Canalization, the stability of phenotypes in the presence of a specific genotype and environment is important for trait selection and understanding gene expression pathways. The goal of this study was to investigate mechanisms involved in the loss of canalization at the maize r1 locus. A specific lightly colored R-sc derivative, R-sc:86-17(L), was mutagenized with ethyl methyl sulfonate (EMS), and the progeny screened for restoration of dark seed color and canalization. Putative revertants/mutants were mapped relative to the r1 locus, tested for complementation to each other to identify a minimum number of genes involved in canalization, tested for cis silencing of the r1 gene Lc, analyzed to determine the genetic basis for loss of canalization and r1 gene expression, analyzed for changes in molecular structure at the r1 locus, and analyzed for changes in cytosine methylation patterns. At least two complementation groups were found to be responsible for increased seed color, one at or near r1 and one elsewhere in the genome. Phenotypic analysis revealed highly variable kernel pigmentation, possible incomplete penetrance and a novel class termed Nc enhancers. Nc enhancers were characterized by light to heavy mottling. Southern blot hybridization analysis demonstrated that 19 out of 20 putative EMS-induced mutants were unchanged in the molecular structure of genes Sc‖nc1, Nc2, and Nc3. One mutant resulted in the loss of one of the Nc genes. The loss of Lc expression was found to be rare in R-sc:86-17(L) Lc, and restoration of seed color in R-sc:86-17(L)/P heterozygotes was found to have resulted from recombination between Sc‖nc1 and P with loss of Nc2 and Nc3. Analysis of cytosine methylation patterns revealed low levels of methylation in the 5’ region of Sc and high levels in the 5’ region of the Nc genes and in the 3’ ends of Sc‖nc1, Nc2 and Nc3 in the homozygous putative EMS-induced mutants as previously found for R-sc:86-17(L). Four out of the twenty EMS-induced mutants tested displayed altered methylation patterns, with changes at both the 5’ and 3’ regions of the r1 genes. These findings suggest that the genes or elements involved in the canalization and/or restoration of seed color of R-sc are located at the r1 locus, at the 3’ end of the Sc gene and that at least one additional site in the genome is involved in seed color expression of r1.

Master of Science / Department of Agricultural Economics / Timothy J. Dalton / Smallholder farmers in Tanzania remain susceptible to food insecurity and poverty. To combat these challenges, the country and development organizations have turned to agriculture. In particular, value chains have been identified as a point of interest. Specifically, the maize value chain is of critical importance since maize is the staple crop of the country as well as the staple carbohydrate in the Tanzanian diet. Markets are beneficial because they enable households to specialize in agricultural production according to their comparative advantage. Specifically, markets have been shown to be one tool for increasing welfare, measured through the proxy income. The objective of this thesis is to identify the determinants of a household’s decision to participate in the maize market as well as identify the determinants of a household’s decision regarding how much maize to sell in a given market. This research examines formal and informal market participation among 908 households during the 2008 long rainy season. Probit models were estimated to determine market participation for the formal, informal, and aggregate sale market levels. A Heckman OLS model was used to further analyze the value sold by the household in a given market. Econometric results indicate that “quantity harvested” positively and significantly impacts market participation decisions as well as value sold decisions. The variable “male-headed households” was positive and significant in the formal market while the variable showed no significant impact in the informal market participation model. Both “radio ownership” and “mobile telephone ownership” proved to be positive and significant in the formal model while only the ownership of a radio was significant in the informal market. Additionally it was found that for the formal market participation decision, “bicycle ownership” was positive and significant. Overall, it appears that households participate in the informal market as a way to meet cash needs since farmers were not price-responsive. However, in the formal market farmers were found to be very price-responsive, following neo-classical economic theory.

Plants are inhabited by diverse species of bacteria and fungi, which affect plant health and fitness. Endophytes are bacteria or fungi that live within plant host tissues without causing symptoms of disease, and mediate important plant traits in agriculture, such as nutrient acquisition, disease resistance, and abiotic stress tolerance. However, we know little about the general ecology of endophytes, including which factors determine their compositions within plants. Seedborne transmission may represent an important source of bacterial and fungal endophytes, which can significantly impact the plant microbiome and plant traits. However, seeds are also a vehicle for transmission of plant pathogens. Seeds are commonly treated to control against seedborne pathogens, and increasingly bacteria and fungi are inoculated onto seeds to serve as biological control against pathogens. My dissertation explores the theoretical and applied ecology of seedborne endophytes of maize, including their interactions with pathogenic Fusarium fungi, and with seed treatments designed to control Fusarium. In Chapter II, I examine factors that affect the transmission of seedborne fungal endophytes and Fusarium into maize seedlings, including the influence of soil microbiota, and the impact of disinfection and biological control seed treatments. In Chapter III, I determine the long-term effects of seed disinfection and biological control inoculants on maize bacterial and fungal endophytes and Fusarium pathogenicity across three different farms. In Chapter IV, I recruit maize seed growers across the Pacific Northwest and U.S. to participate in a broadscale study of seedborne endophytes. Across submitted seed samples, I find commonly occurring seedborne endophyte taxa, and delineate how maize varieties interact with environmental factors to affect the composition and diversity of seed-associated endophytes in seeds. Throughout these chapters, I explore the potential applications of seedborne endophytes in agriculture, particularly as a source for biological control against Fusarium in maize, and speculate how seed treatments can have significant, lasting impacts on the plant microbiome.

Thesis (M.Sc. (Crop Science)) --University of Limpopo, 2008 / Stenocarpella ear rot caused by Stenocarpella maydis (Berck) Sutton is the most important disease of maize in South Africa. It is a sporadic disease which makes it difficult for farmers to prepare for its occurrence and consequently of the control measure. The objectives of this study were to genetically characterise the resistance of Stenocarpella maydis ear rot and to identify agronomically suitable Stenocarpella ear rot resistant inbred lines with good combining ability for grain yield. The experimental design was a randomised complete block design with three replications. Studies were conducted at Bethlehem, Cedara and Potchefstroom. To facilitate the comparison, separate trials were established for inbred lines and top cross hybrids. Fifty-four inbred lines were compared against four inbred lines vs. E739, DO620Y, H111 and Mo17 that are well adapted and stable yielders possessing variable resistance to Stenocarpella maydis ear rot. Fifty-four top crosses were compared against one open pollinated variety (SAM 1066), which was used as a tester line as well as three commercial hybrids vs. PAN 6124BT, PAN 6026 and CRN 3505. At Potchefstroom there was an inoculation trial using both inbreds and top crosses. The inbred and top cross materials were obtained from 2004/05 breeding nursery under natural infestation of Stenocarpella maydis at Agricultural Research Council-Grain Crops Institute, Potchefstroom. Data collected were number of days to 50% silking, plant and ear height in centimetres, husk cover, ear position, stand count, total number of ears, number of diseased ears and lodging resistance,. Entries 43 and 4 were the most stable inbred lines with a beta close to 1, while entries 9 and 25 had the smallest deviation from regression. Among the tested inbred lines entry 47 was superior over other inbred lines for grain yield followed by entry 4. Entry 47 showed grain yield of 2.84 tons ha-1 at Bethlehem and 4.42 tons ha-1 at Potchefstroom. While entry 4 had a grain yield of 2.19 tons ha-1 at Bethlehem and 4.58 tons ha-1at Potchefstroom. The two lines, however, are poor combiners for both grain yield and Stenocarpella maydis ear rot resistance. Using SAM 1066 as a tester the grain yield observed for top crosses at Bethlehem, Cedara and Potchefstroom were 5.94, 7,15 and 9.95 tons ha-1, respectively. Entries 57 and 14 were the most stable top cross hybrids with a beta close to one, while entries 46 and 47 had the smallest deviation from regression. Entries 56 and 28 were the most superior top cross hybrids. Entry 56 showed grain yield of 5.58 tons ha-1 at Bethlehem, at Cedara it showed the yield of 5.90 tons ha-1 and at Potchefstroom it was 9.95 tons ha-1 and for the average of three sites it was 7.14 tons ha-1. Entry 28 showed grain yield of 5.80 tons ha-1 at Bethlehem, at Cedara it was 5.80 and at Pothefstroom it was 9.35 tons ha-1 and the combined average was 6.98 tons ha-1. These values compared favourably with the commercial standards. The checks entries 58 and 57 had proved to be resistant over locations. The best combiners for Stenocarpella maydis resistance were entries 29 and 52. Stenocarpella maydis ear rot was found to be of polygenic resistance with additive genetic effects. / The government of Lesotho, Agricultural Research Council-Grain Crops Institute (ARC-GCI), and the Maize Trust

Thesis (MSc. (Agricultural Economics)) -- University of Limpopo, 2014 / Maize is the most important crop in South Africa, being both the major feed grain for livestock and the primary staple food crop for the majority of the South African population. Furthermore, the maize industry contributes substantially to employment, manufacturing, foreign exchange and food security. The importance of maize in contributing to national growth is critical; this makes it meaningful to investigate the nature of maize farmers’ production decisions. This study quantifies the supply response of maize farmers to price and non-price factors in South Africa using econometric techniques. The non-price factors considered in this study are rainfall, technology and market policy. A modified Nerlovian partial adjustment model was applied on historical time series data spanning from 1980-2012 to estimate the supply response of maize in South Africa. To deal with the expected problems associated with time series data the study adopted several diagnostic tests. Results indicate a short-run supply elasticity of 0.49 and a long-run supply elasticity of 0.65, signifying that maize farmers are less sensitive to price changes. The results confirm that non-price factors seem to have more effect on maize supply in South Africa. These findings coincide with those obtained in supply response studies for field crops conducted in other developing African countries. The study also showed that non-price factors such as, rainfall, technology and market policies have a positive impact on maize production. Given the findings, the study recommends policies that focus more on non-price factors as a means of stabilising maize production. The study also recommends that Industry stakeholders and policymakers should find means to integrate the significant relationships between non-price factors and production output into future decisions and marketing policies to safeguard a healthy, growing and sustainable maize industry in South Africa. Key words: Maize supply response, Nerlovian partial adjustment model, price factors, non-price factors.

As maize plants undergo vegetative phase change, they both exhibit heteroblasty, an abrupt change in pattern of leaf morphogenesis, and gain the ability to produce flowers. Both processes are under the control of microRNA 156, whose levels decline at the end of the juvenile phase. Gain of ability to flower is conferred by expression of miR156 targets that encode Squamosa Promoter-Binding (SBP) transcription factors, which in turn induce the expression of MADS-box transcription factors that promote maturation and flowering. What gene expression differences underlie heteroblasty, as well as what causes the reduction in miR156 levels, remain open questions. Here, we compare the gene expression in primordia that will develop into juvenile or adult leaves to identify genes that define these two developmental states and may influence vegetative phase change. In comparisons among successive leaves at the same developmental stage of plastochron 6, three-fourths of approximately 1,100 differentially expressed genes were more highly expressed in juvenile primordia. This juvenile set was enriched in photosynthetic genes, particularly those associated with cyclic electron flow at photosystem I, and genes involved in oxidative stress and retrograde redox signaling. Pathogen responsive pathways including jasmonic acid, salicylic acid, and benzoxazinoids were also up-regulated in juvenile primordia and indeed, we found that exogenous application of jasmonic acid, and hydrogen peroxide delays vegetative phase change in maize seedlings. These results suggest that the timing of vegetative phase change in maize is coordinated in part downstream of photo-oxidative stress signaling. Photo-oxidative stress during greening likely amplifies heterotrophic energy insufficiency. The successful amelioration of these stress signals may ultimately determine the duration of miR156-mediated juvenility.

1. Fusarium roseum �Graminearum� was the predominant fungus associated with stalk rot of maize in eastern Australia in the 1972, 1973 and 1974 growing seasons. All isolates of this pathogen were of the Group 2 type. Thus Group 2 contrasts with Group I which is normally isolated :Erora crown rot of wheat and grasses. Other fungi isolated in order of frequency were Diplodia maydis, F. rnoniliforme �Subglutinans�, Bipolaris sorokiniana, Nigrospora oryzac, F. roseum �Semitectum�, F. moniliforme, F. roseum �Equiseti�, F. roseum �Concolor�, Macrophomina phaseolina, Rhizoctonia sp., F. roseum �Acuminatum�, F. oxysporum, F. solani, F. tricinctum and F. roseum �Heterosporum�. The relative isolation frequencies of the fungi varied according to the seasonal conditions. Stalk rots were not of major importance in 1973, a relatively dry growing season. However, in 1974, a wet growing season, stalk rot diseases were common in all areas investigated. 2. Isolates of F. roseum �Graminearum�,derived mainly from wheat and maize but also from other sources and from various regions of eastern Australia, were examined for perithecia formation, colony characteristics, fertility, colony growth, conidia production and conidia size. The distribution of the fungus in field colonized maize and wheat plants was also studied. The Group 1 isolates did not produce perithecia, were heterothallic and very infertile, had a mean colony growth of 4.4 cm per 3 days (range, 3.9- 5.1) and produced relatively large numbers of conidia. In contrast, Group 2 isolates were homothallic and produced perithecia readily, had a mean colony growth of 5.4 cm per 3 days (range, 4.7�6.1) and produced relatively low numbers of conidia. Group 1 isolates were found to be commonly associated with crowns and roots of plants and Group 2 isolates were commonly associated with aerial plant parts. 3. The ability of a number of Group 1 and Group 2 isolates to produce the fungal hormone, zearalenone was assessed. Group I isolates produced three to four times more zearalenone than Group 2 isolates. In addition, a. culture which had previously produced perithecia but had lost that ability following numerous transfers, produced no detectable zearalenone. The results provided good evidence that the observed difference in perithecia formation was directly related to the ability to produce zearalenone. 4. The pathogenicity to wheat, maize and carnations of Group 1 isolates from crown rot affected wheat plants and Group 2 isolates from stalk rot affected maize plants was tested. Pathogenicity of 11 other isolates from teosinte, carnations, pearl millet, wheat and barley scab, banana, ginger and common wheat grass was also assessed. The results indicated that pathogenic specialization exists within F. roseum �Graminearum�. Wheat isolates were the most pathogenic to wheat, carnation isolates were the most pathogenic to carnations and all maize isolates were pathogenic to maize while those from wheat and common wheat grass were not as pathogenic to maize. Moreover, Group 2 isolates were more pathogenic when inoculated in aerial plant parts, and the Group I isolates were more pathogenic when inoculated in plant parts in soil. Inoculations on wheat seedlings in sterile field soil demonstrated that the inherent pathogenicity to wheat seedlings of isolates from wheat and maize were similar. 5. Some factors which could contribute to the observed pathogenic differences between isolates from wheat and maize to wheat seedlings in field soil were examined. Conidia volume, germination rate and inherent germinability in the soil were studied. The Group I isolates had the largest volume, the most rapid germination and the highest inherent germinability. Pathogenicity was positively correlated with conidium volume and inherent germinability. In addition, the inherent germinability and conidium volume were positively correlated. Thus, it was established that pathogenic behaviour of conidia of Group 1 and Group 2 reflected differences in conidia morphology.

The estimation of evapotranspiration (ET), a key process within the Earth's surface water and energy balance, remains an important challenge for a wide range of disciplines such as surface hydrology, irrigation management and meteorology. However, notwithstanding the considerable progress recently made in our understanding of the physical and biological processes governing ET, the accurate quantification of ET is very tricky to achieve, even at a limited spatial scale. In this study, we combine field measurements with numerical experiments to tackle issues related to the quantification of ET and the associated uncertainties for a maize cropped field using two different approaches, i.e. the agro-hydrological modelling and the soil water balance approach. For the agro-hydrological modelling, we mainly focus on the estimation of field-scale soil water content and on the identification of root water uptake parameters. With regard to the field-scale soil water content, we put forward that the within-field variability is large and that the maize crop plays a non-negligible role in the development of the soil water content patterns both at the field and at the maize row scale. For deriving root water uptake parameters (RWUP), we develop and test two different approaches, i.e. the simplified soil water balance and the inverse modelling approach. Using numerical experiments, we show that the simplified soil water balance approach produces quite accurate RWUP. On the other hand, the inverse modelling approach is only successful for some soils and for some conditions due to instability and nonuniqueness issues. For the soil water balance approach, we show that the accuracy of the local ET estimate is strongly dependent on the estimation method used to derive the bottom fluxes and that the use of pedotransfer functions is of little interest. For field-scale ET estimates, we show that the variability of ET is large both at the field scale (due to the variable crop growth) and at the maize row scale (due to the maize row layout). To produce accurate field-scale ET estimates, we suggest to scale up maize row scale ET estimates using the concept of temporal stability or using a covariant such as the Leaf Area Index. The results of our study suggest that the estimation of water fluxes or associated state variables for a row cropped field requires a two-step upscaling strategy, from the local scale to the row, then from the row to the field scale.

Sorghum downy mildew (SDM) of maize is caused by the oomycete Peronosclerospora sorghi (Weston and Uppal) C. G. Shaw. The disease can cause devastating yield losses in maize (Zea mays L.). Quantitative trait loci (QTLs) mediating resistance to SDM were mapped using both restriction fragment length polymorphisms (RFLPs), and simple sequence repeats (SSRs) in 220 F2 individual maize progeny derived from a cross between two extremes; highly susceptible inbred parent SC-TEP5-19-1-3-1-4-1-1 (white) and highly resistant inbred P345C4S2B46-2-2-1-2-B-B-B (yellow). The phenotypic expression was assessed on F2:3 families in a wide range of environments under natural field infection and in a controlled greenhouse screening method. Heritability estimates of disease reaction ranged from 93.3% in Thailand sit 1 to 48% in Thailand sit 2. One hundred and thirty three polymorphic markers were assigned to the ten chromosomes of maize with LOD scores exceeding 4.9 covering about 1265 cM with an average interval length between markers of 9.5 cM. About 90% of the genome was located within a 10 cM distance to the nearest marker. Three putative QTLs were detected in association with resistance to SDM in different environments using composite interval mapping. Despite environmental and symptom differences, one QTL on chromosome 2 bin 9 had a major effect in all trials and explained up to 70% of the phenotypic variation in Thailand where the highest disease pressure was experienced. Two other QTLs on chromosome 3 bin 5 and chromosome 9 bin 2 had a minor effect, each explaining no more than 4% of the phenotypic variation. These results revealed one major gene and two minor genes that control sorghum downy mildew resistance. These markers should be very useful in breeding programs in facilitating the introgression of the resistance genes into commercial varieties. Marker-assisted selection for these loci should be useful in incorporating SDM resistance genes in maize across environments, even in the absence of the pathogen.

Fusarium verticillioides (Sacc.) Nirenberg (teleomorph Gibberella moniliformis Wineland) is a fungal pathogen of maize that causes ear rots and stalk rots worldwide. In addition, it produces a group of mycotoxins called fumonisins when the fungus colonizes maize and maize-based products. Fumonisin B1 (FB1), the predominant form occurring in nature, can cause detrimental health effects in animals and humans. Several efforts were made to study the host and pathogen factors that contribute to the production of fumonisins. Using the available genomic resources, three genes with a potential role in FB1 regulation and development were identified. The genes are GBP1, GBB1 and GAP1. This research describes molecular characterization of these genes with respect to regulation of FB1 and development in F. verticillioides. GBP1 is a monomeric GTP binding protein with similarity to DRG and Obg sub-classes of G-proteins. GBB1 encodes heterotrimeric GTP binding protein β subunit. GAP1 is a GPI (Glycophosphotidylinositol) anchored protein, which belongs to a family of cell wall proteins. Targeted deletion and complementation studies indicated that GBP1 is negatively associated with FB1 biosynthesis but had no effect on conidiation in F. verticillioides. GBB1 plays an important role in regulation of FB1 biosynthesis, conidiation and hyphal growth, but not virulence. GAP1 is associated with growth, development and conidiation but not in positive regulation of FB1 or pathogenicity. The outcome of this study revealed new molecular genetic components that will help scientists better understand signal transduction pathways that regulate FB1 biosynthesis and conidiation in F. verticillioides.