Rice is an important crop ranking third after maize and wheat in Kenya. Its demand is growing at 12% per annum, while production has stagnated for quite a number of years. This situation has lead to consumption outstripping production by about 84%. There is therefore an urgent need to step up domestic production. To understand farmers’ preferences, the first survey on rice production was carried out. To supplement on this survey information, focus group discussions and key informants were incorporated to further shed more information. The farmers demonstrated their preferences for varieties that were high yielding, hybrid rice and with high nutrient use efficiency and these constituted 53.7% of their wishes. Among the crops grown by the selected farmers, rice was the most important followed by maize, however, the hectarage of maize was higher followed by rice. The farmers also identified labour costs as a factor limiting production especially for irrigated rice and thus they preferred upland rice due to its ease of production. Farmers identified land preparation, inputs, planting, weeding and harvesting as the most expensive activities. The existing varieties were viewed as being highly dependent on inputs which they could not afford. The main fertilizers used were Diammonium Phosphate (DAP), Sulphate of Ammonia (SA), Calcium Ammonium Nitrate (CAN) and NPK (23:23:0), the amounts used were low even though the farmers were aware that soil fertility was low. No studies or attempts had been carried out to determine performance of rice genotypes and their heritability parameters for adaptation to low soil nitrogen (N) and phosphorous (P) conditions identified by the farmers as a major constraint in Kenya. Since the existing genetic base was narrow, accessions were acquired to broaden the variability of the local cultivars. However, their adaptation to local conditions was important for them to be useful. Evaluation of 390 accessions showed that genotypes and soil environments were highly significant for all the ten traits studied. The degree of genetic determination (H(2)) ranged from 8.0% for 1000 grain weight to 27% for top biomass. The phenotypic coefficient of variation of genotypes ranged from 12% for days to maturity to 149% for top biomass, while, that of days to maturity ranged from 14% to 160% for top biomass. The genetic advance (GA) had values ranging from, 0.2 for phosphorous tolerance to 1081 for grain yield, while the genetic advance expressed as percent of the mean was 6% for days to maturity and 88% for top biomass. The mean values for the ten characters studied had wide variability under the four soil environments with days to maturity ranging from 188 for genotype ARCCU1Fa1-L4P3-HB under both N and P application (N+P+) to 177 for genotype CT16333(1)-CA-1-M under none N and P application (N-P-) condition. The highest yielding genotype was CT16328-CA-18-M under none N and P application with 5916 kg ha(-1). The germplasm revealed usable variability under low soil N and P adaptation and thus warrant rice improvement for traits of interest to farmers. In order to establish the genetic factors controlling upland rice adaptation to contrasting soil N and P a study was conducted to determine genotypes with better performance under the prevailing farmers’ production environments. The GCA and SCA mean squares were significant and their interactions with environment were highly significant. The GCA:SCA ratios were mostly less than 1.0 for the majority of the traits under most of the soil N and P environments, indicating preponderance of nonadditive genetic effects. The maternal and nonmaternal mean squares were significantly different from zero (P<0.05) for most of the ten traits under study, indicating influence of cytoplasm effects and cytoplasm by nuclear gene interactions, respectively. The GCA effects for the parents were significant under different experimental environments but they had both positive and negative signs indicating different directions of influencing the trait of interest. The genotypes had both specific and broad adaptation as exhibited by their diverse rankings under different environments. The relationship between leaf and grain nitrogen (N) and phosphorous (P) with actual tolerance to low and high soil N and P conditions indicated significant genotypes, environments and genotypes by environment interactions. The analysis of genetic components gave highly significant GCA and SCA mean squares for the days to heading, anthesis and maturity, phosphorous and nitrogen tolerance, top biomass, plant height, number of panicles, 1000 seed weight and grain yield under the four soil experimental environments. The general combining ability (GCA) effects for parents were significant for both F(2) and F(3) segregants for the above ten traits and under the experimental conditions. The leaf and seed N and P contents gave significant genotype mean squares values for the three mega-environments. The GCA and SCA mean squares were significant for leaf and seed N and P for the three locations. The same case was observed for GCA effects for the parents, with all the nine parents showing significant values for leaf N and P for the three locations. The GCA:SCA mean square ratios were generally larger than 1.0 values for leaf N and grain P for the three locations. This clearly manifested the predominant role of additive gene action over the dominance effects and that improvement for tolerance to low soil N and P condition was practical. The fragrance in rice is an important quality traits and an experiment was conducted to establish the association of organoleptic test and the variations in SSR marker (RM223) among the parents. Plant leaves of the parental genotypes were sampled for DNA analysis using SSR markers RM223 and RM284. The RM223 was polymorphic while, RM284 gave monomorphic results. Four alleles were detected as follows: 146, 155, 161, and 163. The GCA:SCA ratio was 1.48 indicating that the fixable additive effects were greater than the nonadditive effects in inheritance of fragrance. Test for independence using Chi-square indicated that there was no association between organoleptic and variations in SSR markers. The performance of the aromatic lines was generally lower than that of non-aromatic lines for the agronomic traits. There was negative relationship between fragrant score and other agronomic traits such as grain yield across the three soil N and P regimes. The NERICA1 was found to be a good donor for aroma based on sensory testing and can be exploited in a breeding programme. Analysis on genetic components governing grain yield was investigated using Hayman’s analysis to generate various components of variation and to elucidate their potential, utilization, and provide a thorough understanding of their role in grain yield development and improvement. The additive gene action was significant for all cases of soil N and P environments and the two mega-environments. They were also far above the dominant gene effects, indicating the need to use mass selection in the early generations of segregating populations. The narrow sense heritability (h2(ns)) for upland rice grain yield was 21.52% and 4.22% under soil P and N conditions, respectively. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2010.

The majority of farmers in Tanzania have not yet adopted modern maize varieties and still cultivate landraces and open pollinated varieties (OPVs) with low production potential and susceptible to diseases like maize streak virus (MSV), grey leaf spot (GLS) and northern corn leaf blight (NLB). The NLB disease is among the major causes of low yield and has been reported in all 21 maize growing regions in Tanzania. Breeding for host plant resistance with high yielding potential and involving the community in the breeding process is expected to address the problem of low yield, NLB disease susceptibility and low rate of F1 hybrid adoption. Therefore, the study was conducted to obtain additional sources of resistance to NLB disease, high yielding cultivars with community acceptable traits adapted to Tanzanian conditions. The main objective was to contribute to increased maize productivity in the western zone of Tanzania. The specific objectives of this study were therefore to : 1) investigate maize production limiting factors for smallholder farmers in western Tanzania, 2) identify farmers and stockist perceptions, opinions and maize variety selection criteria in western Tanzania, 3) establish NLB disease status in farmers’ fields of western Tanzania, 4) determine the genetic relationships among landraces and assess maize landraces as sources of breeding materials, 5) determine the combining ability and heterosis for NLB disease resistance of eleven maize inbred lines adapted to Tanzanian conditions, and 6) determine the gene action and inheritance of resistance to NLB disease in five maize inbred lines adapted to Tanzanian conditions. The study was conducted from 2008-2011 in three diverse environments which represent all the maize growing regions in the country The participatory rural appraisal (PRA) was conducted in three districts to investigate farmers’ and stockists preferred traits for maize selection in western Tanzania, determine maize production constraints facing farmers and assess NLB disease prevalence in the same area. A focus group of 30 farmers was selected in each of the three villages. Transect walks, wealth ranking and historical profiles were used in an informal survey. One hundred and fifty questionnaires were used in a formal survey. The recorded yield was only 1 t haˉ¹. Thirteen major maize production constraints, 13 insect pests and vermin and, 11 diseases were recorded. The NLB disease was reported to be increasing in severity in all farmers’ fields. Farmers’ preferred traits included resistance to abiotic and biotic stresses, early maturity, preferred milling qualities, high storage qualities and high yielding potential. Stockists mentioned 12 preferred maize variety traits which included high yielding, disease and insect pest resistance, heavy grain, large cob size and large grain sizes. Similarity between farmers and stockist variety preference ranking were found to exist. The occurrence and distribution of northern leaf blight (NLB) disease study was conducted to assess the incidence and severity of NLB disease in farmers’ fields in seven districts. The study was conducted for two seasons. In each season, 175 fields with 5600 plants were sampled. There were sixteen varieties grown with wide NLB disease reaction variation. Gembe, a landrace, was among the three observed resistant varieties. The NLB disease has changed its distribution pattern affecting all districts of the western zone. The disease incidence in season two (2009/2010) significantly increased from season one (2008/2009) t= -3.25 (348), P= 0.001. About 30% of both means of blight incidence and severity were recorded in the area. Characterization and screening of maize landraces for northern leaf blight disease resistance was conducted to determine the genetic relationships among landraces, assess maize landraces as sources of NLB disease resistance and assess important agronomic traits for future maize improvement. Ninety breeding materials consisting of 71 landraces and 19 commercial varieties were evaluated. The average yield of landraces under research management was 2.3 t haˉ¹. Landrace TZA 3075 was identified as NLB disease resistant. Yield potential, dent grain texture, white endosperm and husk cover were important agronomic traits observed among landraces. There were high variations in terms of morphology and NLB disease resistance among the landraces. Five principal components contributed to 71.98 % of total variation. Clusters analysis revealed five distinct groups of landraces. Leaves/plant, infested leaves/plant, lesion number, lesion length, lesion width and NLB disease incidence traits highly contributed to variation and grouping of landraces. Combining ability analysis for northern leaf blight disease resistance was conducted to estimate the combining ability for NLB disease resistance of 11 maize inbred lines adapted to Tanzanian conditions, determine maternal effects which are involved in NLB disease resistance in maize germplasm, and determine the heterosis in the F1 hybrids. A full 11 x 11 diallel cross was performed. All top ten experimental hybrids in each of the three sites had negative midparent heterosis for NLB disease severity. The overall mid-parent heterosis means for yield across sites was 152%. The mean sum of squares for GCA was highly significant (P< 0.001) on disease severity indicating additive gene action effects. Mean sum of squares for SCA were highly significant for disease severity and yield implying non-additive gene action effects. The mean squares for reciprocal effects were highly significant on yield and non-maternal sum of squares had significant effect (P<0.05) on yield. The GCA contribution was high for disease severity (91%) and lesion number (85%). Almost, all GCA effects for NLB disease resistance were negative implying contribution to disease resistance. Due to preponderance of the additive gene action, recurrent selection could be used to improve the resistance of inbred lines while the non-additive gene action could be exploited in breeding for disease resistant hybrids. Generation mean analysis of northern leaf blight disease resistance was conducted to determine the mode of gene action involved in the inheritance of resistance to NLB disease in five inbred lines adapted to Tanzania at contrasting environments, estimate heterosis and heritability in five tropical inbred lines. Generation mean analysis was conducted using a six parameter model comprising P1, P2, F1, F2, BCP1 and BCP2 generation progenies. The mean sum of squares for environment, replication with the nested environment, generations, generations x environment interactions were highly significant (P<0.001). The full model of additive, dominance, additive x additive and additive x dominance epistatic effects was highly significant (P<0.001). Nonetheless, the additive gene effects were predominant ranging between 57% and 89% which was matched by large heritability (54%-85%). The average degree of dominance ranged between -0.52 and 0.88 supporting observations of partial dominance. The NLB disease severity showed a continuous distribution in all three sets for F2, BCP1 and BCP2 populations which is an indication of quantitative nature of inheritance and additive gene effects. The mid parent heterosis ranged from -19 to 1%. Therefore, resistance to NLB disease could be improved through selection by exploiting the additive gene effects. The epistatic gene effects would cause less complications because they were negligible (<25%). The client oriented breeding for maize northern leaf blight disease resistance was carried out to perform farmers and stockists assessment on the 110 F1 experimental maize hybrids and compare them with breeders selection criteria. Breeders selection criteria ranked 10 top high yielding experimental hybrids. Farmers developed 14 while stockists developed 13 selection criteria. The most preferred hybrids by farmers were VL 05616 x CML 159, CML 159 x KS03- 0B15-47 and EB04-0A01-304 x CML 442 while stockists preferred VL 05616 x CML 395, EB04-0A01-304 x CML 442 and VL 05616 x CML 159. Two F1 experimental hybrids EB04- 0A01-304 x CML 442 and CML 159 x CML 442 appeared in all top five ranked hybrids by breeders, farmers and stockists. Generally, findings showed that, farmers, stockists and breeders coincide in some selection criteria but also differ in other cases. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

Soybean (Glycine max (L.) Merr.) occupies an important position in the world economy of the feedstock of high quality protein and vegetable oils. However, its production is threatened by, Asian soybean rust (ASR), caused by the rust fungus Phakopsora pachyrhizi Syd. & P. Syd. This fungus is highly dependent on environmental conditions, has a wide range of hosts, and evolves rapidly into novel races, making it difficult to control. In addition, most commercial varieties are susceptible to rust, the rust has already developed resistance to triazole fungicides, and most small-scale farmers cannot afford expensive systemic fungicides to control the disease. The use of resistant varieties is the most viable, long-term option to manage ASR, especially in the small-holder soybean farming sector. This study was therefore designed to undertake the following goals: (i) to identify farmers’ preferred varieties and desired traits, their knowledge of ASR, and other key constraints affecting soybean production in Kenya; (ii) to evaluate soybean accessions for rust resistance, and to determine the correlation of rust resistance with other agronomic traits; (iii) to determine the mode of inheritance for ASR resistance and selected agronomic traits; and (iv) to determine yield stability of soybean advanced lines at multiple sites in Central and Eastern Kenya. To understand farmers’ preferred varietal characteristics, knowledge of ASR and other key constraints to soybean production, a survey was conducted using a structured questionnaire in the major soybean growing areas of Kenya. The farmers preferred local varieties because of their desirable characteristics, which included high yields, early maturity, drought tolerance and seed availability. Although the majority of the participating farmers expressed a willingness to grow improved varieties, financial limitations, seed unavailability and lack of information were the major barriers to their use of improved varieties. High yield, early maturity, adaptability and grain quality were the traits that most farmers sought in an ideal soybean variety. Knowledge of the cause of ASR was limited, and its occurrence was largely attributed to environmental factors, poor soil fertility conditions, poor agronomic practices, physiological maturity and specific species of weeds. Their investments in control methods were minimal due to a lack of technical knowledge, poor access to fungicides, and limited resources. Other constraints faced by soybean farmers included: lack of access to grain markets; lack of knowledge in processing and utilization of soybean grain; the unavailability of seeds; losses to pests and diseases; the lack of inputs such as fertilizers; frequent dry spells; and low yielding varieties. A total of 110 soybean accessions were evaluated for their rust reactions and correlations with selected agronomic traits. These included plant introductions possessing single rust resistant genes (Rpp1-4), tolerant lines, gene bank accessions, commercial varieties and advanced lines. Soybean genotypes varied significantly in their reactions to rust severity, sporulation, lesion type and area under disease progress curve (AUDPC) values. Genotypes possessing Rpp4 (G10428) and Rpp2 (G8586) resistant genes, and non-characterized genotypes MAK BLD 11.3, GC 00138-29 and Namsoy 4M, were the most resistant accessions, as indicated by low rust severity scores, low AUDPC values, red brown lesions and low sporulation scores. Other genotypes with known resistant genes including G7955 (Rpp3), G58 and Tainung 4 (Rpp1), a few tolerant lines, and one advanced line (BRS Sambaiba) were moderately resistant. All the other advanced lines, commercial varieties, gene bank accessions and collections from the farmers’ fields were highly susceptible to rust. Rust severity was positively correlated with rust sporulation, indicating that reduction of sporulation made a significant contribution towards rust resistance. An F2 population was generated from a half diallel mating design, involving 4 resistant, 2 moderately resistant and 2 susceptible genotypes selected as parents. The F2 populations along with their parents were evaluated in two environments to determine the type of gene action for rust resistance and other quantitative traits in soybeans. The results revealed that both general combining ability (GCA) and specific combining ability (SCA) were significant for most of the traits studied, indicating that both additive gene action and non-additive gene action played a major role in the inheritance of rust resistance and selected agronomic traits. The GCA/SCA ratio was close to unity for rust severity, rust sporulation, days to flowering, days to maturity and plant height. This indicated that additive gene action played a more significant role in the inheritance of these traits than non-additive gene action. Non-additive gene action was only predominant for soybean grain yield. Parental lines G10428, G8586 and Namsoy 4M were the best general combiners for improving rust resistance across the environments. The most promising parents for early flowering were G7955, G8586 and G58. Parent Maksoy 1N was the best general combiner for early maturity while parents Maksoy 1N, G58, G7955 and Nyala contributed effectively towards reduced plant height. Yield stability analysis was conducted for 30 genotypes in 6 environments, using additive main effects and multiplicative interaction (AMMI), genotype main effect and genotype x environment interaction (GGE) biplot analyses. Genotypes 916/5/19 and G7955 were identified as the high yielding and most stable across the environments. On the other hand, genotypes BRS MG46 and Sable were high yielding but unstable and specifically suitable for the environments EM2 and MW2, respectively (both environments have long rainy seasons). Environment EM2 was identified as the most discriminating and representative among the six environments. Environments IG1 and MW1 (short rainy seasons) were less informative on genotypes tested, as confirmed by short environment vectors. Environment EM1 was better for discriminating genotypes but was a poor representative of the test environments, hence it should only be utilized for developing specifically adapted genotypes. Further analysis using GGE biplot approach grouped the environments into three putative mega-environments in Central and Eastern Kenya. Overall, this study established the need to educate farmers on the cause of ASR, to develop ASR resistant varieties, and to incorporate farmers’ desired traits in the breeding programme, especially by the use of participatory breeding approaches. The resistant and moderately resistant genotypes identified in this study could be used as sources of resistant genes to develop ASR resistant varieties in Kenya. This study also established that genetic improvement for ASR resistance and selected agronomic traits in soybeans is possible based on the use of recurrent selection breeding procedures that result in the accumulation of additive gene effects. Selection of late segregating generations would be effective for soybean grain yield improvement. This study identified potential parents for ASR resistance and selected agronomic traits, but they require further breeding to improve on farmers’ desired traits. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

Fusarium root rot (FRR) disease, caused by the fungus Fusarium solani f. sp. phaseoli (FSP), is an important soil-borne disease reducing common bean (Phaseolus vulgaris L.) yields, and hence food security, in Uganda and elsewhere in developing countries where the crop is grown without fungicides. The key aim of this study was to elucidate the significance of bean root rot (BRR), appraise methods for screening germplasm for resistance to FRR, determine the genotypic variability of resistance, and the inheritance of resistance to FRR in common bean. This information was deemed useful in devising an appropriate strategy for breeding FRR resistance in beans. A participatory rural appraisal (PRA) was conducted in south-western and eastern Uganda to ascertain farmers’ awareness of BRR and their influence on preferred bean varieties. Bean root rot is considered to be the most devastating and most recognised disease, especially in south-western Uganda. Control measures for BRR were very minimal, and in some cases, non-existent. Use of resistant varieties to control the disease was not evident, because the most popular varieties were susceptible to the disease. The resistant bean varieties currently available have undesirable characteristics such as small seed size, black seed and late maturity. Large-seeded bean varieties, even though cited as being more susceptible to BRR than the small-seeded varieties, are still very popular. The study highlighted the need for breeding FRR resistance in the large-seeded bean varieties that are highly preferred by farmers. Four isolates of FSP (FSP-1, FSP-2, FSP-3 and FSP-4) were tested for pathogenicity under screenhouse and laboratory conditions. In addition, three methods of storing and maintaining the viability of FSP isolates were appraised. The isolate FSP-3, was found to be the most pathogenic, resulting in 100% disease incidence on all bean varieties tested, with high severity scores. The potato dextrose agar (PDA) slants stored at 5oC were found to be the best method of storage for pathogenic isolates. The FSP-3 isolate was subsequently utilised for screening bean lines for resistance to FRR. The influence of soil composition, irrigation frequency, and inoculation technique on the severity of FRR was studied on six bean lines. Interactions of irrigation frequency, soil composition, and bean lines were not significant. The 50% swamp soil:50% forest soil composition and forest soil alone categorized the varieties most distinctly according to their reaction to FRR. Also, the best distinct classification for the varieties was obtained under treatments that were watered daily and once in a week. Based on economic considerations, the standard forest soil and daily irrigation were subsequently adopted for screening bean germplasm for resistance to FRR. It was also found that sorghum seed as a medium for pathogen inoculation was better than the agar slurry medium. One hundred and forty seven common bean varieties were evaluated for resistance to FRR (isolate FSP-3) under screenhouse conditions. In order to confirm this resistance, 46 common bean lines selected from the screenhouse trial were further evaluated using natural inoculum in a BRR-infested field. Forty-four varieties comprising ten large-seeded, four medium-seeded and 30 small-seeded varieties showed moderate resistance to FRR; but none were resistant or immune to the disease. Based on adaptability, eight moderately resistant varieties were selected for use as parents in the study of inheritance of resistance to FRR. A 12 x 12 diallel mating design was utilised to develop 66 F1 and F2 populations, plus their reciprocal crosses, with the aim of studying the mode of inheritance of resistance to FRR. The F1 and F2 progeny evaluations showed that FRR resistance was mainly governed by additive genes in most populations. However, there were a few crosses which displayed highly significant specific combining ability (SCA) effects, implying that dominant effects were important in some populations. Maternal effects were also highly significant at both the F1 and F2 generations, suggesting that resistance was modified by cytoplasmic genes. The non-maternal effects were also significant in some populations, suggesting that the cytoplasmic genes were interacting with nuclear genes. The number of genes governing resistance to FRR varied from two to nine among the eight sources of resistance. The allelism test of resistant x resistant populations, and the observation of continuous distributions of severity scores, suggested the presence of many loci governing FRR resistance in beans. Broad sense heritability of disease resistance varied from 0.22-0.69, while heritability in the narrow sense was estimated as 0.35-0.49 in the populations. These results suggested that selection and backcrossing to both parents would be the best breeding procedures for improving resistance in the popular large-seeded bean varieties in Uganda. However, there could be complications in breeding for resistance to FRR in beans, because resistance was modified by cytoplasmic gene effects and their interaction with nuclear genes in some of the populations. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2008.

Abstract not available. / Thesis (Ph.D)-University of KwaZulu-Natal, Pietermaritzburg, 2008.