The importance of maize in sub-Saharan Africa and the potential of quality protein maize (QPM) to alleviate the nutritional gap caused by lack of access to adequate protein rich foods were highlighted. Frustrations from complex inheritance systems of the QPM trait leading to calls for more information on the inheritance and stability of the QPM trait, fear of total loss of the QPM trait due to the recessive nature of the opaque-2 gene to the wild type gene in normal endosperm maize when QPM and normal endosperm maize coexist, lack of information on the nutritional value of contaminated QPM grain, and poor linkages with the smallholder farmers were all cited as drawbacks in the promotion and adoption of QPM. Therefore the objectives of the study were: 1) To solicit the participation of smallholder farmers in the development and setting up of QPM breeding goals, objectives and dissemination strategies; 2) To estimate general combining ability (GCA), specific combining ability (SCA) and reciprocal cross effects on anthesis days, quality traits and grain yield among the publicly available elite QPM inbred lines; 3) To compare experimental QPM hybrids with selected check cultivars, and normal endosperm maize hybrids for grain yield performance and kernel endosperm modification scores; 4) To evaluate QPM hybrids for grain yield and kernel endosperm modification scores in selected sub-Saharan Africa target environments. 5) To determine the level of normal endosperm maize pollen contamination that can occur in quality protein maize without loss of nutritional superiority; 6) To estimate the average levels and the patterns of foreign maize pollen contamination in QPM crops coexisting with normal endosperm maize varieties. The contribution of smallholder farmers in setting breeding goals and dissemination strategies for QPM was solicited. One major finding was that the kernel endosperm qualities of landrace “Hickory King” need to be incorporated into new QPM varieties so as to encourage adoption. Farmers preferred getting information on QPM varieties through their local Agricultural Research and Extension (AREX) officers. A diallel study of 36 F1 QPM hybrids and their reciprocals was conducted across seven environments for agronomic traits and three environments for nutritional value traits. There were significant differences for all traits analysed using Griffing Method 3 model 1. General combing ability effects were significant and important in the control of anthesis days, kernel endosperm modification, protein content, tryptophan content, and Quality Index (QI). Specific combining ability effects were highly significant and important in the control of grain yield. There were significant SCA effects for anthesis days and QI but the proportions were lesser than the corresponding GCA effects in both traits. Kernel endosperm modification had significant GCA effects and nonsignificant SCA effects. Reciprocal-cross differences were significant for anthesis days, tryptophan content and QI. Nonmaternal effects were significant for tryptophan content whilst both maternal and nonmaternal effects were significant for QI and anthesis days. Nonmaternal effects were relatively more important than maternal effects in all the cases where there were significant reciprocal-cross differences. The cross with the highest SCA effects for grain yield was CZL03016/CML144. The most desirable cross with the lowest anthesis days was CZL03016/CML144 whilst the most desirable inbred line with the lowest anthesis GCA effects was CZL03016. The inbred line with the most desirable GCA effects for protein content, tryptophan content and QI was CML264Q. Inbred line CML264Q crossed to CZL03016 had significant SCA effects for QI. The most desirable GCA effects for kernel endosperm modification were associated with inbred line CZL03016 followed by CZL01006. Maternal effects for both tryptophan content and QI were associated with inbred line CML264Q. Genotype by environment interaction effects across all the seven environments were significant for grain yield and kernel endosperm modification. Check hybrids performed better than experimental hybrids for grain yield but were not different for kernel endosperm modification. The normal endosperm maize hybrids were significantly better for both grain yield and kernel endosperm modification. However, in all the comparisons the best check or normal endosperm maize hybrid was not significantly better than the best experimental or QPM hybrid, respectively. The most desirable score for kernel endosperm modification was from the cross of CZL01006 to CZL03016 though not significantly different from the check hybrid with the best score. AMMI1 was the best model for kernel endosperm modification scores and AMMI2 was suitable for grain yield. Both environments and hybrids were diverse. Grain yield of most hybrids was not stable with specific adaptation to environments. The most stable hybrid with no specific adaptation was CML176/CML181f with a mean yield of 6.51t ha-1. The putative nutritional superiority of normal endosperm maize pollen contaminated QPM as measured by the QI depended on the environmental conditions. The moisture stressed environment (CIMMYT Harare) had a lower QI value (0.858) and a lower tolerance to pollen contamination of 15.3% whereas the grain produced under near to optimum growing conditions (ART farm) had a higher QI value (0.915) and a higher tolerance to pollen contamination of 31.9% before total loss of nutritional superiority. Thus contaminated QPM grain had nutritional superiority up to a certain point before total loss of nutritional superiority. Geostatistical analysis was used to determine the levels and patterns of pollen contamination that occur when QPM and normal endosperm maize crops coexist under conditions minimising both temporal and geographical isolation to the lowest possible levels for the two independent crops. Higher pollen contamination levels were restricted mostly to the sections of the QPM crop proximal to the rows of normal endosperm maize crop, with the central parts of the QPM crops experiencing relatively low levels of contamination. For the four experiments (QCS200711, QCS200712, QCS200721 and QCS200722) in which the thresholds to nutritional superiority were determined, 87.9%, 94.8%, 62.2% and 65.6% of the crop areas passed for superior QPM grain, respectively. Estimates for average contamination levels of homogenous mixtures of grain from each of the nine experiments were below 20% contamination. The contamination levels were far less than previously thought. “Hickory King” kernel quality attributes were important in breeding QPM varieties for the smallholder farmers. Parents of the 72 hybrids were diverse for the agronomic characters studied and three of the experimental hybrids were found to be adapted and comparable to the check varieties. Quality protein maize tolerance to foreign pollen contamination without loss in nutritional superiority depended on growing conditions. The coexistence of QPM and normal endosperm maize without total loss of QPM nutritional superiority was feasible. / Thesis (PhD.)-University of KwaZulu-Natal, Pietermaritzburg, 2008.

Maize grain contains high levels of phytic acid which chelates iron, zinc and other micronutrients as it passes through the digestive systems of monogastric consumers reducing their bioavailability. Breeding for low phytic acid (LPA) content to improve micronutrient bioavailability is hampered by a tedious and destructive colorimetric method on the grain, low yields compared to the wild-types and reduced seed germination and vigour of LPA mutants. Breeding for LPA therefore should also incorporate breeding for improved germination and vigour in the mutants. Molecular markers to speed up the selection process and studies on gene action and combining ability for germination, vigour and yield parameters of the LPA mutants in combinations with other different maize germplasm will speed up breeding for this trait. The objectives of this study were: to develop a molecular marker linked to the lpa1-1 gene and apply this marker for foreground selection in a backcross breeding programme and to use amplified fragment length polymorphism (AFLP) markers for background selection to recover the recurrent parent genome to speed up the backcrossing process; to study gene action and combining ability for seed germination, vigour and yield from diallel crosses involving LPA mutants, QPM and normal endosperm maize inbred lines by replicated laboratory seed tests ( standard germination test and accelerated aging test) and field evaluations in South Africa and Zimbabwe. A co-dominant single nucleotide polymorphism (SNP) marker which detects the transition base change of C/T nucleotides was developed from the gene sequence to identify the lpa1-1 trait. The 150 bp lpa1-1 SNP marker was validated by forward and reverse DNA sequencing of the parental amplification products which confirmed the C to T base change resulting in the LPA phenotype. The lpa1-1 SNP marker was used for foreground selection in 250 BC(2)F(1) progenies of CM 32 (LPA) x P 16 as the recurrent parent. This SNP marker was used to genotype the lines into homozygous dominant (wild type) and homozygous recessive (LPA) genotypes by their melting profiles and heterozygous genotypes by the normalised difference plots using high resolution melt (HRM) analysis. Seventeen heterozygous and 11 homozygous recessive lines were identified for background selection by fingerprinting with AFLP markers to determine the amount of recurrent parent (P 16) genome present. There were six EcoRI/MseI primer combinations tested with 277 data points scored (84% polymorphism rate). The amount of recurrent parent (P 16) genome recovered ranged from 62% to 92% with 13 lines showing greater than 83% of the recurrent parent genome. The effects of diallel crosses generated between four LPA, three QPM and three normal endosperm maize lines were determined for seed germination and vigour using the standard germination and accelerated aging seed tests under laboratory conditions in accordance with the procedures of the International Seed Testing Association. The specific combining ability (SCA) effects and general combining ability (GCA) effects were significant for the seed germination and vigour traits, indicating that genes with non-additive and additive effects were important in controlling these traits. However, the SCA effects were greater than GCA effects suggesting that genes with non-additive effects were predominant. The LPA parents showed reduced vigour compared to the normal and QPM inbred lines under both conditions, with LPA lines CM 31 and CM 32 showing stress tolerance. There were some combinations involving LPA lines, such as LPA x normal, LPA x QPM and LPA x LPA that retained high vigour and high germination rates under accelerated aging conditions, suggesting that they could be stress-tolerant.. A 10 x 10 diallel involving four LPA, three QPM and three Nm inbred lines was evaluated in replicated trials across six environments. Results show that both additive and non-additive gene effects were significant for resistance to northern corn leaf blight (NCLB), grey leaf spot (GLS) and Phaeosphaeria leaf spot (PLS) diseases. The additive gene effects were predominant for the yield and associated secondary traits such as days to mid-pollen shed (DMP), days to mid-silking (DMS), ear per plant (EPP) and grain moisture content (GMC) and grain yield. The LPA lines were early flowering and had quick grain dry down rate but all showed undesirable negative and significant GCA effects for yield. The yield of the LPA x LPA, LPA x Nm and LPA x QPM group of crosses was lower than the check hybrids by about 32 to 67% showing the need for yield improvement of the LPA combinations. An eight x eight diallel involving two LPA and six normal endosperm lines was evaluated over two seasons in five locations with two replications for grain yield components and foliar diseases. There was significant additive and non-additive gene action for both seed germination and vigour traits with predominance of non-additive gene effects. Both additive and non-additive gene effects were significant for yield and associated traits such as anthesis dates and number of ears per plant. However, the additive gene action was predominant for yield and associated traits. Generally the LPA lines and their combinations showed lower germination and vigour. The LPA line, CM 32 showed stress tolerance under accelerated aging conditions. There were three LPA x Nm crosses that showed improvements to the means of seed germination and vigour and yield traits. Results indicated that there was not any significant correlation between yield and seed germination and between yield and vigour. Yield was, however, significantly and positively correlated with anthesis dates and GMC, indicating that higher yield was associated with longer growing cycles. This study was able to successfully develop and apply the lpa1-1 SNP marker for foreground selection and AFLP markers for background selection in a backcross breeding programme. Problems of low seed germination, seedling vigour and grain yield of LPA lines and their combinations were confirmed. However results also indicated some potential of combining the LPA and QPM traits in a single cultivar. In general, procedures such as reciprocal recurrent selection, that emphasise both GCA and SCA effects would be recommended to improve seed germination, seedling vigour and yield in developing varieties with LPA trait. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2010.

There are few maize varieties that are drought tolerant in semi-arid eastern Kenya and farmer perceptions of drought tolerant maize cultivars have not been studied in this region. Farmers in this region use maize landraces that have not been studied for their potential future hybridization. The main objectives of this study were therefore to: (i) study farmer perceptions of drought and preference for maize varieties, (ii) improve drought tolerance in maize populations in the semi-arid eastern Kenya using S1 family recurrent selection, and (iii) classify maize landraces according to their heterotic patterns. A participatory rural appraisal (PRA) was conducted in Machakos and Makueni districts in semi-arid eastern Kenya. A total of 175 farmers were involved in focus group discussions. An open ended questionnaire and a checklist were used to guide the farmers during the discussion sessions. Scoring and ranking techniques were used to assess farmers’ preferences of maize varieties and constraints to maize production. The farmers grew maize as their major crop followed by beans. Nearly 60% of the farmers grew local maize landraces, whose seed they recycled from season to season; 40% grew improved varieties, but mainly composites rather than hybrids. The key farmers’ criteria for choosing a maize variety in order of importance were drought tolerance, early maturity, high yield, and disease resistance. The major constraints to maize production were drought, lack of technical know-how, pests, poor soils, and inadequate seed supply. Maize traits preferred by farmers in a drought tolerant variety included high yield, recovery after a dry spell and the stay green characteristic. Two maize landrace populations MKS and KTU from semi-arid eastern Kenya and three CIMMYT populations V032, ZM423, and ZM523 were subjected to two cycles of S1 progeny recurrent selection for drought tolerance in yield and traits indicative of drought tolerance were measured during flowering and grain filling from February 2005 to September 2007. Evaluation to determine selection gains was done in one trial replicated five times. It was laid out as a 4x4 lattice design and drought was imposed at reproductive stage by withholding irrigation one week before flowering and resumed during grain filling. The trial was repeated under well-watered conditions which served as a control experiment. After two cycles of selection under drought stress conditions, KTU population had a realized gain in yield of 0.2 t ha-1, MKS population 1.2 t ha-1 and ZM423 0.4 t ha-1, whereas in V032 and ZM523, grain yield reduced by 1.1 t ha-1 and 0.6 t ha-1, respectively. Under well watered conditions, the realized gains in grain yield were positive in all the populations except V032, where there was a reduction of 0.1 t ha-1. Selection increased the genetic variability and heritability estimates for yield in S1 lines of MKS and ZM423 populations, but decreased in KTU, V032 and ZM523 populations. The research to identify heterotic patterns was undertaken using ten maize landraces from the semi-arid eastern Kenya, six maize landraces from coastal Kenya, and three maize populations from CIMMYT. These populations were planted at Kiboko Research Farm during the short rains of October-December 2005 and crossed to two population testers, Embu 11 and Embu 12. The evaluation of the test crosses was done during the long rains of March-June 2006. Percentage heterosis for yield ranged from -17.7% to 397.4%, -79.4 to 22.2% for anthesis-silking interval, -23.9% to 29.2% for ear height, -0.1 to 1.1 for ear diameter, -7.1 to 21.2% for ear length and -5.9% to 30.3% for plant height. iii General combining ability (GCA) effects were significant (p=0.05) for all the traits, while specific combining ability (SCA) effects were not significant (p>0.05), implying that variation among these crosses was mainly due to additive rather than nonadditive gene effects. Since SCA was not significant (p>0.05) for yield, maize populations were classified based on percentage heterosis for yield alone. The maize populations therefore, were grouped into three different heterotic groups P, Q and R. Twelve landrace populations and two CIMMYT populations showed heterosis with Embu 11 and no heterosis with Embu 12 were put in one group P. Two landrace populations that showed no heterosis with either tester were put in group Q. Two landrace populations and one CIMMYT population showed heterosis with both testers were put in group R. None of the populations showed heterosis only with Embu 12 and no heterosis with Embu 11. The main constraint to maize production was drought and the farmers preferred their landraces whose seed they recycled season to season. After two cycles of recurrent selection, the landrace populations showed improved progress in yield. Thus, further selection will be beneficial in the populations where genetic variability increased. Therefore, these populations can further be improved per se and released as varieties and/or incorporated into the existing maize germplasm to broaden their genetic base, given that their heterotic patterns have been identified. Considering that farmers recycle seed, breeding should be towards the development of open-pollinated varieties which are drought tolerant. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2007.

Bt maize expressing Cry1Ab was approved for release in South Africa for control of Busseola fusca (Fuller) (Lepidoptera: Noctuidae) and Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) in 1998. During 2012, a stacked Bt maize event, expressing Cry2Ab2 + Cry1A.105, was also approved for control of these abovementioned pests. The aim of this study was to determine the effects of two Bt maize events expressing Cry1Ab (MON810 and Bt11) and a Bt maize event expressing Cry2Ab2 + Cry1A.105 (MON89034) on selected lepidopteran non-target pest species and certain lepidopteran stem borer species in South Africa. Results from previous studies and this study will provide information regarding efficacy of Bt maize against pests which have not been evaluated yet. Insects with significance in maize agro-ecosystems in South Africa as well as the rest of Africa, were prioritised and laboratory bioassays were conducted to evaluate the effect of Bt maize against these selected target and non-target pest species. Studies were conducted on three stem borers C. partellus, Eldana saccharina and Sesamia calamistis and three nontarget lepidopteran pest species Agrotis segetum, Helicoverpa armigera and Spodoptera exempta. Results showed that MON810 maize was not effective against A. segetum larvae feeding on maize seedlings. Differential levels of survival were observed between two A. segetum populations on MON89034 with a population from Polokwane showing survival on the stacked maize event. No S. exempta 1st instar larvae survived on MON810 and MON89034 but 3rd instar larvae survived on MON810 maize. Helicoverpa armigera larvae survived on ears of MON810 maize plants but not on events MON89034 or Bt 11. Results further indicated that C. partellus larvae were highly susceptible to these three Bt maize events. Larval survival of S. calamistis was recorded for larvae feeding on MON810 and Bt11 maize ears but not on MON89034 maize ears. Bt maize during the vegetative growth stages therefore effectively controlled C. partellus, S. calamistis and E. saccharina but the latter two species was not effectively controlled when feeding on ear tissue. This study provides important information on the effects of Bt maize on the most important non-target pest species of maize in sub-Saharan Africa. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Bt maize expressing Cry1Ab was approved for release in South Africa for control of Busseola fusca (Fuller) (Lepidoptera: Noctuidae) and Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) in 1998. During 2012, a stacked Bt maize event, expressing Cry2Ab2 + Cry1A.105, was also approved for control of these abovementioned pests. The aim of this study was to determine the effects of two Bt maize events expressing Cry1Ab (MON810 and Bt11) and a Bt maize event expressing Cry2Ab2 + Cry1A.105 (MON89034) on selected lepidopteran non-target pest species and certain lepidopteran stem borer species in South Africa. Results from previous studies and this study will provide information regarding efficacy of Bt maize against pests which have not been evaluated yet. Insects with significance in maize agro-ecosystems in South Africa as well as the rest of Africa, were prioritised and laboratory bioassays were conducted to evaluate the effect of Bt maize against these selected target and non-target pest species. Studies were conducted on three stem borers C. partellus, Eldana saccharina and Sesamia calamistis and three nontarget lepidopteran pest species Agrotis segetum, Helicoverpa armigera and Spodoptera exempta. Results showed that MON810 maize was not effective against A. segetum larvae feeding on maize seedlings. Differential levels of survival were observed between two A. segetum populations on MON89034 with a population from Polokwane showing survival on the stacked maize event. No S. exempta 1st instar larvae survived on MON810 and MON89034 but 3rd instar larvae survived on MON810 maize. Helicoverpa armigera larvae survived on ears of MON810 maize plants but not on events MON89034 or Bt 11. Results further indicated that C. partellus larvae were highly susceptible to these three Bt maize events. Larval survival of S. calamistis was recorded for larvae feeding on MON810 and Bt11 maize ears but not on MON89034 maize ears. Bt maize during the vegetative growth stages therefore effectively controlled C. partellus, S. calamistis and E. saccharina but the latter two species was not effectively controlled when feeding on ear tissue. This study provides important information on the effects of Bt maize on the most important non-target pest species of maize in sub-Saharan Africa. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

A Dissertation submitted to the Faculty of Science, University of the Wfitwatersvand, Johannesburg for the Degree of Master of Science. Johannesburg, 1977,

O milho (Zea mays) é considerado como uma das culturas mais importantes cultivadas mundialmente devido a sua composição química, valor nutritivo e o seu potencial produtivo, apresentando assim, considerável relevância nos aspectos socioeconômicos. Diversos fatores interferem no desempenho da cultura e, dentre eles, o clima está entre aqueles que oferecem os maiores desafios para planejamento e manejo da cultura. Diante da importância da cultura no contexto nacional e mundial, é importante considerar as projeções futuras da produção do grão diante das mudanças climáticas e, consequentemente, na segurança alimentar nos próximos anos. Assim, avaliou-se neste estudo o impacto da mudança do clima sobre o crescimento e desenvolvimento da cultura do milho, utilizando um modelo de crescimento de plantas, baseado em processos biofísicos. Para a calibração do modelo foram utilizados dados obtidos experimentalmente e a simulação de cenários de mudanças climáticas foi realizada de acordo com a abordagem do programa AgMIP. Trabalhou-se com o modelo CERES-MAIZE/DSSAT, e três modelos de circulação climática global (GCM\'s) regionalizados e dois cenários econômicos (ou de emissão) para o período 2040-2069 (representando 2050). Com base nos resultados obtidos, pode-se concluir que se as práticas de gestão se mantêm como presentes, o rendimento de milho deverá diminuir em meio do século, no entanto, a diminuição dos rendimentos reais pode não ser tão dramática quanto previsto nos casos em que apenas o fator climático é considerado. Para isso fatores econômicos e tecnológicos devem ser considerados para aumentar os rendimentos. O aumento da [CO2] terá um efeito positivo sobre o crescimento do cultivo, mas não parece ser suficiente para compensar os efeitos negativos do clima futuro, notadamente o aumento da temperatura do ar. / Maize (Zea mays) is considered one of the most important crops cultivated worldwide due to its chemical composition, nutritional value and its productive potential, thus presenting considerable relevance in socioeconomic aspects. Several factors interfere in the performance of the crop and, among them, the climate is among those that offer the greatest challenges for crop planning and management. Given the importance of culture in the national and global context, it is important to consider the future projections of grain production in the face of climate change and, consequently, food security in the coming years. Thus, the impact of climate change on maize crop growth and development was evaluated in this study using a plant growth model based on biophysical processes. For the calibration of the model, data obtained experimentally were used and the simulation of climate change scenarios was performed according to the AgMIP program approach. We worked with the CERES-MAIZE / DSSAT model, and three regional climate circulation models (GCM\'s) and two economic (or emission) scenarios for the period 2040-2069 (representing 2050). Based on the results obtained, it can be concluded that if management practices remain as present, corn yields should decrease in the middle of the century, however, the decrease in real incomes may not be as dramatic as predicted in cases where that only the climatic factor is considered. For this economic and technological factors must be considered to increase incomes. The increase in [CO2] will have a positive effect on crop growth, but it does not appear to be sufficient to compensate for the negative effects of future climate, notably the increase in air temperature.

Maize (Zea mays L.) is the principal crop of Southern Africa but production is threatened by gray leaf spot (Cercospora zea-maydis L.) and phaeosphaeria leaf spot (Phaeosphaeria maydis L.) diseases, drought and the use of unadapted cultivars, among other constraints. There are few studies of gray leaf spot (GLS) and Phaeosphaeria leaf spot (PLS) resistance, drought tolerance, yield stability and maize cultivar preferences in Southern Africa. The objective of this study was to: a) determine farmers’ preferences for cultivars; b) investigate the gene action and heritability for resistance to GLS and PLS, and drought tolerance; and c) evaluate yield stability and its relationship with high yield potential in Southern African maize germplasm. The study was conducted in South Africa and Zimbabwe during 2003 to 2004. A participatory rural appraisal (PRA) established that farmers preferred old hybrids of the 1970s because they had better tolerance to drought stress. Farmers also preferred their local landrace because of its flintier grain and better taste than the hybrids. The major prevailing constraints that influenced farmers’ preferences were lack of appropriate cultivars that fit into the ultra short seasons, drought and low soil fertility. Thus they preferred cultivars that combine high yield potential, early maturity, and drought tolerance in all areas. However, those in relatively wet areas preferred cultivars with tolerance to low soil fertility, and weevil resistance, among other traits. A genetic analysis of 72 hybrids from a North Carolina Design II mating revealed significant differences for GLS and PLS resistance, and drought tolerance. General combining ability (GCA) effects accounted for 86% of genetic variation for GLS and 90% for PLS resistance indicating that additive effects were more important than non-additive gene action in controlling these traits. Some crosses between susceptible and resistant inbreds had high resistance to GLS suggesting the importance of dominance gene action in controlling GLS resistance. Resistance to GLS and PLS was highly heritable (62 to 73%) indicating that resistance could be improved by selection. Also large GCA effects for yield (72%), number of ears per plant (77%), and anthesis-silking interval (ASI) (77%) under drought stress indicated that predominantly additive effects controlled hybrid performance under drought conditions. Although heritability for yield declined from 60% under optimum to 19% under drought conditions, heritability for ASI ranged from 32 to 49% under moisture stress. High heritability for ASI suggested that yield could be improved through selection for short ASI, which is positively correlated with high yield potential under drought stress. The stability analyses of the hybrids over 10 environments indicated that 86% had average stability; 8% had below average stability and were adapted to favourable environments; and 6% displayed above average stability and were specifically adapted to drought stress environments. Grain yield potential and yield stability were positively correlated. In sum, the study indicated that farmers’ preferences would be greatly influenced by the major prevailing constraints. It also identified adequate genetic variation for stress tolerance, yield potential and yield stability in Southern African maize base germplasm, without negative associations among them, suggesting that cultivars combining high yield potential, high stress tolerance and yield stability would be obtainable. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2005.

Maize genetic diversity includes an array of kernel colors (red, blue, purple) with blue concentrated in the aleurone and red primarily in the pericarp. Quality protein maize (QPM) is improved over normal maize in regards to grain concentration of the essential amino acids lysine and tryptophan but has not been widely adapted in part due to lower than conventional yields. These are minimally-utilized specialty corns when compared to the yellows and whites commonly grown. Red, blue, and purple pigments are antioxidant phytochemicals produced by the plant as secondary metabolites. Antioxidants have been linked to anti-cancer and other anti-inflammatory health benefits. QPM hybrids are desirable in developing countries where subsistent agriculture is commonly practiced and quality protein cereals are non-existent. These two diverse maize categories have been the subject of little breeding research compared to normal maize and the potential for high phenolic content as well as the characterization of these QPM hybrids has not been previously investigated. We evaluated 153 maize hybrids (84 colored, 69 QPM) across three locations. High heritability estimates were found for phenolic content (0.80), tryptophan (0.46), and endosperm opacity (0.82). It was encouraging that all three traits observed little genotype by environment (GxE) interaction across diverse environments. This proved the trait analysis procedure to be robust in detecting and separating genotypes for both total phenolic content in colored maize, and amino acids in QPM. Top combiners for phenolics were the purple maize "maize morado" and red lines, with blue, yellow and white maize performing in descending order. Within the tested hybrids, high per kernel antioxidants (measured by total phenolics) may be the answer for producing the most total phenolics, with the top hybrid yielding greater than twice the total phenolics as the top yielding yellow hybrid. The top QPM hybrid out yielded the top normal hybrid by 35 and 30% for lysine and tryptophan. Additionally, QPM endosperm opacity primarily followed an additive, mid-parent trend, with some hybrids (20%) from diverse germplasm backgrounds deviating from that trend displaying the complexity and recessive nature of multiple modifier loci. Additional agronomic and composition traits were minimally correlated with phenolics.

Modern agriculture is dependent on both global supply chains and crop monocultures. These features aid the evolution and spread of novel plant pathogens. Limited genetic diversity in commercial crop lines can result in widespread susceptibility to emerging pathogens. Pathogen resistance may be developed through conventional breeding approaches, or a number of transgenic strategies. This thesis focuses on the characterisation of an emerging maize disease, Maize lethal necrosis (MLN), and engineering resistant maize lines using an artificial microRNA (amiRNA) approach. MLN is a synergistic viral disease caused by the interaction of Maize chlorotic mottle virus (MCMV) with any maize-infecting member of the potyviridae. I used next-generation RNA sequencing to characterise the MLN outbreak in East Africa, discovering that local and Chinese strains of the potyvirus Sugarcane mosaic virus (SCMV) typically coinfect with MCMV. A first global MCMV phylogeny was constructed using these samples combined with new Sanger sequencing of samples in Ecuador and Hawaii. The phylogeny supported previous hypotheses of a link between the Chinese and African outbreaks, and suggested a novel link between the Hawaiian and Ecuadorian outbreaks. The SCMV sequences generated demonstrated strong evidence of extensive recombination, in line with previous reports on SCMV and potyviruses. These data also produced first reports of a number of RNA viruses in East Africa, and five novel viral-like sequences, with their presence confirmed by RT-PCR. RNA silencing is an important component of the plant immune response to viral infection. amiRNAs can be used to generate specific and effective viral resistance through Watson- Crick base pairing between the amiRNA and the (RNA) viral genome. Previous amiRNA approaches have targeted invariable genomic regions using consensus sequences. However, the high mutation rate of RNA viruses means single cells contain a variety of mutant genomes, collectively called a quasispecies. To deter the evolution of resistance breaking I devised a novel strategy to include intra-sample variation from NGS data in amiRNA design, and constructs, each containing five of these amiRNAs, were transformed into tropical maize lines. RNA silencing may be hampered by the expression of viral suppressors of silencing (VSRs). Local VSR assays demonstrated that there are no local VSRs in the MCMV genome, while systemic VSR assays showed a possible systemic VSR role for the unique P32 protein, and an interesting link between photoperiod and systemic silencing more generally.