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).

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

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.

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.

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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.

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Call number: LD2668 .T4 1957 R68 / Master of Science

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’.