Wheat is one of the major food crops consumed by man and is grown in a wide range of environments. One constraint in the production of wheat is the different diseases attack the crop. One such a diseases is leaf rust. Leaf rust is caused by Pucdnia recondita f.sp. trifid and is the most widespread and regularly occurring rust on wheat. Researchers are continually searching for new resistance genes and to date 47 leaf rust resistance genes (Lr) have been designated in wheat. Three molecular techniques RAPDs (random amplified polymorphic DNA), AFLPs (amplified fragment length polymorphism) and SSRs (microsatellites) were used to identify and analyse the distances between different cereal genotypes. Four RAPD primers, three AFLP primers and two SSR primers were used to analyse the wheat genotypes, x-tritosecale and rye. The average polymorphisms obtained from the AFLPs were 100 polymorphisms per AFLP primer combination, and is much higher than with the RAPD primers (11-16 polymorphic loci). The four RAPD primers failed to identify unique molecular markers for the wheat genotypes. The AFLP primers were able to distinguished between the 'Kiewiet', rye, 'SA463/*4Palmiet', 'SA684', TA2460' and 'KG90WGRClO' genotypes. The SSR primer pair XGWM122150 was able to amplify a fragment from the A or B genome. The pairwise distances between the genotypes revealed that the wheat genotypes were genetically very close, with an average distance value of 0.29 between the genotypes. The genotypes, 'TA2460', 'TAMI07' and 'KS90WGRCI0', were not closely related to the South African wheat genotypes and were genetically very close to each other. The rye and 'Kiewiet' genotypes were grouped as an outgroup by the UPGMA analysis and were the least closely related to the cereal genotypes. RAPD (Random amplified polymorphic DNA) and AFLP (amplified fragment length polymorphism) analysis were used to identify molecular markers linked to leaf rust resistance gene Lr41. Bulk and parental lines were screened with 380 RAPD primers and 64 AFLP primer combinations. A total of 3190 RAPD and 1859 AFLP loci, respectively were screened for linkage to the resistance gene. Twelve fragments (seven RAPD and five AFLP), nine in coupling phase and three in repulsion phase, were identified as putative markers for the leaf rust resistance gene Lr41. Segregation analysis of these markers in a BC2F2 population revealed varying linkage distances that ranged from 2.8 to 33 cM. The coupling phase AFLP marker E-AAG:M-CTA300 was converted into a sequence characterised amplified region (SCAR) marker. AFLP markers have potential for marker assisted selection breeding programs, provided it can be converted into SCARs or equivalent marker typed systems. / Dissertation (MSc (Genetics))--University of Pretoria, 2007. / Genetics / unrestricted

This doctoral thesis presents three original research papers investigating aspects of agricultural production in small-farming households in two regions of Ethiopia. While answering specific research questions, the articles are connected and motivated by an interest in essential themes of agricultural development: access to seed, the use and conservation of agrobiodiversity as well as strategies to manage production risk in smallholder agriculture. The first article analyses patterns of agrobiodiversity in three communities with comparatively favourable farming conditions and good market access in the East Shewa zone of Eastern Ethiopia. Using original panel data of more than 300 households collected in 2011 and 2013, the study shows that the least vulnerable households grow a larger portfolio of food crops and wheat varieties. Based on these findings, the role of agrobiodiversity for ex ante risk management and alternative incentives for portfolio diversification are discussed. The second article investigates the effects of a fungal crop disease on agricultural production of households in East Shewa using household level panel data during and after an epidemic outbreak of yellow rust in 2010/11. Findings suggest that while varietal diversity in wheat does not increase, roughly thirty percent of households make changes in their varietal portfolio and reduce wheat cultivation in response to the disease. Disease resistant varieties are only available to 16 percent of all households with preferential access to agricultural resources. The third article presents a mixed methods study of a highly developed informal seed insurance network among subsistence‐oriented small farmers in two communities in the West Hararghe zone of Ethiopia. Based on a survey and interviews with 150 farmers, we find that the vast majority of small farmers actively participate in informal seed assistance by giving or receiving small quantities of seed without compensation. We argue that the seed assistance through gifts is practiced to insure against hunger ex ante and facilitate access to crop genetic resources in a centre of crop origin and diversity.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is an economically important foliar disease of wheat (Triticum aestivum). In the last decade, losses from stripe rust in North Dakota (ND) have increased, peaking at 5% in 2015. Three research studies were conducted to address questions on the pathogen, varietal resistance, and integrated management. The objective of the first study was to (i) identify virulent phenotypes of Pst isolates collected from ND from 2015 to 2017 and assign races, and (ii) determine the effect of temperature on in vitro urediniospore germination, latency, and lesion spread. Across the three years, five races were detected with PSTv 37 being the most common. The highest urediniospore germination occurred at 12oC followed by 16oC. Pst isolates had shorter latency at 21oC and larger lesion spread at 16oC. The objective of the second study was to evaluate seedling resistance and adult plant resistance in the North Dakota State University spring wheat breeding program using races PSTv 37 and PSTv 52. Results from seedling experiments indicated only four and two lines were resistant to PSTv 52 and PSTv 37, respectively. Adult plant resistance experiments were unsuccessful in 2019, and will be conducted again in the future. The objective of the third study was to develop fungicide timing recommendations for wheat rust (stripe and leaf) based on varietal resistance and time of disease onset. Rust developed in five of the eight field trials, and timing of disease onset was categorized by growth stage (tillering, flag leaf, or early-flowering). Results indicated fungicide application timing was influenced by timing of disease onset and varietal resistance. When rust was detected at the tillering growth stage on the susceptible variety, the best time to apply a fungicide was at Feekes 9. When rust was detected at flag leaf or beyond on a susceptible variety, a fungicide application at Feekes 10.51 provided the adequate disease reduction and protection of yield. Results from these research studies provide a better understanding of Pst, determined seedling resistance in the breeding program, and provides field data to refine management recommendations for wheat rusts in ND. / North Dakota Wheat Commission / State Board of Agricultural Research and Education

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Plant diseases are among the major causes of food insecurity. In South Africa the wheat fungal diseases including stem rust caused by Puccinia graminis f. sp. tritici, leaf rust caused by P. triticina and stripe rust caused by P. striiformis f. sp. tritici are the most important. Genetic resistance is a viable way of protecting wheat crops against the wheat rusts, especially cultivars carrying multiple genes that confer durable resistance. In order to breed for multi-gene resistance an effective breeding strategy that allows for selecting multiple resistance genes and other desirable traits needs to be devised. The aim of this study was to identify a number of genotypes with combinations of different rust resistance genes, good grain yield and end-use quality out of an existing pre-breeding population and thereby identify superior parents. In order to achieve the stated aim the following objectives have been identified: identify wheat lines through marker-assisted selection (MAS) carrying the gene complexes, Sr31/Lr26/Yr9, Lr24/Sr24, Lr37/Sr38/Yr17, Lr34/Yr18 and Sr2; to develop inbred lines to evaluate selected lines under field trials. From the initial subset of 64 lines, 60 were chosen and advanced to the doubled haploid (DH) phase and seed multiplication. The 60 lines either carried one or more of the three rust resistance gene complexes. The genes that were the most prominent were Sr31/Lr26/Yr9 and Lr24/Sr24. The selected lines were incorporated into a DH seed multiplication phase. After 4 cycles of seed increases and preliminary field evaluation during multiplication, 15 lines were chosen and subjected to multi-location field trails. The extensive multi-location field trails carried out in this study aided in identifying genotypes from the 15 MS-MARS lines with good adaptability and stability in regards to yield and baking quality. An important observation was that the molecular markers employed to indentify quality loci correlated well with the genes encoding the HMW-GS 5, 10 and 12 as observed with the Agilent© 2100 Bioanalyzer. In future studies the lines which performed the best could be re-introduced into the existing MSMARS pre-breeding programme of the Stellenbosch University’s Plant Breeding Laboratory (SUPBL). The frequencies of desired alleles could be increased in this manner. Since the majority of these characteristics are influenced by quantitatively inherited alleles, using these lines as recurrent parents will increase the frequencies of these alleles in the existing SU-PBL pre-breeding population. / AFRIKAANSE OPSOMMING: Plantsiektes is van die belangrikste oorsake van voedselonsekerheid ter wêreld. In Suid-Afrika is die roesswamme van die belangrikste plantsiektes wat koring produksie beïnvloed. Hierdie siektes sluit in, stamroes wat veroorsaak word deur Puccinia graminis f. sp. tritici, blaarroes wat veroorsaak word deur P. triticina en streeproes wat veroorsaak word deur P. striiformis f. sp. tritici. Genetiese weerstand is ‘n uitstekende manier om koring te beskerm teen hierdie swamsiektes. Weerstand wat gebasseer is op veelvuldige weerstandsgene is veral ‘n goeie middel om genetieseweerstand op ‘n volhoubare basis in koringteling toe te pas. Om veelvuldige weerstandsgene in koringkultivars in te teel word ‘n effektiewe telingstrategie benodig. Die doel van die studie was om genotipes te identifiseer met kombinasies van veelvuldige weerstandsgene vir roes, sowel as goeie eienskappe belangrik vir graanopbrengs en bakkwaliteit. Lyne is geïdentifiseer uit ‘n bestaande voortelingspopulasie van Stellenbosch Universiteit se Planteteelt Laboratorium (SU-PTL) wat geteel was met spesifiek weerstand en opbrengs potensiaal in gedagte. Om die doel van die studie te bereik is sekere doelwitte daar gestel. Hierdie doelwitte sluit in om lyne uit die populasie te selekteer deur middel van merker bemiddelde seleksie (MBS) vir gene naamlik Sr31/Lr26/Yr9, Lr24/Sr24, Lr37/Sr38/Yr17, Lr34/Yr18 en Sr2; om die geselekteerde lyne suiwertelend te maak; sowel as om die suiwertelende lyne in veld proewe in te sluit. Van die oorspronklike stel van 64 lyne, is 60 gekies vir verdere studie. Deur middel van die verdubbelde haploïed (VH) tegniek is die lyne suiwertelend gemaak. Die 60 lyne het een of meer van die geselekteerde gene bevat. Die mees prominente gene was die twee geen komplekse Sr31/Lr26/Yr9 en Lr24/Sr24. Na vier siklusse van saadvermeerdering en voorloppige seleksies is 15 lyne ingesluit by ‘n multi-omgewing veldproef. Hierdie uitgebreide multi-omgewing veldproewe het gehelp om individue uit die 15 lyne te identifiseer wat oor goeie aanpasbaarheid en stabiliteit beskik met betrekking tot opbrengs en bak kwaliteit. Die molekulêre merkers gebruik om die gene verantwoordelik vir die kodering van HMGGS 5, 10 en 12 op te spoor het goed gekorreleer met die HMG-GS bande bepaal met behulp van die Agilent© 2100 Bioanalyzer. Toekomstige studies kan moontlik insluit die gebruik van die lyne wat geïdentifiseer was met goeie kenmerke in die bestaande MS-MARS teelprogram van die SU-PTL. Die frekwensies van die verlangde allele kan op hierdie manier in die populasie verhoog word.

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.

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