Bambara groundnut (Vigna subterranea [L.] Verdc.) is an under-utilized indigenous African legume crop which has substantial potential to contribute to food security in sub-Saharan Africa. The crop is well adapted to severe agro-ecologies and grows where other legumes may not survive. The seed is highly nutritious with an ideal balance of carbohydrate (55-72%), protein (18-20%) and fats (6-7% oil), which is particularly beneficial in balancing protein deficiencies in cereals. Also, the seed contains essential and non-essential amino acids of about 33% and 66%, respectively. These attributes make Bambara groundnut an ideal crop to alleviate food insecurity, and to reduce protein malnutrition in rural communities of Africa. However, small-scale farmers grow low-yielding landraces in most production regions in sub-Saharan Africa. Bambara groundnut landraces exist as heterogeneous mixtures of seeds of a few to several seed morpho-types that embrace wide genetic potential for breeding. The objectives of this study were: 1) to determine the production status and constraints associated with Bambara groundnut production in Kano State of Nigeria through the use of a participatory rural appraisal (PRA); 2) to determine the genetic diversity of Bambara groundnut landraces through seed morphology; 3) to assess the inter- and intra-genetic diversity of the Bambara groundnut landraces; 4) to determine the yield and yield component responses among selected Bambara groundnut genotypes, 5) to determine the genomic diversity in Bambara groundnut landraces, using simple sequence repeat (SSR) markers; and 6) to develop a crossing protocol. Using a structured questionnaire, 150 Bambara groundnut farmers were interviewed. The respondents interviewed were male and aged between 36 to 50 years, while Qur’anic education was the most popular among them. Most of the farmers practiced a combination of sole and mixed cropping, and allocated between 0.38 to 1.68 hectares of land to Bambara groundnut growing. They selected Bambara groundnut landraces, especially looking for large seeds that were pure and oval in shape, with a cream seed coat colour and which were early maturing. A total of 27 diverse landraces bearing different names were identified in the hands of the farmers. Most popular among them were Gurjiya, Kurasa, Hawayen-Zaki, Fara Mai-Bargo and Silva. Production was largely for home consumption and for sale on local markets. Common production constraints of the crop were identified as a lack of improved varieties (70.7%), frequent droughts (9.3%), low yield (4%) and limited access to large markets (3.3%). Diverse collections of Bambara groundnut landraces from seven geographic origins were characterized using seed morphology, including seed coat, seed eye colour and pattern, and hilum colour and pattern. Out of 58 original seedlots, a total of 353 different seed morpho-types were further identified. The selected morpho-types- can be used for large-scale production or true-to-type lines could be used in genetic improvement of the crop. Genetic variability within- and between-landraces was investigated among 262 Bambara groundnut landraces, forty nine were studied for agronomic traits, and 213 were investigated for pod and seed variability. Most (47.9%) of the landraces developed pods with a point on one pole, and a round end on the other. Most had a creamy (37.1%) and yellow (76.1%) pod colour, and the pods were usually rough textured, and contained an oval seed. A further 158 landraces were evaluated for leaf morphology where 49.4% had round leaves, while 21.5% had elliptic leaves, with 55.7% of the landraces being heterogeneous, possessing more than one form of leaf shapes. These discrete characters can be utilized for genetic studies and improvement of Bambara groundnut. Single plant selections of 49 Bambara groundnut genotypes were evaluated for yield and yield components using 26 yield and yield related traits. Highly significant variations (P<0.001) were detected among the genotypes for canopy spread, petiole length, weight of biomass, seed weight and seed height. Principal component analysis (PCA) identified nine useful components, where two components, PC1 and PC2, contributed strongly to the total variation, at 19% and 14%, respectively. The PCA revealed that leaf colour at emergence, petiole colour, leaf joint pigmentation and calyx colour were highly correlated with PC1, while seed length, seed width and seed height had strong association with PC2. Both the principal component and cluster analyses showed that most genotypes associated with one another with respect to agronomic and seed yield traits, irrespective of geographical location. The genotypes 211-57, MO9-4 and TV-27 displayed high seed yield performances, while TV-93 and 45-2 had higher biomass production. These genotypes can be used as breeding lines to enhance productivity of Bambara groundnut. Fifty Bambara groundnut genotypes, representing seven geographical regions across Africa, were genotyped using five pre-selected polymorphic simple sequence repeat (SSR) markers developed specifically for Bambara groundnut. The results detected a total of 53 alleles among the 50 Bambara groundnut genotypes, while the neighbor-joining analysis generated seven major genetic groups, which were clustered regardless of their geographic origin. Close relationship were found between 211-68 on one hand and 211-83-2, N211K and M09-3 with 211-68 on the other. Genotypes M02-3, 211-55-1 and 211-57 displayed close similarities. These associations suggested the likelihood that the two pair groups had common origins or may possess similar genes. A preliminary protocol was developed for crossing Bambara groundnut using eight selected parents, using the diallel mating system. Emasculation and crossing of Bambara groundnut was effective when conducted on the same day, with the two procedures being carried out sequentially between 4:30 am and 9:00 am. This protocol generated a number of F1 seeds, with the most success being from crosses between 211-40-1 x N211-2, N212-8 x 211-40-1 and M09-3 x 211-82-1. These F1 seeds can be advanced to confirm whether they are true F1 or selfs. The most important production constraint of Bambara groundnut production is the lack of improved varieties, suggesting that further breeding is needed to enhance productivity. Bambara groundnut landraces need to be sorted using discrete morphological features before breeding for genetic enhancement. The SSR markers used in the study demonstrated their ability to distinguish the existing diversity among the Bambara groundnut genotypes, which could be useful for both germplasm conservation and for breeding. Genotypes that displayed outstanding performance in seed yield and biomass can be used as breeding lines for the genetic improvement of Bambara groundnut. Overall, the study generated valuable and novel Bambara groundnut genetic material, useful in the development of improved cultivars for large-scale production in sub-Saharan Africa. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2014.

The maize weevil (Sitophilus zeamais Motschulsky) is one of the most destructive storage insect pest of maize (Zea mays L.) in tropical Africa and worldwide, especially when susceptible varieties are grown. Therefore, grain resistance against the maize weevil should be part of a major component of an integrated maize weevil management strategy. The specific objectives of this study were to: i) determine farmers’ perceptions about weevil resistance in maize cultivars; ii) determine the genotypic variation for maize weevil resistance in eastern and southern Africa maize germplasm lines; iii) study the gene action conditioning weevil resistance in the inbred line populations from eastern and southern Africa maize germplasm and to measure their combining ability for yield and weevil resistance; iv) determine the effectiveness of two cycles of modified S1 recurrent selection in improving a tropical maize population “Longe5” for weevil resistance and agronomic superiority and v) evaluate the effectiveness of the “weevil warehouse techniques” compared to the “laboratory bioassay technique” as methods of maize screening against the maize weevil. A participatory rural appraisal (PRA) was conducted in three districts between December 2010 and January 2011, to gather information on the maize weevil pest status in Uganda and farmers’ perceptions about improved maize varieties and the major attributes desired in new maize varieties. Over 95% of farmers knew the maize weevil and its pest status, and were reportedly controlling the maize weevil using wood ashes, red pepper and Cupressus sempervirens. The estimated postharvest weight losses attributed to weevil damage was over 20% within a storage period of four months. The most highly ranked attributes desired in the new maize varieties included high grain yield, tolerance to drought and low nitrogen stresses, resistance to field pests and diseases, good storability and resistance to storage pests. In the search for new sources of weevil resistance, a total of 180 inbred lines from three different geographical areas were screened for weevil resistance using the laboratory bioassay technique. Eight inbred lines (MV21, MV23, MV75, MV102, MV142, MV154, MV157, and MV170) were consistently grouped in the resistant class, and therefore selected as potential donors for weevil resistance in the maize improvement programs. Large significant genetic variations for weevil resistance, and high levels of heritability (89 – 96%) were observed. The results revealed that there was no significant association between maize weevil resistance andgrain yield; suggesting that breeding for maize weevil resistance can be achieved without compromising grain yield. Eight weevil resistant and two susceptible inbred line parents were crossed in a 10 x 10 full diallel mating design and the resulting 45 experimental hybrids and their reciprocal crosses evaluated for grain yield and secondary traits under four environments, and also to determine the gene action regulating their expression. The F1 hybrid seed, F2 full-sib and F2 half-sib grain generated from the 45 experimental hybrids and their reciprocals under two environments in Namulonge, were evaluated for weevil resistance using F1 weevil progeny emergence, median development period (MDP), Dobie’s index of susceptibility (DIS), and parental weevil mortality as susceptibility parameters. The general combing ability (GCA), specific combining ability (SCA), and reciprocal effects were all significant for grain yield, with SCA accounting for over 80% of the hybrid sum of squares. Inbred line parent MV44 exhibited positive significant GCA for grain yield and thus can be utilized in the development of synthetics and hybrids. Hybrids MV21 x MV13, MV154 x MV44, and MV154 x MV102 and all hybrids between parent MV142 and the rest of the parental lines exhibited positive and significant SCA effects. For the weevil resistance parameters, the general combining ability (GCA), specific combining ability (SCA) and reciprocal effects were all significant for F1 weevil progeny emergence, MDP, and DIS in the three seed categories. The results revealed that weevil resistance was governed by additive gene action, non-additive, and maternal effects. Parents MV170 and MV142 were consistently exhibiting weevil resistance in the three seed categories and thus recommended for future breeding strategies. Furthermore, most of the hybrids generated from parental line M142 were noted to exhibit outstanding performance in terms of grain yield and weevil resistance. Another study was conducted to determine the effectiveness of two cycles of modified S1 recurrent selection towards the improvement of weevil resistance in a maize population Longe5. Over 540 selfed ears were selected from the source population (C0) and screened for weevil resistance in the laboratory at Namulonge. Based on weevil resistance characteristics, 162 genotypes were selected from C0 and recombined in an isolated field to generate cycle C1. The same procedure was used for generating cycle C2 from cycle C1, but instead 190 weevil resistant C1 genotypes were selected and recombined to form C2. Seed from cycles C1 and C2, together with that from the source population (C0), was used to plant an evaluation trial in three locations, to compare the performance of the three cycles in terms of grain yield and reaction to the major foliar diseases, and also to produce seed for subsequent screening against weevil ii infestation. A total of 54 seed samples were screened for weevil resistance in a laboratory at Namulonge, in an experiment laid out in a randomized complete block design. A reduction in grain weight loss of 65% was registered in the C2 seed, whereas in C1 seed it was 15%. A similar trend was observed for F1 weevil progeny emergence and grain damage. Grain yield results indicated a yield gain of 19% realized from cycle C2 while a yield gain of 7% was realized from cycle C1. Furthermore, reductions in disease severity of 27%, 10% and 13% were exhibited for Turcicum leaf blight (TLB), grey leaf spot (GLS) and rust disease, respectively in cycle C2. The results indicated that Longe5 can be improved for maize weevil resistance, grain yield, and resistance to foliar diseases through selection. Further recurrent selection cycles would be recommended. The last study was aimed at evaluating the potential of shelled grain and suspended ear options of the weevil warehouse technique in discriminating maize genotypes into different susceptibility classes, based on genotype response to weevil attack. It involved comparing the effectiveness of the two options under the weevil warehouse technique with the laboratory bioassay technique using grain damage and grain weight loss as the maize grain susceptibility parameters. Fourteen maize genotypes were screened using the weevil warehouse and the laboratory bioassay techniques at Namulonge. On grouping the 14 genotypes into different response classes, high levels of consistency were observed in the three screening techniques. Therefore, the two weevil warehouse screening options being faster and effective in discriminating maize cultivars towards weevil attack, they were found to be better than the laboratory bioassay technique. The minimum evaluation period required to discriminate genotypes by the two weevil warehouse options was two months from the onset of the experiment. The maize weevil was noted to be an important storage pest constraining maize production in Uganda. The major weevil control measures included proper postharvest handling procedures and use of indigenous technical knowledge. The results also revealed that host plant resistance could significantly reduce grain damage. It was further revealed that grain resistance against the maize weevil could be enhanced through hybridization and recurrent selection; thus the germplasm identified in the study can provide new sources of maize weevil resistance for commercial deployment and further breeding. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

Sorghum [Sorghum bicolor (L.) Moench] is a major food security crop for millions of people in sub-Saharan Africa and the fourth most important crop in Africa. The potential sorghum yields are limited due to a number of abiotic, biotic and socio-economic constraints. Among the biotic stresses is the parasitic weed, Striga hermonthica, which inflicts yield losses ranging from 30-100%. Various control options have been recommended to reduce levels of Striga damage. However, these techniques need to be integrated for effective control and to boost sorghum productivity. A series of experiments was conducted to integrate host resistance improvement and the use of a biological control agent, Fusarium oxysporum f.sp. strigae to control Striga hermonthica. These studies were also focused on improving breeders‟ awareness of the traits that farmers‟ desire, on the assumption that farmers‟ variety preference traits are the missing link in technology development and adoption process for S. hermonthica management. The objectives of the study were to: 1) determine farmers‟ views on sorghum production opportunities; threats; indigenous knowledge and perceptions; breeding priorities; Striga infestation; and the coping mechanisms of farmers in the north eastern and north western Ethiopia, 2) evaluate sorghum genotypes for compatibility to F. oxysporum inoculation where grown in Striga infested soil in controlled environments, 3) determine field responses of sorghum genotypes and F. oxysporum compatibility for integrated Striga management (ISM), 4) determine the variability present among selected sorghum genotypes exhibiting S. hermonthica resistance, and compatibility with the biological control agent using phenotypic and simple sequence repeat (SSR) markers, 5) identify F. oxysporum compatible sorghum parents and hybrids with high combining ability for grain yield, yield components, and Striga resistance for ISM, and 6) undertake farmers‟ participatory assessment, and identify their preferred traits for sorghum genotypes under ISM, simultaneously with the breeders‟ evaluation. A participatory rural appraisal (PRA) research was conducted involving 315 farmers in nine districts of three administrative zones within two provinces in Ethiopia. Sorghum landraces were preferred by >85% of participants rather than previously improved released varieties. The participating farmers listed and prioritized their sorghum production constraints. In the North Shewa and North Wello zones drought was the most important constraint, followed by Striga. In the Metekel zone Striga was the number one constraint followed by a lack of genotypes with high grain quality. Controlled environment experiments were conducted involving greenhouse and laboratory tests in order to evaluate 50 sorghum genotypes for their compatibility with F. oxysporum and for possible deployment of the bio-control agent to control Striga. Striga population was reduced by 92% through the application of F. oxysporum, resulting in yield increment of 144%. Twelve sorghum genotypes were identified as promising parents for breeding and to control Striga through integration of host resistance and F. oxysporum seed treatment. During field and sick plot plot evaluations differential responses to F. oxysporum application among the sorghum genotypes were observed for various attributes including Striga plant height. Most traits showed highly significant (p<0.001) genotype X site interactions. Similarly, the main effects of F.oxysporum application were highly significant (p<0.001) across sites for most of the traits. The genotype and genotype X environment biplot identified 13 genotypes that consistently performed well following Fusarium application. The variability present among 14 selected sorghum genotypes exhibiting S. hermonthica resistance, and compatibility with a biological control agent, Fusarium oxysporum, were determined using phenotypic and 20 polymorphic simple sequence repeat (SSR) markers. Highly significant (p<0.001) differences were detected among genotypes for phenotypic traits. Principal component analysis showed three components that accounted for 73.99% of the total variability exhibited among genotypes. Cluster analysis allocated the genotypes into two major groups, one with a further two subgroups based on morphological traits, showing clear demarcations between the genotypes. The SSR markers revealed high levels of polymorphisms among genotypes, with the mean number of alleles per locus being 6.95 and the mean polymorphic information content being 0.80. The observed genetic diversity was relatively wide, with the allele sizes ranging from 203.6-334 bp. The SSR markers allocated genotypes into two distinct clusters close to the phenotypic markers. Forty sorghum hybrids were developed through a line by tester mating design involving 10 lines selected for their compatibility with F. oxysporum and high agronomic performances and four Striga resistant tester parents. The F1s and their parents were field evaluated with complementary in-vitro tests. Field evaluations were conducted at two locations: Kobo and Shewa Robit in Ethiopia, which are well known for their severe Striga infestation. Significant (p<0.05) general combining ability (GCA) effects were observed among testers and lines at both sites for days to 50% flowering and maturity, plant height, biomass, number of Striga plants and Striga plant height. Furthermore, significant (p<0.05) specific combining ability (SCA) effects were detected for days to 50% flowering, biomass, grain yield and number of Striga plants. From the complementary in-vitro experiment, highly significant variation (p<0.01) was exhibited due to line x tester interaction for maximum Striga germination distance. The study identified paternal parents with high GCA effects including SRN-39 and Birhan and maternals 235761, 2384443, IC9830, 235466, 237289,235763, and 235929 to be useful for breeding for ISM in sorghum. At Kobo, cross 235763 x N-13 and Shewa Robit IC9830 x SRN-39 had significantly negative SCA effects for the numbers of Striga plants. Progenies of these crosses will be selected in the Striga resistance breeding program. In the participatory sorghum genotypes assessment, farmers were invited to assess and select the genotypes based on their preferences at maturity and harvesting. The standard agronomic traits and Striga parameters relevant for breeding were collected by the breeders. Earliness, Striga resistance, high yield and high grain quality and threshability were the most important farmers‟-preferred traits for sorghum genotypes. Comparative analyses between farmers‟ and breeders‟ evaluations revealed highly significant correlations (p<0.01) except between Striga resistance and Striga damage and pest resistance and insect damage. Repeatability of scoring genotypes among farmers was consistent (>0.80) for all traits except Striga and pest resistance. The prioritized traits through farmers‟ participation are important for further breeding program. Overall, the study established farmers‟ preferred traits, the effectiveness of ISM to boost sorghum productivity, and identified useful parents and crosses for effective sorghum breeding to control Striga in Ethiopia. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

Finger millet is the second most important cereal in Uganda after maize. The yields however, have remained low due to several constraints, such as finger millet blast disease and limited technology options. Therefore breeding investigations were conducted to determine farmer preferred traits, genetic variation, combining ability and genetic effects for head blast disease and head shapes, and other quantitative traits in finger millet. Among other traits, farmers preferred high grain yield potential, brown seed colour, compact head shape, tolerance to blast disease, high tillering ability, medium plant height, early maturity, tolerance to shattering and ease of threshing in new finger millet varieties. Path coefficient analysis indicated that the most important traits were grain mass head-1, tillering ability and reaction to head blast disease. Overall, the high heritabilities and genetic advance (GA) as a percentage of mean revealed the existence of variability which can be utilised through selection and/or hybridisation. The genotype x environment interaction (GEI) and stability analysis showed significant differences due to genotypes (58%), environments (10%) and GEI (32%). Twelve genotypes that combined high yield potential and stability were identified for advancement in the program. Both general (GCA) and specific combining ability (SCA) were significant for most traits, but GCA effects were more important for all the traits except for number of fingers head-1, finger width and panicle width. The Hayman genetic analysis confirmed importance of additive gene action for most of the traits and that additive-dominance model was adequate for explaining genetic variation in finger millet. The results also indicated that yield was controlled by recessive genes whereas blast resistance was controlled by dominant genes. At least two genes, probably three gene pairs and their interactions seemed to control head shape in finger millet. The interactions observed suggest recessive and dominant epistasis, and probably an inhibitor were involved. Seemingly, the gene for curving of fingers, when present in a dominant form prohibits opening of the heads; whereas the recessive form leads to open head shape irrespective of the gene conditions in the other loci. This study forms the baseline for future investigations and the basis for devising breeding strategy on finger millet head shapes. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

Cassava (Manihot esculenta Crantz), is the world’s most widely grown starch storage root crop. It is a principal food staple in sub-Saharan Africa where it accounts for approximately one-third of the total production of staple food crops. It plays a key role as a food security and an income-generating crop for millions of smallholder farmers. In Uganda, cassava ranks second to bananas (Musa spp.) in terms of area occupied, total production and per capita consumption; however, nearly 5% of the total population experiences hunger with the prevalence of food energy deficiency at the country level standing at 48%. Cassava is a crop with high potential to alleviate food shortages and energy deficiencies, owing to its unique advantages of producing acceptable yields and starch on infertile soils amidst erratic rainfall, when most other crops would fail. Hoewever, its yield potential has not been fully realised since most of the cassava cultivars grown are susceptible to pests and diseases, low yielding and late bulking. The main objective of the research was to develop high yielding, early bulking cassava genotypes that combine resistance to cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) with farmer preferred traits for cultivation in Uganda. The specific objectives were to: (i) evaluate farmers’ attitudes to and/or perceptions of cassava early bulking, production constraints and cultivar preferences; (ii) determine the extent of genetic variability in storage root bulking and other important traits of selected cassava genotypes; (iii) assess the effects of genotype x environment interaction on early bulking and related traits of selected cassava genotypes; (iv) develop and evaluate cassava F1 families for early bulking in terms of the attainment of early, high fresh storage root yield (FSRY) and resistance to CBSD and CMD; and (v) determine the combining ability and gene action controlling early bulking and yield-related traits, as well as resistance to CBSD and CMD. Through the farmer participatory survey, a number of cassava production constraints were identified, key of which were: diseases, especially CBSD and CMD; lack of early bulking cultivars; rodents and insect pests. Farmers rated early bulking as the second most important preferred trait after FSRY, but suggested that early bulking should be complemented with high dry mass content (DMC), sweetness, high FSRY and resistance to pests and diseases. The analysis of variance of 12 cassava genotypes selected for evaluation in three diverse locations and at five different harvest times indicated significant variation among genotypes, harvest times, locations and their interactions for FSRY and most of the other traits evaluated. Fresh storage root yield and the other traits evaluated were predominantly under the control of genetic variation, indicating that genetic advance would be achieved through hybridisation of the test genotypes. Additive main effects and multiplicative interaction (AMMI) analysis of the data collected at nine months after planting (MAP) indicated a non-significant GEI for early FSRY, but significant GEI for other traits assessed. Eight of the 12 genotypes analysed had relatively low interaction with locations for early FSRY, signifying that these genotypes were relatively stable for early FSRY. Thirty-six F1 families were generated from a 9 x 9 diallel and exhibited a high degree of variation between and within families for all the traits assessed at the seedling evaluation stage. Diallel analysis at the seedling evaluation stage at 10 MAP indicated that additive gene effects were predominant in the expression of early FSRY and most of the other traits analysed. At the clonal evaluation stage, the 36 families were assessed for early FSRY at 8 MAP and this trait together with most of the other traits assessed were found to be predominantly under the control of non-additive gene effects. High mid- and better-parent heterosis for early FSRY was recorded in most families at the clonal evaluation stage with NASE3 x Nyara, Nyara x B11 and NASE3 x B11 recording the highest. Selection from the 36 families at the clonal evaluation stage based on farmers’ top two preferred traits, viz. early bulking for FSRY and DMC, plus resistance to CBSD and CMD identified 50 genotypes that had early FSRY of ≥25 t ha-1 at 8 MAP compared to the best parent, CT1 that had 15.9 t ha-1 at 8 MAP. The selected genotypes also had high DMC and dual resistance to CMD and CBSD. Advancement of the selected genotypes should go a long way towards increasing cassava yield per unit time, reducing food shortages and increasing the income of smallholder farmers in Uganda. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

The soybean programme in Zimbabwe is over seventy years old. However, there is lack of information on breeding gains, genetic diversity, heritability, genetic advance, combining ability, gene action and relationships between grain yield and secondary traits available for breeding. Therefore, the aim of the present study was to characterise the genetic diversity of the available germplasm, determine gene action conditioning grain yield and estimate the breeding gains that have been realised since the inception of the breeding programme. Evaluation of 42 soybean genotypes for genetic diversity conducted during 2010/11 and 2011/12 cropping seasons, using phenotypic and molecular characterisation approaches, revealed evidence of wide diversity among the genotypes. The phenotypic traits and SSR markers assigned the soybean genotypes to 8 and 15 clusters respectively. The SSR marker technique was more polymorphic, informative and highly discriminatory. The clustering pattern and relatedness from SSR data was in agreement with the pedigree data while the phenotypic clustering was divorced from pedigree data. Genotypes, G41 and G7; G41 and G1; G41 and G42 were the most divergent; therefore, they could be utilized as source germplasm in cultivar development and commercial cultivars. Investigations on breeding gains involving 42 cultivars (representing a collection of all the varieties that were released in Zimbabwe from 1940 to 2013) showed that improvement in grain yield was slowing down. However, annual genetic gain was estimated to be 47 kg ha-1 year-1 representing an annual gain of 1.67%. Furthermore, grain yield ranged from 2785 to 5020 kg ha-1. Genotypes, G16, G15, G17, G1 and G42 exhibited superior performance in grain yield and other agronomic traits and are therefore, recommended for utilisation in the hybridisation programme. Seed protein concentration decreased by 0.02 year-1 while oil increased by 0.02, 100 seed weight increased by 0.21 g year-1 over time. In addition, number of days to 95% pod maturity and pod shattering increased by 0.35 and 0.38 days year-1 respectively while lodging declined by 0.31%. Results indicated that emphasis should be refocused on grain yield to restore the original linear increase. Assessment of the magnitude of GEI and stability of 42 released cultivars was done over 13 environments and two seasons using additive main effects and multiplicative interaction, cultivar superiority and rank analyses. Results showed that environment and GEI captured larger portion of the total sum of squares, which reveals the influence of the two factors on grain yield, hence, the need for evaluating soybean genotypes in multi-environment trials and over years. Further, the data revealed that GEI was of a crossover type because of differential yield ranking of genotypes. The three stability parameters selected two genotypes, G1 and G15, as the most productive, consistent and stable, thus they could be produced in diverse environments while G2, G4, G5, G7, G16, G40, G17, G18 and G31 were identified as unstable and suitable for specific adaptation. Correlation and path analyses showed that grain yield was positively and significantly correlated with number of branches per plant, number of nodes per plant, shelling percentage, and number of days from 95% pod maturity to first pod shattering, implying that breeding and selection for these traits probably improved grain yield. Number of nodes per plant, plant height and 100 seed weight exhibited highest direct effects on grain yield while, number of nodes per plant and plant height presented the highest indirect effects on grain yield. These results demonstrated that number of nodes per plant and plant height could be recommended as reliable selection traits for developing high yielding genotypes of soybean. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

Maize (Zea mays L.) supports millions of livelihoods in sub-Saharan Africa (SSA) in terms of food and feed. Production of the crop is however limited by several factors, among these, maize streak virus (MSV) disease. Although extensively studied, MSV remains a serious problem in SSA due to several challenges in breeding MSV resistant maize varieties. These include integration of MSV resistant germplasm from different backgrounds, reliance on a few resistant sources, and genotype x environment interactions. This study was designed to assess the breeding potential of several MSV resistant lines in hybrid combinations. Understanding architecture of genetic divergence and background of these genotypes would greatly aid in breeding high yielding and stable MSV resistant hybrids. Experiments were conducted during 2010 to 2012 seasons in Kenya. Diallel crosses and SSR markers were used to characterize MSV resistant maize inbred lines from three programs of CIMMYT, KARI and IITA. In general, this study revealed that MSV is still an important problem in Kenya with high incidence and severity levels in the farmers’ fields. The levels of MSV resistance in locally grown hybrids needs to be improved. Farmers challenged breeders to develop new hybrids that combine early maturing, high yield potential and MSV resistance. The study was successful in identifying the best eight inbred lines for use in breeding new maize hybrids with MSV resistance. The nature of gene effects was established for the first time, in particular the role of epistasis and G x E in conditioning MSV resistance in hybrids. Results indicate serious implications for previous models that ignored epistasis in studying MSV resistance in maize. The inbreds Z419, S558, CML509 and Osu23i, displayed high levels of epistasis for MSV resistance. Unless strong sources of MSV resistance, such as MUL114 and CML509, are used, breeding resistant hybrids will require parents that carry dominant resistance genes. The additive-dominance model was adequate to explain northern leaf blight (NLB) resistance in hybrids, indicating fewer complications in breeding NLB resistant hybrids. The study also reveals that SSR genetic distance data can be used to predict hybrid performance, especially when the correct set of markers is used. Many previous studies have not found any significant relationship between genetic distance and heterosis, due to large G x E and use of a wrong set of markers. The diallel analysis and SSR data established the important heterotic groups, which will be exploited for efficient development of MSV resistant maize hybrids. These strategies will be recommended to programs that emphasize MSV resistance in maize hybrids. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

Alternaria leaf petiole and stem blight is an important disease of sweetpotato (Ipomoea batatas (L.) Lam.) causing yield losses in both landraces and improved cultivars. The most important species causing economic yield loss in Uganda are Alternaria bataticola and A. alternate with A. bataticola the most aggressive and widely distributed. The study was conducted to: i) establish farmer-preferred sweet potato attributes, production constraints and Alternaria leaf petiole and stem blight awareness; ii) evaluate Ugandan sweet potato germplasm for Alternaria leaf petiole and stem blight resistance; iii) determine the mode of inheritance of resistance to Alternaria leaf petiole and stem blight and storage root yield components of sweet potato through estimation of the general combining ability (GCA) of the parents and the specific combining ability (SCA) of the parents for each cross; and iv) determine the adaptability and farmer acceptability of selected F1 genotypes across environments. The participatory rural appraisal was conducted to establish farmer preferences and production constraints revealed that farmer preferred sweet-potato traits were high yield, sweetness (taste), early maturity, high dry mass, resistance to pests and diseases, and in-field root storability after maturity. A majority of the farmers considered Alternaria leaf petiole and stem blight a serious production constraint causing yield loss of over 50%. The main control measures against the disease were roguing of infected plants, spraying with fungicides, use of healthy planting materials and planting resistant genotypes. Thirty sweet potato land races and improved cultivars were evaluated for Alternaria blight severity; yield, dry mass, harvest index, sweetpotato weevil (Cylas spp.) damage and sweetpotato virus disease at two sites (Namulonge and Kachwekano) over three seasons (2010B, 2011A, 2011B) under Alternaria inoculum and fungicide spray treatments. Landrace Shock was more resistant to Alternaria blight than Tanzania, the resistant check. Genotypes NASPOT 1, NASPOT 7, New Kawogo and Dimbuka were the most susceptible. Thirty two F1 families were generated from 16 parents in two sets in a North Carolina II mating scheme. The families were evaluated at two sites using a 5 x 7 row-column design with two replications. There were significant (P<0.05) differences among the families in Alternaria blight severity. Both GCA and SCA mean squares (MS) for Alternaria blight were highly significant (P<0.001) but the predominance of GCA sum of squares (SS) for Alternaria blight at 67.4% of the treatment SS versus 32.6% for SCA SS indicated that additive effects were more important than the non-additive effects in controlling this trait. For the yield components, the GCA MS were significant (P<0.05) and accounted for more than 60% of the treatment SS except for percentage dry mass composition where SCA SS accounted for 53.0% of the treatment SS implying that non-additive genetic effects were slightly more important than additive for this trait. Some parents that had desirable high, negative GCA effects for Alternaria blight produced families with undesirable positive SCA effects and the reverse was also true. This implied that the best parents should not be chosen based on GCA effects alone but also on SCA effects of their best crosses. The promising F1 genotypes selected from previously evaluated crosses together with one Alternaria blight resistant check (Tanzania) and one susceptible check (NASPOT 1) were evaluated at three sites (Namulonge, Kachwekano and Serere) using a randomised complete block design with three replications. Scientists and farmers evaluated the agronomic performance and also quality traits of the genotypes before and at harvest. Genotypes G14, G16, G24, G29, G49, G59 and G69 were the most stable across the sites for low Alternaria blight severity and can, therefore, be recommended for further evaluation under both low and high disease pressure areas. Genotypes G67, G13, G14, G24, G29 and G53 were the most high yielding and stable across the sites and were therefore the most widely adapted. In the participatory selection, before harvest and at harvest, Spearman’s rank correlation of the scientists and farmers’ mean ranking of the genotypes at each site was positive and significant. This indicated that the scientists in the study were capable of selecting for farmer preferred traits. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

Common bean (Phaseolus vulgaris L.) is an important legume crop in Kenya and is a cheap source of proteins. The small scale farmers in Kenya produce common bean under low agricultural input systems and this predisposes the crop to pests and diseases. Among the diseases, angular leaf spot (ALS) is a major constraint to common bean production and contributes to yield losses as high as 80%. The causative pathogen Pseudocercospora griseola (Sacc.) Crous & Braun is highly variable and several races have been reported. There are few common bean genotypes with resistance to this disease. Therefore breeding for resistance to ALS is important for the country. This study was carried out to; i) evaluate the common bean production systems, constraints and farmer varietal preferences in Kenya, ii) evaluate local landraces and selected introductions of common bean for yield performance and reaction to ALS, iii) study the genetics of resistance to ALS in common bean and iv) develop a breeding method for durable resistance to ALS in common bean. To determine the common bean production systems, farmers’ preferred traits and their knowledge on common bean constraints including ALS, a survey was conducted in Kiambu county using a semi-structured questionnaire, interviews, and focus group discussions. The study revealed that farmers cultivate common beans during the short and long rain seasons. However, they experience better yields in the short rains due to reduced disease incidence. The majority of the farmers (71%) intercrop common bean and this ensures maximum utilisation of space. A high percentage (70%) of the farmers utilise their retained seed for production. The farmers identified ALS as one of the most important constraints to production. The only preventative measure they undertake to control the disease is weeding. The farmers reported that they would prefer improved varieties that were resistant to ALS. Farmers have a preference for particular common bean traits that include high yield (80%), resistance to insect-pests and diseases (72%), type I growth habit (52%), early maturity (68%), seed size and colour (21%) and cooking time (20%). These should be incorporated in breeding programmes. Two hundred common bean landraces and market class varieties were evaluated for ALS resistance in a nethouse at University of Nairobi, Kabete Field Station and for ALS resistance and yield in the field in KARI-Tigoni. The results showed that disease severity scores for the genotypes were similar in the two locations, with the top three resistant genotypes being Minoire, GBK 028123 and Murangazi with disease severity scores of 2.9, 2.9 and 3.2 in Kabete and 2.6, 2.8, and 2.9 in Thika respectively. These resistant genotypes can be used as sources of resistance in a breeding programme or they can be used as resistant varieties. All the market class varieties were susceptible to ALS (disease severity score 6.7-8.0). There was a non-significant correlation between disease and yield most likely because most of the resistant genotypes were exotic and hence not adapted to the local conditions. There was also a non-significant correlation between disease and seed size. The two hundred common bean genotypes were evaluated for yield at University of Nairobi, Kabete Field Station and KARI-Thika. The results indicated that the 2011 and 2012 seasons had similar mean yields and that yields at Kabete were higher than at KARI-Thika. The highest yielding genotypes across the two locations were; GLP 2 (766 kg ha-1), Nyirakanyobure (660 kg ha-1), GBK 028110 (654 kg ha-1), GLP 585 (630 kg ha-1) and Mukwararaye (630 kg ha-1). There was a significant genotype x environment interaction and hence it is important for breeders to carry out stability analysis, so as to recommend varieties for a wide range of environments. To study the genetics of ALS resistance in common bean, three inter-gene pool crosses: Super-rosecoco x Mexico 54, Wairimu x G10909 and Wairimu x Mexico 54 were made. The resistant genotypes were Mexico 54 and G10909, while Super-rosecoco and Wairimu were susceptible. The generations F1, F2, BC1P1 and BC1P2 for each of the crosses were developed. The parents P1, P2 and the five generations of each cross were evaluated for resistance to ALS in Kabete Field Station. Results showed that both dominance and additive gene action were important in the expression of resistance to ALS. However, additive gene action was predominant over dominance gene action. There was a moderately high narrow sense heritability estimate (52.9-71.7%). The minimum number of genes controlling resistance to ALS was between 2 and 3. The predominance of additive gene effects and the moderately high narrow sense heritability estimates recorded imply that progress in resistance to ALS could be made through selection in the early segregating generations. A double cross followed by selection against resistant genotypes was used to develop a method to breed for durable resistance to ALS in common bean. The method was used to accumulate minor genes of ALS resistance into single genotypes. Four intermediate resistant landraces were used to develop a double cross population that was screened using a mixture of ALS races. Selection in F1 and F2 population was done on the basis of intermediate resistance (disease severity score 4.0-6.0), while selection from F3 population was based on resistance (disease severity score 1.0-3.0). Ten advanced F4 lines along with their parents were evaluated for ALS resistance. The F4 advanced lines had a significantly improved resistance to ALS compared to their parents. Hence the method was successful in accumulating minor genes for resistance thus showing significant breeding progress in breeding for durable resistance. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

Finger millet (Eleusine coracana) productivity in East Africa has remained low in all production agro-ecologies for decades owing to the low yielding potential of existing that are susceptible to the blast disease caused by the fungus Magnaporthe grisea (Hebert) Barr. and the limited research on the crop. The region holds large finger millet germpasm collections whose value is not yet been fully exploited. However, with the ongoing breeding efforts through hybridization, there is a need to comprehensively characterize the germplasm to identify valuable traits to address biotic and abiotic stresses that affect finger millet productivity. Studies on gene action and inheritance of key traits that contribute to yield improvement are also required to help formulate an effective breeding strategy for finger millet improvement. The objectives of this study were to (i) determine the genetic diversity in a set of germplasm from East Africa (ii) determine association between grain yield and its component traits (iii) identify genotypes for target production agro-ecologies (iv) identify blast resistant finger millet genotypes for use in breeding and production and (v) generate information on the inheritance of blast, grain yield and yield components for the development of an effective breeding strategy. A total of 340 finger millet accessions were collected from three countries in East Africa: Kenya, Tanzania and Uganda and 80 global minicore accessions sourced from ICRISAT-India. High phenotypic variability in the germplasm was recorded for 23 quantitative traits, blast reaction and five qualitative traits. Both morphological and molecular characterization (using SSR markers) of the 340 accessions revealed higher diversity within than among the countries Kenya, Tanzania and Uganda. Seven morphological clusters and three major genetic clusters were detected. Morphological diversity delineation was largely influenced by leaf sheath length, plant height, peduncle length, panicle exertion and grain yield. The mean polymorphic information content (PIC) of 19 polymorphic markers was 0.606 with mean alleles of 195 with sizes that ranged from 148-474 base pairs. The Kenyan and Tanzanian accessions had higher diversity than the Ugandan with the Kenyan and Ugandan, and the Kenyan and Tanzanian accessions being closely related than the Tanzanian and Ugandan. The low diversity in the Ugandan accessions could be attributed to higher research intervention in the country leading to the promotion and use of improved cultivars. Efforts have to be directed towards collection and conservation of valuable diversity before it is lost. The diversity in plant height, maturity, yield and blast reaction and the cluster groups detected in the germplasm should provide a basis for finger millet improvement through hybridization and selection. Higher genotypic than phenotypic correlations were recorded for most of the traits studied with grain yield having high positive correlations with finger width, grains per spikelet, threshing percent, peduncle length and panicle exertion. Both grain yield and days to flowering had negative correlations with all three blast types (leaf, neck and finger). Path coefficient analysis revealed that productive tillers per plant, 1000 grain mass, grains per spikelet and threshing percent had positive direct genetic effects on grain yield with strong indirect effects from several of the other traits which necessitates simultaneous selection for those traits with strong direct effects and those with strong indirect effects for grain yield improvement. High broad sense heritability estimates and high genetic advance as percent of mean were recorded in fingers per panicle, flag leaf sheath length, 1000 grain mass, finger length, peduncle length, panicle exertion, number of leaves per plant and leaf sheath length probably indicating the predominance of additive gene effects in controlling these traits hence the potential for improvement through selection. Adaptation and stability analysis using the GGE biplot model identified Lanet 2012 long rains, Serere 2012 long rains and Miwaleni 2012 long rains as the most discriminating environments for the low temperature, sub-humid mid altitude and dry lowland areas, respectively. Alupe 2012 long rains was the ideal environment for genotype discrimination for blast while Lanet 2012 long rains was best for grain yield. Genotypes G3, G5, G17, G25, G28, G36 and G71 were identified as being stable across environments and G1, G18, G19, G37, G54, G61, G74, G75, and G77 were found ideal for specific adaptation. Disease severity scores were highly negatively (P<0.01) correlated with days to flowering and grain yield suggesting that early lines suffered more disease damage leading to reduced yield. Resistant genotypes were slow blasting (probably associated with horizontal resistance) which may enable them to withstand blast pathogen variability for longer periods. Nine genotypes were identified with high resistance to blast and will be useful for breeding as blast resistance sources. Resistant genotypes had low AUDPC values and disease severity rating for the three blast types and vice-versa for susceptible genotypes. Further investigations need to be carried out to determine the possibility of the three blast types being controlled by the same genes. Early maturing blast susceptible genotypes with good yield potential could be utilized in areas with low blast prevalence. To understand the gene action for inheritance of the various traits 16 F2 families plus their four female and four male parents were evaluated at Alupe and Kakamega western Kenya under artificial blast inoculation. Significant additive genetic effects were recorded for all traits (except for finger width and grains per spikelet) meaning that improvement for these traits would be possible through the common selection methods for self pollinating crops. Parent lines KNE 392, and KNE 744 and IE 11 were found to be suitable for blast resistance breeding while Okhale 1 was found to be suitable for high grain yield and blast resistance improvement due to their high desirable GCA effects. Most of the F2 families showed transgressive segregation for the three blast types in either direction which gives hope for the development new pure lines with better blast resistance than the parents. Crosses IE 3104 x KNE 796, KAT FM 1 x Okhale 1, IE 11 x Okhale, IE 11 x P 224 and KNE 744 x KNE 392 have potential to generate lines with blast resistance due to their high desirable SCA effects. The F2 segregation distributions for blast indicated quantitative inheritance. However the one to four minimum number of genes (effective factors) detected for resistance control in all the three blast types was not in sync with the segregation patterns in the F2 families and further investigations are required. There were differences in segregation patterns between crosses which may suggest the presence of different resistance genes in the different parents used. This would call for gene pyramiding for durable resistance. These results confirm the potential of sourcing valuable parental stocks in the local germplasm for the development of genotypes to improve finger millet productivity in East Africa. Already some of the high yielding and blast resistant genotypes identified here have been incorporated in the regional cultivar trials. The diversity information generated will facilitate effective conservation and utilization of this germplasm. Results of gene action for inheritance of the various traits from this study will enable breeders to develop sound breeding strategies for finger millet improvement in the region. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.