (Triticum dicoccoides) = one RAPD and two SCARs; S13-translocation (Aegilops speltoides) = four RAPDs, three RGAPs and five SCARs; S15-translocation (Ae. peregrina) = one RAPD and two SCARs; S20-translocation (Ae. neglecta) = two RAPDs, two RGAPs and one SCAR. The markers are already being employed in current projects aiming to map and shorten these translocations. Some of the markers can be combined in multiplex reactions for more effective mass screening. No repeatable markers could be identified for the four remaining translocations (S12 from Ae. sharonensis; S14 from Ae. kotschyi; Smac from Ae. biuncialis and Lr19-149-299 from Thinopyrum ponticum).

Thesis (MSc (Genetics))--University of Stellenbosch, 2010.
Includes bibliography.
ENGLISH ABSTRACT: Wheat rust is a significant contributor to the total impact of diseases on sustainable wheat production. Genetic resistance, produced by using resistance genes from wheat and other related wild species, is the simplest and most cost-effective way to guard against these diseases. The pyramiding of resistance genes in a single line is a vital practice in bringing about durable resistance. This study aimed to develop a series of doubled haploid (DH) wheat lines containing combination's of wild species genes for rust resistance. Rust resistance genes Lr19 (7BL), Sr31/Lr26/Yr9/Pm8 (1BS) and Lr54/Yr37 (2DL) were combined by means of crossing. Breeders. lines which have complex resistance including Lr24/Sr24 (3DL), Lr34/Yr18 (7D), Sr36 (2BS) and Sr2 (3BS), were used. Marker assisted selection (MAS) was used to type populations for the above mentioned genes. Using the DH method (maize pollination technique), an inbred population was developed from the selected lines, after which the lines were characterised molecularly for the resistance gene translocations which they contain. The study produced 27 lines with diverse genetic profiles. Seven lines contain four translocations (Lr24/Sr24, Lr34/Yr18, Sr2 and Lr19 or Sr31) each, 11 lines contain three genes each, six lines contain two genes each and only three lines contain a single translocation (Lr24/Sr24). The reality that rust pathogens have already overcome three of the resistance genes in the final population . Lr19, Sr31 and Sr24 . is a clear indication of the value of using non-major gene resistance for bringing about durable resistance. The focus should fall ever more greatly upon the application of quantitative trait loci (QTL) for this purpose, which will result in MAS contributing to the development of more durable resistance. The value of the integration of MAS and DH in combination with conventional breeding practices in breeding programmes has already been illustrated internationally for increasing the rate of cultivar development and this is reaffirmed by this study.
AFRIKAANSE OPSOMMING: Koringroes lewer jaarliks .n beduidende bydrae tot die totale impak van siektes wat volhoubare koringverbouing belemmer. Die mees eenvoudige en koste-effektiewe verweer teen hierdie siektes is genetiese weerstand, wat deur weerstandsgene vanaf koring, sowel as wilde verwante spesies, bewerkstellig word. Die stapeling van weerstandsgene in .n enkele lyn word as .n onontbeerlike praktyk om duursame weerstand tot stand te bring, geag. Hierdie studie het ten doel gehad om .n reeks verdubbelde haploiede (VH) koringlyne te ontwikkel wat kombinasies van wilde spesie gene vir roesweerstand bevat. Roesweerstandsgene Lr19 (7BL), Sr31/Lr26/Yr9/Pm8 (1BS) en Lr54/Yr37 (2DL) is deur middel van kruisings gekombineer. Telerslyne wat oor komplekse weerstand beskik wat Lr24/Sr24 (3DL), Lr34/Yr18 (7D), Sr36 (2BS) en Sr2 (3BS) insluit, is gebruik. Merker-bemiddelde seleksie (MBS) is gebruik om populasies vir bogenoemde gene te tipeer. .n Ingeteelde populasie is vanaf die geselekteerde lyne met behulp van die VH metode (mielie-bestuiwing tegniek) ontwikkel, waarna die lyne molekuler vir die weerstandsgeentranslokasies waaroor hul beskik, gekarakteriseer is. Die studie het 27 lyne met diverse genetiese profiele opgelewer. Sewe lyne bevat vier weerstandsgeentranslokasies (Lr24/Sr24, Lr34/Yr18, Sr2 en Lr19 of Sr31) elk, 11 lyne beskik oor kombinasies van drie gene elk, ses bevat twee gene elk en slegs drie lyne beskik oor .n enkele translokasie (Lr24/Sr24). Die realiteit dat die roespatogene reeds drie van die weerstandsgene in die finale populasie . Lr19, Sr31 en Sr24 . oorkom het, benadruk die waarde van die gebruik van nie-hoofgeenweerstand vir die daarstelling van duursame weerstand. Die fokus behoort toenemend meer op die aanwending van kwantitatiewe kenmerk-loci (QTL) vir hierdie doel te val en sal sodoende teweegbring dat MBS bydra tot die ontwikkeling van meer duursame weerstand. Die waarde van die integrasie van MBS en VH in kombinasie met konvensionele telingsmetodiek is reeds internasionaal vir die versnelling van kultivarontwikkeling aangetoon en word ook deur hierdie studie herbevestig.

Cephalosporium stripe of wheat (Triticum aestivum), caused by the soilborne fungus Cephalosporium gramineum, results in significant yield reductions in dryland winter wheat crops of the U.S. Pacific Northwest. The development of resistant cultivars offers the best hope for disease control. Breeding for resistance is hampered by the long trial times inherent in screening adult plants, and by cultivar x environment interactions in field tests. The principal objective of this research was to develop and test a procedure for screening wheat seedlings in controlled environments for resistance to Cephalosporium stripe. Wheat seedlings were raised hydroponically in growth chambers, and the fungus was increased in large fermentation tanks. The seedlings were inoculated at about 12 days post-germination. Disease severity was assessed approximately seven days later using a chlorophyll meter to measure the symptoms of chlorosis and striping. In three trials, five soft white cultivars from the Pacific Northwest and four hard red cultivars from the Southern Great Plains with known levels of field resistance were tested with a Pacific Northwest fungal isolate. With one exception, chlorophyll readings ordered the cultivars appropriately, with moderately resistant cultivars ranking above susceptible cultivars. Three other moderately resistant cultivars from the Pacific Northwest also appeared in one or two trials, and were ranked properly by chlorophyll level. Chlorophyll levels of uninoculated plants were assayed to determine if differences in chlorophyll content were innate in the cultivars. The chlorophyll levels of uninoculated and inoculated seedling treatments were only significantly correlated when the cultivar Madsen, which ranks high both in resistance and in chlorophyll content, was included. In adult plants, flag-leaf chlorophyll level corresponded to intensity of Cephalosporium stripe symptoms where disease was present, and was independent of known field resistance in undiseased cultivars. The seedling screening technique was used to investigate pathogenic variability in C. gramineum. In two experiments, a total of eight cultivars from the Pacific Northwest and the Southern Great Plains were tested with three fungal isolates from each region. No evidence of virulence/vertical resistance was found. There was also no significant adaptation of isolates to greater virulence on cultivars from the same region.
Graduation date: 1998

M.Sc. (Botany)
Cereals such as oats, rye, rice, barley, maize and wheat are a major source of food worldwide. Wheat (Triticum aestivum L.) is the largest winter cereal crop produced in South Africa (Crop Estimates Committee, 2011; South African Department of Agriculture, Forestry and Fisheries, www.daff.gov.za/crop estimates). Wheat production in South Africa includes both the summer and winter rainfall areas. Like other crops wheat is cultivated under monoculture conditions to increase yield per hectare. This increases the risk to pathogen exposure, as monocultures are genetically very similar or even identical, which makes them particularly vulnerable to both abiotic and biotic stresses (Haile, 2001). Both of these stressors negatively influence crop yield (Peterson and Higley, 2001; Wang et al., 2003).

M.Sc. (Botany and Plant Biotechnology)
Wheat (Triticum aestivum L.) is the one of the three most extensively cultivated cereal crops worldwide (Shewry, 2009). In South Africa, wheat is cultivated in both summer and winter rainfall regions as monocultures typical to modern industrialised agriculture. Monocultures provide uniform crop quality and allow processes such as planting and harvesting to be mechanised (Altieri et al., 2009). However, the genetically homogeneous nature of monocultures increases the vulnerability of the crop to both biotic and abiotic stresses (Faraji, 2011). Future food production is challenged by predicaments such as an increasing human population while the ratio of arable land to population is decreasing. Yield losses of wheat due to biotic factors alone were estimated as 29 % (2001-2003) (Oerke, 2006). The need to reduce the gap between attainable yield and actual yield is therefore crucial in order to maximise crop production for future food security (Duveiller et al., 2007). One of the most damaging pests to worldwide wheat production is the Russian wheat aphid (RWA), Diuraphis noxia (Kurdjumov) (Arzani et al., 2004). A native pest of central Asia, the RWA has spread to all cereal producing areas of the world with the exception of Australia (Burd et al., 2006). While feeding on susceptible hosts, the aphid injects an eliciting agent into the host, which causes the breakdown of the chloroplast and cellular membranes, leading to the appearance of symptoms typical of RWA feeding, including leaf rolling (Botha et al., 2005). Leaf rolling creates a sheltered environment for the aphid from insecticides and predators, and this together with their parthenogenic and viviparous reproductive nature makes their rapid increase in numbers extremely difficult to control (Goggin, 2007). Resistant wheat genotypes currently represent the most effective long term solution to control RWA infestations; however resistance breaking aphid biotypes are rapidly overcoming the incorporated resistance genes under field conditions (Burd et al., 2006; Jankielsohn, 2011). Understanding the molecular basis of plant resistance to the RWA is crucial in creating cultivars with durable resistance (Botha et al., 2005).

Mycosphaerella graminicola (anamorph Septoria tritici) causes Septoria tritici blotch, a globally important disease of winter wheat. Resistance and pathogenicity generally vary quantitatively. The pathogen reproduces both sexually and asexually, and the pathogen population is highly genetically variable. Several unresolved questions about the epidemiology of this pathosystem are addressed by this research. Among them are whether cultivar-isolate specificity exists, how partial host resistance affects pathogen aggressiveness and sexual reproduction, and how host genotype mixtures influence epidemic progression and pathogenicity. At its release in 1992, the cultivar Gene was highly resistant to M. graminicola, but that resistance had substantially dissolved by 1995. Six of seven isolates collected in 1997 from field plots of Gene were virulent to Gene seedlings in the greenhouse, while 14 of 15 isolates collected from two other cultivars were avirulent to Gene. Gene apparently selected for strains of M. graminicola with specific virulence to it. In a two-year experiment, isolates were collected early and late in the growing season from field plots of three moderately resistant and three susceptible cultivars, and tested on seedlings of the same cultivars in the greenhouse. Isolates were also collected from plots of two susceptible cultivars sprayed with a fungicide to suppress epidemic development. Isolate populations were more aggressive when derived from moderately resistant than from susceptible cultivars, and more aggressive from fungicide-sprayed plots than from unsprayed plots of the same cultivars. Over 5,000 fruiting bodies were collected in three years from replicated field plots of eight cultivars with different levels of resistance. The fruiting bodies were identified as M. graminicola ascocarps or pycnidia, or other. In all three years, the frequency of ascocarps was positively correlated with cultivar susceptibility, as measured by area under the disease progress curve, and was also positively associated with epidemic intensity. For three years, four 1:1 mixtures of a moderately resistant and a susceptible wheat cultivar were planted in replicated field plots. Isolates from the plots were inoculated as bulked populations on greenhouse-grown seedlings of the same four cultivars. Mixture effects on disease progression varied among the years, and were moderately correlated with mixture effects on pathogenicity.
Graduation date: 2002

Septoria leaf blotch of wheat is a major biotic factor limiting the grain yield. To determine the nature of inheritance involving selected genotypes, three resistant semidwarf spring wheat lines exhibiting durable global resistance and one susceptible cultivar were crossed in all possible combinations, excluding reciprocals. Parents, Fl, F2, and F3 generations were inoculated with one pathogenic strain of Septoria tritici and evaluated under field conditions. Data were collected on an individual plant basis. F2 and F3 frequency distributions were computed to determine the nature of inheritance. Combining ability analysis of the 4x4 diallel cross and narrow-sense heritability were employed to estimate the nature of gene action. Phenotypic correlations were obtained to examined the possible association between disease severity traits and their relationship with heading date and plant height. The continuous distribution of the F2 and F3 populations among crosses made it impossible to classify plants into discrete classes in crosses between resistant x susceptible genotypes. Mean values of the disease traits Septoria progress coefficient, Relative coefficient of infection, and Septoria severity of flag leaf among the segregating populations were similar to the midparent values. Transgressive segregation was also observed in the F2 and F3 suggesting that parents had different resistance genes. Additive gene effects were found to be the major component of variation although nonadditive gene action played an important role in the expression of all three disease traits. The resistant parents Bobwhite"S" and Kavkaz /K4500 L.A.4 were found to have the largest negative general combining ability effects for the disease traits suggesting that these parents would be the best source for resistance to Septoria leaf blotch. High general combining ability and high narrow sense heritability estimates in the F3 population, indicated that substantial progress for resistance to Septoria tritici would be effective selecting in this generation. Of the three disease measures it would appear that selection for the lowest percentage of Septoria infection on the flag leaf would provide the most progress in developing resistant cultivars. Moderate and low negative phenotypic correlations were found among generations for the disease traits with heading date and plant height. From the results of this study the selection of early maturing short stature progeny would be possible within the genetic materials employed in this study.
Graduation date: 1993

M.Sc.
Wheat is one of the most extensively grown small grain crops in Southern Africa. It is a staple food source used by humans, animals and other living organisms around the globe (Feldman, 2001). One of the major threats of wheat production in South Africa is the Russian wheat aphid (RWA), (Kurdjumov), (Diuraphis noxia, Homoptera: Aphididae) (Brooks et al., 1994; Du Toit & Walters, 1984). The RWA was first described as a pest in South Africa in 1978 and in the US in 1986. Thereafter it was rapidly reported as becoming a major pest of cereals in these countries (Brooks et al., 1994; Du Toit & Walters 1984). A short life span, asexual reproduction, the development of resistance towards insecticides and rapid colonisation of the host plant are all factors that have made the management of the RWA a difficult task (Dogimont et al., 2010; Hein et al., 1998). As a result of complications such as these, host plant resistance is the most viable option to counter the RWA (Dogimont et al., 2010). The method of feeding of the RWA is detrimental to the plant as they insert their stylets into, and feed primarily from, the phloem sieve elements. This damages the plants through nutrient drainage (Dixon, 1985; Klingler et al., 2009) and results in a variety of symptoms, the most common being chlorosis, necrosis, wilting, stunting, curling of the leaves (which provides the pest with a sheltered environment protected from predators and pesticides), misshapen or nonappearance of new growth, and localised cell death at the site of aphid feeding. The RWA elicits an increase in essential amino acids in the phloem sap, by triggering the breakdown of proteins in infested wheat leaves (Burd & Burton, 1992; Du Toit, 1986; Haley et al., 2004; Ma et al., 1998; Miller et al., 2001; Walters et al., 1980). It also reduces transport of labelled tracers (amino acids) from the feeding site to the roots and other sinks in the plant. This increases the nutrient concentration at the site of aphid feeding by increasing the import of resources from other sites in the plant, mobilising local resources and blocking their export to other organs. The damage of the foliar tissue that occurs as a result of the RWA feeding is thought to play a role in the pest’s ability to increase the nutritional quality of the host plant (Botha et al., 2006; Goggin, 2007; Shea et al., 2000).

Strawbreaker foot-rot is a major limiting factor to cost efficient winter wheat production in the Pacific Northwest. Development of resistant cultivars has been hindered by the lack of adequate levels of genetic resistance and screening techniques which can consistently detect desired genotypes. Studies were conducted to determine if the reported strawbreaker foot-rot resistance of the cultivar "Rendezvous" is effective on isolates of Pseudocercosporella herpotrichoides found in the Pacific Northwest. Protected, naturally infected and artificially inoculated treatments were employed to determine the level of resistance of 10 cultivars including Rendezvous. Different concentrations of inoculum and stages of development were also used to determine if observations on leaf sheath penetration of seedlings obtained in the greenhouse were related to disease severity index readings taken in the field for selected cultivars. In addition, the nature of inheritance of strawbreaker foot-rot was studied in two crosses involving Rendezvous. Experiments were conducted at three locations and over two years at one location. Despite cultivar x treatment interaction, consistent levels of infection were observed in all experiments at each location. Significant differences were found for treatments and cultivars for most attributes. Yield losses, including the components of yield spikes per square meter, 1000 kernel weight, and kernel number per spike were proportional to the severity of the disease. Losses were greater when lodging occurred, which was also associated with disease severity. However, even in the absence of lodging losses were recorded in the naturally and artificially inoculated plots. Traits measured involving Rendezvous and Vpm/Mos 95//*2Hill were only slightly influenced by the treatments. Under greenhouse conditions, it was possible to distinguish the level of resistance of Rendezvous from susceptible cultivars at concentrations of 100 spores/ml, two weeks after inoculation at the seedling stage. Leaf sheath penetration of seedlings was found to be closely associated with the disease severity index obtained under field conditions. Generation means analysis performed in crosses involving Rendezvous indicated that additive and additive x additive gene action were responsible for most of the genetic variability associated with resistance. Narrow-sense heritability estimates also confirmed these fmdings. It would appear that Rendezvous has at least two major genes for resistance to strawbreaker foot-rot.
Graduation date: 1992

This study quantified the frequency of simple versus complex races of Puccinia striiformis Westend. in mixtures of wheat cultivars possessing different race-specific resistance genes. A simple race of a pathogen can infect only one component, and a complex race of the pathogen can infect two or more components of an intraspecific plant mixture. The treatments were designed so that the race that was complex changed depending on the host mixture, thus enabling us to observe the influence of pathogen complexity in different host genetic backgrounds. Six cultivar mixtures and one pure stand of winter wheat were inoculated with three races of P. striiformis (CDL 27, CDL 29, and CDL 41) at two locations for two seasons. Potted plants of three winter wheat cultivars (Paha, Tres, and Tyee) that were each susceptible to one of the three races of the pathogen were used to sample the pathogen during the field epidemics. Disease incidence on the differential cultivars was used to calculate the proportion of the three races in each treatment. The specific cultivars included in the mixtures influenced the frequencies of the three races. Increasing the number of virulent races in a mixture reduced the frequency of the complex race relative to the other two races. When two of the races (races 29 and 41) were complex on the same mixture, location had an effect on which of the races was more frequent. When race 29 was the complex race in the mixture, it was more frequent than when race 41 was the complex race. The results suggest that environmental interactions, genetic background of the pathogen race, host composition, and interaction among pathogen races may be as important in determining race frequencies in mixtures as is stabilizing selection sensu Vanderplank (1968).
Graduation date: 1993

Errata slip inserted.
Bibliogaphy: leaves [93-109].
x, 92, [17] leaves, [20] leaves of plates : ill. ; 30 cm.
Title page, contents and abstract only. The complete thesis in print form is available from the University Library.
Identifes and maps markers associated with the quality traits of grain protein content, milling yield and flour colour, and with genes resistant to stem- and leaf-rust diseases in wheat.
Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, Waite Agricultural Research Institute, 1998

Despite many investigations genotype by environment interaction remains one of the least understood factors in plant improvement. Understanding genotypic differences responsible for such interactions could assist in making more informed breeding decisions. The components of yield being less complex than grain yield per se may be useful for selection to improve adaptation of genotypes and enhance grain quality. However, the potential compensatory response among the components of yield could compromise their usefulness as selection criteria. To evaluate this aspect fifteen cultivars, including Soft White, Hard White and Hard Red wheats, were planted at three diverse locations over two growing seasons. Genotypes were ranked based on measurements for specific traits in each environment. The genotype by environment interaction for grain yield, protein concentration and hardness were investigated according to the AMMI model. Influence of environmental factors and genotype by environment interactions on associations among selected traits were determined. The results of this study showed that genotypic differences in adaptation to the Pacific Northwest and resistance to Septoria spp. were responsible for interactions for grain yield. However, no consistent patterns of response were found among the similar cultivars for quality traits. Those environments that favored expression of biomass and grain weight potential provided for enhanced performance of the adapted cultivars. The environments with suppressed biomass accumulation and grain filling interacted positively with the unadapted cultivars. A large compensatory relationship between tillering and apical growth was detected. No or low compensation was observed between grains per spike and thousand kernel weight. Two different strategies were proposed for improvement of Soft and Hard White wheat cultivars under the conditions of the Pacific Northwest. Both strategies accentuate importance of increasing biomass while maintaining harvest index. When selecting for higher yielding Soft White cultivars, plants with larger leaves, stronger stems, larger spikes and heavier grains should be emphasized. For Hard Whites - higher number of tillers and grains m����� is desired, as they provide for harder grains with higher protein content.
Graduation date: 2000

Bibliography: leaves 318-347.
ix, 347 [24] leaves : ill. (some col.) ; 30 cm.
Title page, contents and abstract only. The complete thesis in print form is available from the University Library.
A major problem in the production of agricultural crops including wheat, is the damage caused by destructive plant parasitic nematodes, among these the root lesion nematode (Pratylenchus spp.) The association of P. neglectus with fungi in ceraeal root disease has been reported. Infection is associated with leaf yellowing, which reduces plant photosynthesis and grain yield. In nematode infested soil, well fertilized crops are usually less affected.
Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 1996?

Bibliography: leaves 133-152
iv, 152 leaves, [47] leaves of plates : ill. (1 col.) ; 30 cm.
Title page, contents and abstract only. The complete thesis in print form is available from the University Library.
Thesis (Ph.D.)--University of Adelaide, 1987

This thesis investigates the effect of Russian wheat aphid (RWA; Diuraphis noxia) infestation on the defence responses of the bread wheat line, PI 137739, on a molecular level. PI 137739 is known to contain the RWA resistance gene, Dn1. The study was conducted by utilising and combining a vast array of molecular biological techniques. Chapter 1 introduces the reader to a summary of the resistance responses observed within infested plants. A detailed description of the Russian wheat aphid follows and the genes responsible for RWA resistance in wheat is discussed. A brief report of research performed on the bread wheat genome is given and the biochemical defence responses of plants against insect infestation are discussed. This is followed by a concise description of resistance (R) genes and resistance gene categories in plants. The last discussion concerns microarray technology, a molecular tool utilised during this study. Chapter 2 aims at identifying genes involved in resistance against RWA infestation; specifically, genes containing the conserved nucleotide binding site¬leucine rich repeat (NBS-LRR) motif. Genomic, as well as complementary DNA (cDNA), was utilised in order to compare functional gene expression in wheat infested with the RWA. This was executed by employing PCR-based methods, single-pass sequencing and basic local alignment search tool (BLAST) analyses. Chapter 3 introduces suppression subtractive hybridisation (SSH) as a tool to further identify NBS-LRR or other resistance-related sequences in RWA infested wheat plants. SSH allows the comparative analysis of differential gene expression in RWA infested and uninfested wheat in order to identify resistance-¬related genes expressed in the infested, resistant wheat plants. The effect of RWA infestation on wheat resistance responses was examined further in chapter 4 through microarray analysis. The aim was the introduction and establishment of the microarray technique and to test the feasibility of using microarrays for differential gene expression and regulation studies. Microarray slides were assembled in order to monitor the up- and down¬regulation of genes at different time intervals - day 2, day 5 and day 8 - of RWA infestation. Clones isolated throughout this study were assembled on microarray slides and probed with control and RWA infested RNA. Differential gene regulation was assessed and further confirmed through Northern blot analyses, as well as quantitative real-time PCR. The thesis concludes with a general summary of the results obtained in chapter 5 and future prospects are outlined.
Thesis (PhD(Genetics))--University of Pretoria, 2005.
Genetics
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