The eldana stalk borer (Eldana saccharina Walker) is the most serious pest of the Southern African sugarcane industry, and it is imperative that effective control measures are available to minimize economic damage. Because conventional control methods have had limited success, cultivar resistance is seen as the most viable method of controlling infestation. However, due to the space- and time-consuming nature of the present screening methods, only small numbers of cultivars can be tested relatively late in the Plant Breeding selection programme. Increased resistance in breeding and selection populations is therefore slow. Buds are a preferred entry point of eldana larvae as they are softer than the rind that is present on the rest of the stalk surface. Preliminary results by other workers suggested that near infrared spectroscopy (NIRS) could provide a rapid screening method for the chemical profile in bud scales, the outer coating of buds and therefore the first contact point of an invading larva. If feasible, analysis of samples using this method could be done in the South African Sugar Experiment Station's (SASEX) stage two selection trials, providing an early indication of eldana resistance on large numbers of cultivars, without the necessity of separate trials. However, knowledge of how environments, position of bud scales on the stalk and age affect NIRS is required in order to determine the feasibility of the method. Planting of a trial with an identical set of genotypes across a range of environments, sampled at a number of ages, would provide the necessary information on environmental effects, whilst simultaneously providing the necessary range of samples to develop a calibration between bud scale chemical profiles and eldana resistance ratings. Inheritance patterns of the characteristics being measured is also required if they are to be used in a breeding programme. The original work by Rutherford (1993) was carried out on only five calibration sets (a set of standard clones with relatively well-known eldana resistance ratings), and different sets were not comparable due to what was assumed to be environmental differences between calibration sets. One aspect of the current experiment was to examine more closely the effect of genotype x environment interaction (G x E) on the performance of the NIRS technique under a range of conditions. Two sites were chosen to represent the conditions encountered in trials carried out by SASEX. The crops were sampled at three ages, representing the range of ages at which sugarcane is harvested in South Africa. Two locations on the stalk were also examined, top and bottom, for removal of bud scales, based on the assumption that aging of bud scales may affect chemical composition. A new NIRSystems 6500 instrument was acquired during the course of this study. Data from the new instrument indicated that there were no longer differences between the different calibration sets, and therefore no longer differences between environments. Spectra for different samples were very close, the differences being of the same scale as those recorded with repeated measures of the same samples, or between the readings for the standard solvent solution. This led to the conclusion that the differences observed on the original NIRSystems 5000 instrument were due to instrument error, not environmental differences. More importantly, the different calibration sets were not comparable despite being similar to each other. Prediction from one calibration set to another was low. These observations led to the conclusion that NIRS was not a suitable method for determining chemical compounds associated with tolerance of sugarcane genotypes to eldana borer. The original NIRS instrument was subject to error, and the small number of calibration sets included in the study led to the erroneous conclusion that NIRS was suitable for the prediction of varietal tolerance to eldana. With the acquisition of the new instrument, the errors generated by the old instrument became apparent. With the increase in number of calibration sets included in the study, it also became apparent that a global calibration covering all environments was not possible. An analysis of the heritability of the chemical compounds associated with eldana resistance was also included in this study. A biparental progeny design of 24 crosses with 33 unselected offspring per cross was used. This trial would have been analysed once the calibration had been developed using the environmental trial, and it would have provided knowledge of the breeding behaviour of the chemical compounds associated with tolerance to eldana. Because the NIRS technique proved to be unsuitable for detection of chemical compounds associated with eldana resistance, the heritability of these chemical compounds could not be studied. As the NIRS study did not produce data, the G x E interaction analysis and determination of heritability was applied to the bud scale mass data set. This study showed a relatively low positive correlation between bud scale mass and resistance to eldana. The broad sense heritability estimate for bud scale mass from the G x E interaction analysis was 0.45, and the narrow sense heritability estimate from parent-offspring regression analysis was approximately 0.27, suggesting a low degree of genetic determination in bud scale mass. The G x E interaction analyses gave varying results depending on the method used. The ANOVA analysis suggested that ages, sites and years had an effect on bud scale mass, while deviation from maximum plot showed no significance for G x E interactions. The number and choice of genotypes selected as unstable also varied with the method used to determine the stability of individual genotypes. Regression analysis and rank order analysis revealed a number of unstable genotypes, whilst stability variance and ecovalence, which produced similar results, detected only two unstable genotypes. In the rank order analysis correction of data to remove genotype effect, reduced the number of unstable genotypes, suggesting that the G x E interaction effect was partially confounded with the bud scale mass of the genotypes. This was a more reliable method than the uncorrected rank order analysis, and would be the preferred analysis type of all those tried. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2003.

Eldana saccharina Walker (Lepidoptera: Pyralidae) is an indigenous insect widely distributed throughout Sub-Saharan Africa that is a major pest of sugarcane in southern Africa. Studies have shown that populations from West Africa have distinct behavioural differences compared to populations from eastern and southern Africa. In addition, the parasitoid guilds attacking populations in these regions are markedly different. This marked behavioural and parasitoid guild variation evoked a hypothesis of genetic diversification. To evaluate this hypothesis a project on the phylogeography of E. saccharina was initiated. The project was planned to include sampling of as many regions as possible in its known range in Africa, to obtain specimens of E. saccharina for genetic analysis. When these surveys were initiated in Ethiopia, it was found that there was no published literature available on the occurrence of stem borers in Ethiopian sugarcane. It was thus clear that no stalk borer/parasitoid surveys had been completed in either sugarcane or any large grass and sedge indigenous hosts in Ethiopia. The study was thus expanded beyond the investigation of only the genetic diversity of E. saccharina, to include area-wide surveys to determine ecological aspects of the borer complex in suspected host plants, including sugarcane, in Ethiopia. In this way the host plant range and distribution of E. saccharina and other sugarcane borers in Ethiopia in particular could be determined, samples for a larger phylogeography project could be collected, and the insect's impact on sugarcane could be assessed. Quantified area-wide surveys of the sugarcane estates and small-scale farmer fields of Ethiopia were conducted between December 2003 and February 2004. The surveys verified the presence of four lepidopteran stem borer species on Ethiopian sugarcane. These were Chilo partellus Swinhoe (Lepidoptera: Crambidae), Sesamia calamistis Hampson (Lepidoptera: Noctuidae), Busseola fusca Fuller (Lepidoptera: Noctuidae) and Busseola phaia Bowden (Lepidoptera: Noctuidae). The surveys indicated that Busseola species are the major and most widely distributed sugarcane stem borers in sugarcane farms of Ethiopia. Over 70% of the peasant sugarcane fields visited were infested by these borers, with the highest levels of infestation (35% and 50%) being in the northern and western part of the country, respectively. Busseola was also the predominant stem borer of sugarcane in two of the three estates (Wonji and Finchawa). Chilo partellus and S.calamistis were recovered in very low numbers at all the commercial estates and from peasant farms in the western part of Ethiopia. However, C. partellus was the predominant sugarcane stem borer in lowland areas of northern, southern and eastern parts of the country. Eldana saccharina was recovered from large sedges in waterways of Metehara and Wonji sugar estates in the central part of the country, and sedges growing around lakes in northern and southern Ethiopia, but not from sugarcane anywhere in Ethiopia. The phylogeographic study conducted on E. saccharina populations from eleven countries of Africa clearly showed the population structure of the insect within the continent. Five hundred and two base pairs of the mitochondrial DNA (mtDNA), corresponding to the Cytochrome Oxidase subunit I (COl) region, were sequenced to clarify phylogenetic relationships between geographically distant populations from eastern, northern, southern and western Africa. Results revealed that E. saccharina is separated into four major populations corresponding to their geographical location, i.e. West African, Rift Valley and two southern African populations. Sequence divergence between the four populations ranged from 1% to 4.98%. The molecular data are congruent with an isolation by distance pattern except for some of the specimens from eastern and southern Africa where geographically close populations are genetically distant from each other. Geographical features such as the Rift Valley and large water bodies in the continent seem to have a considerable impact on the genetic diversity in E. saccharina. Identification of field-collected stem borer specimens was done using classical taxonomic techniques, except for Busseola spp. where DNA barcoding was used. As field-collected larval material of Busseola died before reaching the adult stage, identification of species using adult morphology was not possible. 'Sequence divergence in the COl gene was used as a tool to identify the species of Busseola attacking Ethiopian sugarcane. Partial COl sequences from Ethiopian specimens were compared with sequences of already identified noctuid species from the East African region. Results of the sequence analysis indicated that the Busseola species complex in Ethiopian sugarcane comprised B. fusca and B. phaia. Sequence divergences between Ethiopian Busseola species was as high as 5.0 %, whereas divergences within species were less than 1% in both species identified. Several larval parasitoids, bacterial and fungal diseases of stem boring caterpillars were also recorded in Ethiopian sugarcane. Amongst these was Cotesia flavipes Cameron (Hymenoptera: Braconidae). This exotic parasitoid has been introduced into several African countries for the control of C. partellus in maize and sorghum, but had never been released in Ethiopia. To investigate the origin of C. flavipes in Ethiopian sugarcane, molecular analyses were conducted on Ethiopian specimens from sugarcane and specimens of C. flavipes from different countries of Africa released from the Kenyan laboratory colony, again using COl sequences. Results of the analysis revealed that the C. flavipes population that had established in sugarcane fields of Ethiopia was similar to the south east Asian populations released against C. partellus in maize in other parts of Africa, and different from other populations of this species, providing evidence that the Ethiopian C. flavipes is likely to be a descendant of the original Pakistani population that was released in different parts of Africa. The study reveals the importance of lepidopteran stem borers in sugarcane production in Ethiopia and highlights the role of molecular methods in species identification and determining phylogenetic relationships. More importantly, this study establishes the continental phylogeographical pattern of the indigenous moth, E. saccharina. The impact of geological events, geographic barriers and cropping systems on the evolution, distribution and abundance of stem borers are discussed. Future areas of research for understanding more about the phylogeographic relationships of E. saccharina and management of stem borers are discussed. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

As is the case in many other regions in the world, sugarcane production in southern Africa is affected by a wide range of climatic conditions, which can vary considerably from location to location and from year to year. As a result, the season length and growth cycles of sugarcane in southern Africa differ greatly. Such conditions include the hot and dry regions of northern KwaZulu-Natal, Swaziland and Mpumalanga, where sugarcane is mostly irrigated, to the humid sub-tropical coastal belt extending from the far north coast of KwaZulu-Natal to areas in the Eastern Cape, as well as the cool frost prone midlands regions of KwaZulu-Natal. Owing to the wide range of climatic conditions in which sugarcane is grown in southern Africa, there are many different external factors that affect sugarcane production, including a range of pests and diseases, frost occurrences and variations in soil water. The objective of this research was to (1) identify a number of important variables that affect cane production in southern Africa, (2) employ suitable models to reflect these variables, and (3) simulate and map the extent and severity of these variables at a high spatial resolution over southern Africa. Such variables include the Eldana saccharina and Chilo sacchariphagus stalk borers, sugarcane rust fungus, heat units with selected base temperatures, frost, soil water content, soil compaction, irrigation water demand, conducive and non-conducive growing conditions, flowering proficiencies for sugarcane, sugarcane yields and yield increments per unit of irrigation. The distribution patterns of the above-mentioned variables relied greatly upon the various models employed to represent them, as well as the accuracy of the temperature and rainfall databases to which the various models were applied. Although not definitive, the models used to reflect the variables which had been identified were considered to be generally satisfactory. The resolution at which the variables which had been identified in this study were mapped, was also found to be adequate. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2008.