Bambara groundnut is an indigenous African legume grown mainly in sub-Saharan Africa; it is an important source of protein to the rural majority. There are no established varieties and subsistence farmers grow locally adapted landraces which are generally low yielding. Bambara groundnut is a predominantly self-pollinating crop and is expected to exist as non-identical inbred lines, although the previous lack of co-dominant markers has prevented a formal assessment of heterozygosity within bambara groundnut genotypes. A total set of 75 microsatellites that were characterised in this study were used to investigate the genetic diversity of a set of 24 bambara groundnut landraces, to provide an evaluation of the markers for polymorphism and provide a link with DArT marker data that were previously analysed. Sixty eight microsatellites were identified that were found to be consistent and reproducible, from which a set of markers were selected and used for genetic variability studies of bambara groundnut, to compare the use of molecular markers with morphological markers, and to investigate using SSR markers in pure line selection. The genetic diversity of bambara groundnut was assessed based on morphological characters for two seasons; in a glasshouse experiment at the University of Nottingham, Sutton Bonington Campus, UK and in a field experiment that was conducted at the Botswana College of Agriculture (Notwane farm), Gaborone in a randomised block design with three replicates. The landraces were characterised for 24 quantitative and 13 qualitative characters. The results indicated considerable variation for quantitative characters, while significant morphological differences were also recorded for most characters. Multivariate data analysis was conducted using principal component analysis, cluster analysis and heritability estimates were developed. The low cost, simplicity and agricultural relevance of morphological characterisation makes it an important tool in germplasm genetic variation studies. Thirty four lines from field experiments were investigated for genetic diversity based on 20 microsatellites. The expected heterozygosity (He) had an average of 1 in agreement with the fact that bambara groundnut is predominantly self-pollinating. Both cluster analysis and principle component analysis (PCoA) grouped landraces based mainly on their areas of origin. A thorough molecular analysis of genetic and morphological variation in bambara groundnut was conducted to investigate the relationship between the two assessment techniques. This comparison will assist in breeders making informed decisions as to which approach is best to use in germplasm characterisation and plant breeding and how best to apply such knowledge in practical situations. DNA markers could then aid with the selection of germplasm for breeding, quality control within breeding programmes and, potentially, direct selection via Marker Assisted Selection (MAS). Euclidean distance estimates for morphological data and (Nei’s 1972) genetic distance estimates for SSR data were strongly correlated (r = 0.7; P < 0.001) in the agronomy bay and (r = 0.6; P< 0.001) in the controlled growth room. These results suggest the two approaches are generating the same pattern of genetic diversity, and as such can be used as a surrogate for each other.

As a major food source potato delivers significant levels of minerals to the human diet. The aim of this study was to understand the control over the mineral concentrations found in tubers. The three-dimensional patterns of mineral distribution in tubers give clues to the processes leading to storage in the tuber. Within the tuber flesh, calcium and phosphorus content decreased towards the centre of the tuber (on FW basis). The elements iron, magnesium, zinc, manganese, sulphur and chlorine were higher at the stem end, while potassium was higher at the bud end. Remobilisation of minerals within the tuber was evident after six months of cold storage. Mineral variation was explored in potato germplasm. Three diverse germplasm collections, the Commonwealth Potato Collection, the Phureja and Tuberosum Core Collection and the Neotuberosum Population demonstrated wide variation for tuber mineral concentrations, an interaction with tuber yield and, on multivariate analysis, consistent parallels between some minerals suggesting unsuspected shared processes affecting their concentrations. The 12601ab1 x Stirling tetraploid mapping population was used to identify QTls for tuber mineral concentration using REML analysis to account for local field variation. Transgressive segregation for tuber mineral concentrations was detected. The genetic map for this population was extended using DArT markers and QTLs were identified on all 12 linkage groups for all minerals studied. Two bulk segregant analyses were performed to add precision to the QTL analysis. One approach identified candidate genes on the potato genome sequence and used nearby SSRs to seek association in the tetraploid mapping population. A second approach used the variation present in the highly diverse Neotuberosum Population to identify DArT markers which were associated with the tails of the distribution of minerals. Using the latter approach, single superscaffolds containing candidate loci and trait-associated DArT markers could be aligned with a small part of mapping population QTLs, providing additional resolution.

Date palm (Phoenix dactylifera L.) is a diploid with 18 pairs of chromosomes and an estimated genome size of 658 Mb. It is a dioecious perennial monocot, with a long generation time (a period of 4-5 years until first flowering). Date palm is one of the major fruit crops grown in the Gulf countries and particularly in the Sultanate of Oman. Approximately 250 varieties of date palm are recorded throughout the country with evaluation and characterization based on morphological and reproductive traits (e.g. fruit color, fruit shape and fruit weight). Limited molecular characterization work has been undertaken for date palm germplasm in general and Omani date palm germplasm, in particular. The principal focus of this study was to: investigate the genetic diversity of Omani date palm germplasm and compare it with 'exotic' germplasm, to differentiate between female and male plants at the molecular level and to construct an initial genetic map for date palm. Samples were taken from eight parents of the available Omani date palm controlled crosses (Khalas 4, Khalas 13 male, Um-Alsela, Khori male, Bami, Naghal, Bahlani male, and Khasab) with 90 date palms from the BC1 and F1 populations, from 194 Omani date palm accessions (151 female cultivars and 43 male trees), together with samples from Italy (Sanremo and Bordighera), USDA-ARS, France, Iraq, Libya, Sudan and Iran. The F-statistics analysis showed that the genetic variation between female and male accessions based on random markers was only 2.1 %, while within the broader group of Omani female and male accessions the molecular variation was 97%, suggesting that the Omani female and male accessions have little consistent divergence, compared to the large-scale divergence within Omani germplasm, so male palm have been derived from most genetic origins in Oman. Additionally, the Principal Coordinates Analysis (PCA) and bootstrap consensus phenetic tree showed that the Omani accessions were closely related to each other and there was no clear genetic differentiation between female and male cultivars. A high degree of genetic variation was observed between germplasm from Oman, Italy, USDA-ARS, France, Iraq, Libya, Sudan and Iran as measured by Fst (19.7 %). The PCA showed that the Europe-Africa (Italy, France, Libya and Sudan) accessions are distinguished from West-Asia (Oman, Iraq and Iran) accessions and have their own autochthonous origin, a finding which was strongly validated by bootstrap consensus tree test. A medium density genetic map in date palm was constructed using 53 individuals from BC1 and 30 individuals from F1 populations. The BC1 map consisted of 270 markers (28 SSR and 242 SNP) distributed into 29 linkage groups with total genetic length of 1.486.7 cM, while the F1 map consisted of 591 markers (21 SSR and 570 SNP) distributed into 30 linkage groups with total genetic length of 2,385.6 cM. A total of 25 combined linkage groups were possible by combining both BC1 and F1 maps through common markers. A sex-link marker locus was developed and found to predict a high level of discrimination between male and female date palms among multiple varieties distributed across the wide range of cultivation, with an accuracy of 100% in the Omani crosses, 96% in the broad Omani material and 86% in the broadest date palm germplasm. This marker was also mapped in both BC1 and F1 at 42.8 cM and 4.9 cM in linkage groups 18 and 29, respectively and on combined group 19 at 42.8cM.

This thesis presents laboratory investigations on the competitive interactions which take place within and between bethylid parasitoids. Part one investigates the compatibility of three bethylids (Cephalonomia hyalinipennis, Cephalononlia stephanoderis and Prorops nasuta) for biocontrol releases against the principal pest of coffee, the coffee berry borer (CBB), Hypothenemus hampei. Cephalonomia hyalinipennis is able to hyperparasitise and consume pupae of C stephanoderis and P. nasuta. Cephalonomia stephanoderis also engages in intra-guild predation, consuming pupae of C hyalinipennis. In contests for CBB hosts, fatal fighting occurs in 69% of inter-specific replicates but never occurs in intra-specific replicates. This suggests that interspecific competition is stronger than intraspecific competition and that species coexistence may be compromised. Cephalonomia tephanoderis is the superior interspecific contestant while P. nasuta is the least successful and never kills an opponent. Where CBB infested coffee berries are provided to the three bethylids, coexistence between species is possible, but rare, within a single coffee berry. Prorops nasuta is the most successful species in interspecific replicates and replicates containing C. hyalinipennis generally have low production, regardless of the species combination added. Part two investigates contest interactions, the variables that influence contest outcome between Goniozus nephantidis females and chemical release. Prior ownership and difference in contestant weight have positive influences on contest outcome. Host weight positively influences the outcome of contests between two 'owners' and 'intruder' take-over success increases when intruders are older than owners. Seven bethylid species are found to release volatile chemicals when stressed. A pilot study identifies the volatile chemical in G. nephantidis and employs Atmospheric Pressure Chemical Ionisation-Mass Spectrometry for real-time analysis of chemical release during contest interactions. The appendix contains an advanced investigation using this technique. Bethylids are useful model organisms for the study of competitive interactions but appear to be generally ineffective as biological control agents.

Wheat (Triticum aestivum L.) is the most widely grown of any crop and provides one-fifth of the total calories of the world's population. Since the 1960s, increases in productivity have been achieved as a result of wide-scale adoption of Green Revolution technologies. However, in spite of growing demand, the challenges of increasing production to feed an estimated world population of 9 billion in 2050 are still considerable. Due to the increased demand, it is estimated that food production must be increased by about 50% by the year of 2050. Improving wheat productivity through developing cultivars with high yield potential and with high adaptability to specific environments is the key objective in the wheat breeding programs worldwide to fill the gap between the production and the demand. The overall aims of the present study were to: (i) investigate the physiological basis of yield potential progress from 1966 to 2009 in spring bread wheats released at the International Center for Maize and Wheat Improvement (CIMMYT) in the irrigated high potential environment of NW Mexico, (ii) investigate the physiological basis of effects of the tiller inhibition Tin1A gene on ear-fertility traits and yield potential and interactions with plant density in NW Mexico and UK environments in lines of a doubled-haploid (DH) population segregating for Tin1A/non-Tin1A alleles and (iii) identify breeding targets for new cultivars with higher yield potential. Four experiments were conducted in NW Mexico at the CIMMYT research station at Ciudad Obregon. Two of these experiments studied a set of 12 historic CIMMYT spring wheat cultivars released from 1966 to 2009 in 2008/9 and 2009/10. The other two experiments examined selected lines from a doubled-haploid (DH) population derived from a cross between CIMMYT spring wheat L14 and UK winter wheat Rialto contrasting for the presence/absence of the TinlA allele for tiller inhibition and their interaction with seed rate in 2008/9 and 2009/10. In addition, two other field experiments were conducted in the UK, one in 2008/09 at KWS UK Ltd in Thriplow, Hertfordshire and one in 2009110 at the University of Nottingham Farm, Sutton Bonington campus, Leicestershire. The plant material for both of these experiments was selected lines from the CIMMYT spring wheat advanced line Ll4 (+Tin1A allele) x UK winter wheat Rialto (-TinlA allele) DH population and the Rialto parent. In the experiment at Thriplow in 2008/09 the DH lines were examined at one seed rate and in the experiment at Sutton Bonington in 2009/10 at two seed rates. At the CIMMYT site in 2008/9 and 2009/10, a randomized complete block design was implemented with four replications for the experiments examining the CIMMYT wheat historic releases and a split-plot randomised complete block design with three replications was implemented for the experiments examining the +/- Tin1A DH lines, with three seed densities (50, 150 and 450 seeds per square metre); seed rates were randomized on main plots and eight genotypes randomized on sub-plots. At the UK site, in the KWS experiment, 24 DH lines (12+Tin1A allele) and (12-TinlA allele) from the L14 x Rialto population were used. There was only one seed rate (300 seeds m-2) and a completely randomised design in three replicates was implemented. The same 24 DH lines were examined in the experiment at the SB site, at two seed rates (40 and 320 seeds m-2) in a split plot randomised complete block design in three replicates. Seed rate was randomized on main plots and DH lines were randomized on sub-plots. In all experiments examining the DH lines of the Ll4 x Rialto population, lines were selected in pairs so that the two groups of +Tin1A and -Tin lA lines were approximately balanced for flowering time and plant height, i.e. every +TinlA line has a non-Tin1A pair with similar height and flowering date. Plots were sampled for destructive measurements of dry weight and DM partitioning and ear-fertility traits at four stages in the historic experiments at (GS3l, GS39, GS61+7d and at maturity) and at two stages in the DH population experiments (GS61+7d and at maturity). The water soluble carbohydrate (WSC) content of the stems plus attached leaf sheaths was also measured at GS61+7d and at maturity. In the historic experiments, at GS 61+14 days, a degraining treatment was implemented by removing all spikelets from one side of the ear (i.e. ca. 50% of the spikletes) in the histories experiment. Non-destructive measurements were taken for stomatal conductance, canopy temperature, fractional photosynthetically active radiation (PAR) interception and normalized difference vegetative index at various dates both pre- and post-anthesis in the historic experiments. In the experiments examining the set of 12 historic CIMMYT spring wheat releases, results showed that from 1966 to 2009 the linear rate of genetic gain in yield potential was 32 ha-1 yr-1 (0.59 % yr-1) (r = 0.76. P = 0.01). Yield progress was primarily associated with harvest index (percentage above-ground DM as grain DM) in the period from 1966 until about 1990 increasing from 43% to 49%, but deceased with year of release thereafter. A non-linear genetic gain in AGDM was evident over the 43-yr period with AGDM increasing from about 1990 from which point it increased rapidly to 2009. There was no association between genetic progress in grain yield and grain number per m2 in this set of 1 cultivars; a small increase in ears per m2 was counteracted by a decrease in grains per ear. However, grain weight tracked the improvement in yield potential over the 43-year period with a linear increase of 0.23 mg yr-1. No change was found in rachis length with plant breeding; however, number of fertile spikelets per ear decreased since about 1990 and was associated with the decrease in grains per ear. There were statistically significant differences in above-ground DM production at all growth stages and a tendency to produce more biomass during the GS31 to GS61+7d phase with year of release. No differences amongst cultivars were found in the amount of radiation intercepted by the whole canopy from GS3l to GS6l+7 days. Although not conclusive, since Bacanora was an exception to the trend and radiation-use efficiency (above-ground biomass per unit PAR interception; RUE), there was a tendency for RUE to increase with year of release which was consistent with a positive association with crop growth rate (above-ground DM per m2 per day; CGR) and the trend for an increase in biomass accumulation during the stem-elongation phase with plant breeding. Although there was a trend for an increase in biomass accumulation from GS31 GS61+7d this was counteracted by a decrease in ear DM partitioning so that ear DM per m2 at GS61+7d and grains per m2 did not change with plant breeding. Results showed that the improvement in the individual grain weight from 1966 to 2009 in this set of cultivars was associated with improvements in the grain filling rate from 1966 to ca. 1990 and in the duration of grain filling from ca. 1992 to 2009. Averaging across years, there was a significant positive association between post-flowering canopy-temperature depression and grain yield. Fractional PAR interception by the canopy layers of the ear, flag leaf and the penultimate leaf was increased with year of release since about 1990. This increase in the fractional interception of PAR correlated significantly with the grain weight and grain yield amongst the 12 cultivars. Grain growth of the cultivars in this historic set was generally sink limited rather than source limited. There was no change in source-sink balance as indicted by grain growth responses to the degraining treatment with year of release.

Herbicide resistance in weeds is a major threat to agricultural productivity, but the incidence of herbicide resistance in agricultural systems continues to increase. It is increasingly recognised that sustainable weed management can only be achieved by considering the ecological and evolutionary drivers of herbicide resistance evolution. Within this context, it has been suggested that selection within pre-existing variation in herbicide susceptibility, underpinned by additive genetic variation, may result in rapid evolution of herbicide resistance. In this thesis, these principles were tested in the major agricultural weed Alopecurus myosuroides (black-grass). Dose-response experiments demonstrated pre-existing phenotypic variation in response to two commercial herbicides with alternative modes of action (the ACCase inhibitor herbicide fenoxaprop-P-ethyl and the ALS inhibitors mesosulfuron-methyl and iodosulfuron-methyl-sodium) in A. myosuroides with no history of exposure to herbicide. Selection within this pre-existing variation was then tested using low doses of the herbicide fenoxaprop-P-ethyl, demonstrating rapid increases in resistance following a single generation of selection. Recurrent selection showed further, but non-significant, increases in resistance. Competition experiments were then performed to compare fitness in the absence of herbicide between the original susceptible population, and a population following two generations of selection for fenoxaprop-P-ethyl resistance. Results suggested that both resistant and susceptible A. myosuroides populations were of similar fitness and competitiveness: seed output was highly variable, and both resistant and susceptible populations were highly competitive against wheat. Finally, the possibility of exploiting dose-dependent selection to limit resistance evolution was tested in a long-term dose rotation experiment using the unicellular alga Chlamydomonas reinhardtii. The results showed that rotating between a very high herbicide dose and no herbicide application could limit resistance evolution, but overall population control was poor. There were indications that rotation between intermediate higher and lower herbicide doses could successfully control population sizes and limit resistance evolution, but these effects were only present in the earlier stages of the experiment.

Due to the lack of published molecular information concerning plant viruses from Iraq, this study was initiated to investigate the diversity of viruses infecting potato and vegetables in Iraq on a molecular basis. Based on the economic importance and incidence worldwide, eight virus genera were investigated in 175 potato and vegetable samples collected from fields in Baghdad, Anbar and Najaf provinces in Iraq. Using genus/family specific primers, published in the literature, polymerase chain reaction (PCR) and reverse transcription-polymerase chain reaction (RT-PCR) were performed to screen samples for potyviruses, begomoviruses, carlaviruses, tombusviruses, potexviruses, cucumoviruses, tobamoviruses and alfamoviruses. Circular DNA viruses were screened by rolling circle amplification (RCA). Products resulting from PCR/RT-PCR and RCA were cloned and sequenced and data obtained were used for sequence analyses. The above approach led to the first molecular characterisation of three potyviruses; Potato virus Y (PVY), Bean yellow mosaic virus (BYMV) and Zucchini yellow mosaic virus (ZYMV), one begomovirus; Tomato yellow leaf curl virus, two carlaviruses, Potato virus S (PVS) and Cowpea mild mottle virus (CPMMV) and one tombusvirus; Grapevine Algerian latent virus (GALV) in Iraqi potato and vegetable samples. Based on nucleotide (nt) sequence analyses, BYMV from broad bean and ZYMV from zucchini were 97% and 99% identical to equivalent sequences from the GenBank sequences, respectively. Two PVY strains were distinguished when sequences from potato and tomato showed 99% maximum nt identity to equivalent PVYO: N and PVYNTN GenBank sequences, respectively. Full-length sequence from tomato amplified by RCA showed 99% maximum nt identity to equivalent TYLCV sequences from the GenBank. Sequence comparison of carlavirus sequences isolated from potato and cowpea were 99% and 96% identical to equivalents PVS and CPMMV sequences from the GenBank, respectively. All tombusvirus sequences amplified from tomato and eggplant showed 93% maximum nt identity to equivalent GALV GenBank sequences. The high similarities (93-99%) of virus sequences isolated suggest, viruses isolated may have been introduced into Iraq from other countries, through international trading of plant materials used for cultivation as Iraq import most of plant materials for agriculture.

The study was undertaken with the objective of developing an IPM control strategy against M. vitrata in cowpea which will replace the existing use of calendar based application of broad spectrum chemical insecticide (Mixture of 30g cypermethrin and 250g dimethoate) in Kebbi State of Nigeria. The study initially made use of a survey backed up by focus group interviews to gather information on the types of farmers’ cowpea cultivation practices, their perceptions on pests and pesticides and the economics of cowpea cultivation with the aim of incorporating those practices that were found to be IPM compatible in the strategy developed. The result showed that most farmers were small scale growers who inappropriately used chemical insecticides due to lack of knowledge of other alternatives. Farmers had good scouting ability as demonstrated by their knowledge of field insect pests of cowpea, the nature of their feeding habit and magnitude of damage due to these insect pests. Cowpea cultivation in Zuru is profitable, labour and insecticides costs were the major profit limiting factors in cowpea cultivation. Therefore, an on-station trial was conducted which initially focused on the evaluation of four potential IPM components for their suitability as control tools against M. vitrata using two cowpea varieties [Danzafi (local) and improved Kanannado (IT89KD-245-1)]. The result showed that neem (nke) at 5% concentration was as effective as chemical insecticide (mixture of cypermethrin and dimethoate) in terms of reducing larval infestation/damage, pods and seeds damage as well as increasing yield of cowpea. In the next season another on-station trial was conducted to validate use of nke on scouting basis as an IPM system for the management of M. vitrata using the same cowpea varieties. The result showed that, the scouting based nke application had significantly higher larval infestation/damage which significantly lowered yield in comparison with the calendar based insecticide application. However,; the highest cost benefit ratio was sustained by the scouting based nke application. During the third season on-farm trial, although nke on scouting based application had significantly higher larval infestation/damage compared to calendar based chemical insecticide application yield was similar, indicating that it was not affected. The application of nke on scouting basis did not affect the abundance of the natural enemies. It was therefore concluded that nke application on scouting basis has the potential as an IPM control strategy against M. vitrata in cowpea.

This study on sweetpotato seed systems was conducted in Mukono, Kamuli, Bukedea and Soroti districts in Uganda, and in Mwanza, Shinyanga and Meatu regions in the Lake Zone of Tanzania during 2007 – 2011. It aimed at developing simple, affordable and applicable technologies for conserving and multiplying sweetpotato planting material for early season planting after the long dry season. The study sought to understand and describe farmers’ existing approaches, improve on rapid multiplication techniques and develop rational use of available planting material. Complete lack of or insufficient planting material for early planting immediately following the long dry season was reported. Farmers recognised that obtaining planting material early was beneficial as it resulted in increased root yield, an early source of food and sales at high prices. The Triple S (Sand, Storage and Sprouting) method of producing ample planting material for early season planting was developed in Uganda after testing various ways of storing the roots during the dry season so as to eliminate dry season mortality. Using roots obtained from crops planted in the conventional time and planting them out in watered gardens 1-2 mths before the rains to act as sources of sprouts for vine cuttings was the most appropriate. The method was validated in Tanzania which has a longer dry season. The use of 20cm cuttings instead of the mini cuttings (10 cm) in rapid multiplication of vines needed less labour and care. Pre-planting fertiliser (NPK: 25:5:5) doubled the quantity of planting material generated, and planting shorter and fewer cuttings than recommended saved planting material to enable more extensive plant coverage and doubled potential production. All these findings greatly contribute to the improvement of the conservation and multiplication of planting material, especially to improving the availability of early planting material.

The mirids, Sahlbergella singularis Hagl and Distantiella theobroma (Dist) (Heteroptera: Miridae), are major insect pests of cocoa, a valuable crop in West Africa. Their control by the application of insecticides is problematic in terms of safety and cost. Therefore, this study was undertaken to determine the potential for use of mirid sex pheromone trapping as an alternative, environmentally-acceptable method of managing the mirids. Based on the behavioural responses of the mirids to pheromones in traps, parameters were standardised for efficient performance of the traps. A range of five blends of the synthetic pheromone, the diester, hexyl (R)-3- ((E)-2-butenoyl)-butyrate and the monoester, hexyl (R)-3-hydroxybutyrate, impregnated in polyethylene vials were assayed with a blank control. Blends of 1000:500 μg and 1000:1000 μg respectively attracted significantly higher numbers of male S. singularis than other blends and the lure attracted male mirids optimally for four weeks with minimal reduction in eight weeks. Field bioassays were conducted to determine the appropriate trap design for pheromone trapping from four models; 2.5 litre and 4.5 litre plastic water bottles, sticky plastic plates, cylinder and standard rectangular traps. All models were equally effective. A field experiment was conducted with sticky glue on the outside of the traps. Combined inside and outside surfaces caught more mirids than the inside surface alone which caught only about 23% of the male mirids. Three field experiments using two different experimental designs were conducted to determine optimal height for trap placement. Traps placed inside the canopy attracted significantly more mirids than below 2.7 m height from the ground. The potential for mass trapping of mirids as a method of control was studied through three mass trapping experiments on research plantations and smallholder farmers’ farms. Catches of male S. singularis in pheromone traps were significantly reduced in mass-trapped fields but pheromone trapping did not control mirid numbers or affect damage on cocoa. Densities of 150 and 230 traps/ha were found to be optimal for trapping S. sahlbergella and D. theobroma respectively. Catches of male S. singularis in pheromone traps, however, predicted the magnitude of total mirid populations, and also shoot and pod damage in cocoa farms, albeit inconsistently.