Thesis (MSc)--University of Stellenbosch, 2006. / Bibliography. Also available via the Internet.

Typescript, etc.

Thesis (Ph.D.) - James Cook University, 2005. / Typescript (photocopy) Bibliography: leaves 179-194.

Increasing the sucrose yield and the disease resistance of plants are two major objectives of the transgenic sugarcane plant programme in South Africa. The sugarcane culm has thus been identified as one of the main target areas for transgene expression. A shortage of reliable promoter elements as well as patent limitations have necessitated the isolation of promoters that are preferentially expressed in the sugarcane culm. In the present study two different approaches were followed to isolate such promoters, and the bacterial promoter, rolC, was evaluated for tissue-specific expression in sugarcane. Differential display is a non-directed technique that was used to identify genes that are differentially expressed in the mature sugarcane culm. The original method was modified, and four putative culm-preferential fragments were isolated. Sequence and hybridisation analyses revealed that these fragments were false positives, and could therefore not be used to obtain a culm-specific promoter. Activity of the Agrobacterium rolC promoter was evaluated by analysing expression patterns of two reporter genes in the mature culm of transgenic sugarcane plants. Nucleic acid analyses indicated that the foreign DNA was incorporated into the sugarcane genome, and that mRNA transcripts were produced. Histochemical analysis was done to visualise rolC-driven GUS and GFP expression in the mature sugarcane culm. In both cases the reporter gene expression was restricted to the vascular bundles and specifically to the phloem. A directed approach was followed to isolate the gene and subsequently the promoter of the β-subunit of pyrophosphate-dependent phosphofructokinase (PFP-β). An incomplete cDNA clone was obtained from a mature culm cDNA library, and was used for the screening of a sugarcane genomic library. Two clones containing different parts of the PFP-β gene were isolated. A Deletion Factory™ system was used to analyse the clone containing the 5' end of the gene. The first five exons and 1747 bp of the 5' flanking region of the gene were sequenced. Preliminary activity analysis of the promoter region was done by constructing two expression vectors, and analysing transient GUS expression in sugarcane callus. Results indicated that the promoter is capable of driving foreign gene expression in callus. Transient expression levels were lower than that of the maize Ubi-1 promoter. Further analysis of the 5' flanking region will be done to establish whether cis-acting elements outside the analysed area have an influence on the activity of the promoter. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1997.

A mathematical model has been developed to represent the extraction of sugar from sugar cane in the diffusion process. As a consequence of the structure of prepared cane, extraction is postulated to occur via two first order relations in parallel. The model was found to represent accurately the extraction behaviour observed in two different experimental configurations. Experiments on a laboratory scale were undertaken to elucidate the mechanism and basic rates of extraction. The results are consistent with the postulate that extraction takes place by a combination of washing and molecular diffusion. The diffusion process was simulated experimentally in a fixed-bed pilot plant diffuser. Model parameter values estimated from this data provide evidence of the effect of liquid hydrodynamics on the extraction process. These results have been interpreted in terms of liquid holdup, liquid velocities and the efficiency of liquid- solid contacting. It is shown how the model can be applied to full scale diffusers of the moving-bed type, which will enable prediction of performance and the choice of optimum operating conditions. / Thesis (Ph.D.)-University of Natal, Durban, 1972.

Sugarcane is an economically important crop and its high demand has necessitated the use of biotechnology methods to produce and accelerate the production of desirable genotypes. One such method is genetic transformation. However, as sugarcane is a highly polyploid crop, which originated from interspecific crosses between Saccharum spontaneum and S. officinarum, efforts to transform it are inhibited by transgene promoter silencing. As ancestral lines have a simpler genetic makeup than modern varieties, they may be useful to test promoter function. Intrinsic to the generation of transgenic plants is the ability to produce plants from specific species and varieties, for which an indirect method of regeneration is needed. Consequently, the first objective of this study was to determine a high yielding protocol for somatic embryogenic calli. The second was to transform such calli and produce regenerated plants to assess transgene expression. A preliminary study was conducted using eight ancestral varieties to determine which were the most responsive in culture. Leaf roll disks were cultured on 5 mg.1¯¹ 2, 4-D and callus production was assessed. Based on these results and the availability of plant material, S. spontaneum Nigeria 1, S. spontaneum Nigeria 2, S. spontaneum Coimbatore, S. officinarum NG 77-69, and S. officinarum Black Cheribon and the commercial polyploid variety NCo376 were selected and tested on 11 different callus induction media. The S. spontaneum variety that generated the highest percentage of leaf disks that produced callus and plant yield was Nigeria 1 (61 % and 259 plants/10 disks, respectively), whilst the S. officinarum variety was Black Cheribon (75 % and 90 plants/10 disks, respectively). The best media for both comprised of MS salts and vitamins, 20 g.1¯¹ sucrose, 0.5 g.1¯¹ casein hydrolysate 5 mg.1¯¹ 2, 4-D and 8 g.1¯¹ agar. NCo376 produced the most amount of callus (93 %) when cultured on media containing 3 mg.1¯¹ 2, 4-D and gave a final yield of 450 plants/10 disks. Based on the yields obtained above and the availability of plant material, the varieties S. spontaneum Nigeria 1 and S. officinarum NG77-69 were selected for genetic transformation studies. Calli of these varieties as well as that of NCo376 were microprojectile bombarded with either pEmuKN + pAHC27 or pEmuKN + pR₁₁F¯. Following bombardment, the calli were cultured onto paromomycin-containing (1 ml.1¯¹) selection media and regenerated plants were obtained after 8-12 weeks. Transgene integration into the plant genome was assessed using PCR and qPCR techniques, and indicated that all NCo376 plantlets contained the GUS and npt II transgenes. However, only 4 out of 5 and 2 out of 3 S. officinarum NG77-69 plants transformed with pAHC27 and pR₁₁F¯- respectively, and 6 out of 10 S. spontaneum Nigeria 1 plants transformed with pR₁₁F¯- contained these transgenes. The transformation efficiencies achieved for NCo376, for the constructs pAHC27 and pR₁₁F¯- was 0.27 and 0.33 transgenic plants/blast, respectively. For NG77-69 it was 0.27 and 0.13 transgenic plants/blast, whilst that of Nigeria 1 was 0.20 and 0.40 transgenic plants/blast. Stable transgene expression in acclimatized plants was then assessed using a histochemical GUS assay and none of the plants expressed the GUS gene. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.

The use of genetic markers that are linked to specific traits in sugarcane has the potential to increase the efficiency of the selection of improved varieties. Conventionally, markers are identified by analysing the segregation of potential markers and traits in the progeny of single crosses. However, this approach is not practical for sugarcane breeding programmes where replicated, well characterized progenies do not exist. The objective of this project was to investigate the potential of using commercial varieties for identifying markers associated with some of the important traits in sugarcane. This approach would be far more effective than dealing with single progenies since the traits of commercial varieties have already been characterized. The DNA of fifty commercial varieties of sugarcane was amplified by RAPD PCR using forty-one arbitrary decamer primers. Analysis of the resulting banding profiles, obtained by agarose gel electrophoresis, yielded fifty-four reliable polymorphic fragments. Two approaches were used to identify putative markers linked to the traits of resistance to eldana, sugarcane mosaic virus, and smut: (1) a correlation approach which attempted to identify whether the presence of any polymorphisms could be used to imply the existence of a particular phenotypic state, and (2) multiple regression analysis, in order to determine whether polymorphisms could be used to predict the performance of the varieties for each of the traits. Both approaches appeared to identify associations between polymorphisms and the traits, although multiple regression analysis yielded the most informative results and was able to assign statistical values to the associations. Using multiple regression, the best predictive model was obtained for sugarcane mosaic virus resistance. This model consisted of four polymorphisms and had an r² of 0.40l. By dividing the resistance ratings into three groups (resistant, intermediate and susceptible), 52% of the varieties were correctly classified and only 2% of the varieties were predicted in opposite groups (i .e. predicted susceptible when actually resistant, and vice versa). The predictive model for eldana resistance consisted offour polymorphisms and had an r² of 0.347. This model classified 30% of the varieties in the correct group of three while none of the varieties were predicted in opposite groups. The predictive model for smut resistance consisted of three polymorphisms and had an r² of 0.316. This model classified 30% of the varieties in the correct group of three while 2% of the varieties were predicted in opposite groups. Further analysis of sugarcane varieties using additional polyrnorphisrns has the potential to identify markers linked to important traits. These markers could be used for marker-assisted selection to increase the efficiency of selecting for improved sugarcane genotypes for commercial release. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 1996.

Over-irrigation and poor internal drainage of soils in the Indus basin of Pakistan have resulted in waterlogging and salinity problems, severely affecting agriculture. These problems may be solved by subsurface drainage or more efficient irrigation water management. Since drainage system installation is relatively expensive Pakistan, efficient irrigation management practices e.g., irrigation scheduling and on-farm water management are cheaper alternatives. / A soil water simulation model, SWAP93, was used to evaluate the effects of water stress on crop yield, water use efficiency (WUE) and crop water use in sugarcane [Saccharum officinarum L.]. This information was used to determine water management practices, which can reduce salinity and waterlogging / Drainage fluxes and evapotranspiration simulated by the model were compared with those measured in drainage lysimeters (water tables controlled at 1.5 m and 2.25 m from the soil surface) for 1989 and 1990. Drainage fluxes were overestimated, and evapotranspiration underestimated. The model's original grass-based evapotranspiration (ET) was changed to an alfalfa-based one, resulting in a better estimation of drainage fluxes and ET. / The effects of soil water balance, simulated by the SWAP93, on the crop yield, WUE and crop water use were assessed using twelve irrigation treatments consisting of four irrigation amounts (1800, 1650, 1200 and 900 mm) factorially combined with three irrigation intervals (7, 10 and 15 days) for seven years of climatic data. / Crop yields increased linearly with irrigation of 1200 mm during the growing season, Crop yield, ET and WUE were not significantly different for irrigation amounts ranging from 1200 to 1800 mm. When the total applied water was above 1400 mm, the crop yield showed a plateau. This maximum yield was reached because irrigation water was remained in the soil profile or percolated into deeper layers at high levels of irrigation application. / For a 7-day irrigation interval, the 1200 mm treatment showed water deficits during the middle of the growing season, whereas for 10- or 15-day irrigation intervals, water deficits were negligible. / A 3rd degree polynomial relationship between cumulative irrigation amount and drainage fluxes was developed, allowing a daily estimation of irrigation amount for a given percolation or capillary rise. This relationship can be used to optimize irrigation amounts, and evaluate their impacts on percolation losses. / From the results of this simulation study, it was predicted that the 1200 mm---15 irrigation application treatment (15 day interval) was best for irrigation scheduling to reduce salinity and waterlogging.

Crop models have great potential as research tools, for crop system management and policy analysis. One of the most promising future uses of crop models is in crop improvement. The limitation in the use of models for crop improvement has been the inability of crop models to predict variety differences. Currently, the CANEGRO model, a sugarcane crop model developed the South African Sugar Association Experiment Station (Inman-Bamber, 1991a) can only model the performance of the NC0376 variety. Experiments were undertaken in the South East Lowveld of Zimbabwe, which is a hot and dry environment where sugarcane is grown under irrigation, to examine the canopy growth and development of four commercial varieties, ZN6, ZN7, N14 and NC0376. The study aimed at determining variety differences in canopy (tillers and leaves) development, develop parameters that can be used to model variety differences and test the improved CANEGRO canopy model for its ability to predict variety differences in canopy growth and development. For the late season, the numbers of leaves and tillers produced by each variety were counted every fortnight throughout the crop cycle. The total leaf area of the varieties and the individual leaf area on a stalk were determined using a Delta-T leaf area meter every fortnight. The date of emergence of successive leaves on a stalk was recorded daily. The leaf angles of each variety were measured every fortnight. The amount of photosynthetically active radiation (PAR) intercepted by the varieties was measured using a SunScan Ceptometer. Tillering and tiller senescence rates, phyllochron intervals, extinction coefficients and base temperatures were determined for the growth and development processes of varieties ZN6, ZN7, N14 and NC0376. Tiller and leaf population development was varietal. Tillering and leaf emergence were highly correlated to thermal time while tiller and leaf senescence were less correlated to thermal time. The poor correlation of the senescence phases to thermal time could mean that tiller and leaf senescence was driven by other factors other than thermal time. PAR interception could be one of these factors. The data showed that PAR interception could be a trigger of tiller senescence. The study showed that the tiller and leaf population development could be approximated by two linear equations. Tillering will be the first linear phase and tiller senescence the second linear phase. The first linear phase is driven by thermal time. While the second linear phase is triggered by PAR interception, the major driving factors need to be determined. This study proposed the use of two linear equations to model tiller and leaf population development as opposed to the polynomial equations used in the current CANEGRO model. Polynomial equations assume the factors driving tillering and tiller senescence are the same. The green leaf numbers per plant showed that all varieties experienced a decline in green leaf numbers with crop age. Varieties NC0376 and ZN7 had the greatest decline in green leaf numbers per plant while varieties N14 and ZN6 had the least decline. Variety ZN7 had the highest number of green leaves per plant while NC0376 had the least. The tiller growth and development was divided into three phases: the exponential phase during the initiation of stalks, the first linear phase during a period of rapid stalk elongation and the second linear phase during sucrose accumulation and maturation. The first two phases of development were driven by thermal time while the sucrose accumulation was not. There were variety differences in tiller growth and development. There were variety differences in base temperature for the development of various components of the canopy. Internode formation occurred at lower air temperatures than stalk elongation and tillering while canopy heights were correlated with higher air temperatures. This implies that internode formation could occur under conditions unsuitable for stalk elongation and may explain the short internodes frequently observed in stalks exposed to winter during rapid stalk elongation. The basic requirements for physiological parameters are that they should be stable across different environments, have significant differences between varieties and have physiological meaning. The parameters studied were thermal time requirement for shoot emergence, leaf appearance, to reach peak tiller population and to start of stalk elongation; surface area of the youngest biggest leaf, leaf number of the youngest biggest leaf, PAR transmission at the start of tiller senescence, extinction coefficients, and peak and mature tiller population. The difference between varieties in thermal time to shoot emergence was least using a base temperature of 16 QC compared to using 10 QC and therefore 16 QC could be a more appropriate base temperature for shoot emergence. The accumulated soil temperatures were less variable than accumulated air temperature and could therefore be a more reliable driver of shoot emergence. However, the limitations in the use of soil temperature are that it is not a readily available measurement and that it is not easy to measure. The gradual increase in phyllochron intervals appeared to be a better method of predicting leaf appearance compared to using a broken stick model. The phyllochron gradient was proposed, as it is likely to be a more robust way of modelling leaf appearance. The varieties had different phyllochron gradients. Variety ZN7 had highest rate of leaf appearance and produced the highest number of leaves per stalk while NC0376 had the lowest rate and produced the least number of leaves. There were statistically significant differences between varieties (P = 0,05) in PAR transmission at the start of tiller senescence and a base temperature of 16 QC was best at determining accumulated thermal time to the start of tiller senescence. Varieties with higher peak tiller population had higher final tiller population, lower thermal time per tiller and a higher ratio of final to peak tiller population. There were differences between varieties in the youngest leaf number attaining maximum leaf area and the leaf area of the youngest biggest leaf. Variety Nl4 had the biggest leaves and NC0376 had the smallest. Variety Nl4 had the highest leaf area index (LAI) while ZN7 had the lowest. There were significant differences (P = 0,01) in PAR intercepted by the varieties but there were no significant differences in extinction coefficients. Extinction coefficients increased with crop age. The varieties had significantly different (P = 0,01) leaf angles and ellipsoidal leaf angle distribution parameters. The measurement of LAI using SunScan ceptometer provided a better estimate of extinction coefficients than LAI measured using Delta-T leaf area meter. Model evaluation showed that CANEGRO canopy model version 2 was improved compared to than version 1. The model (version 2) was accurate in predicting tiller heights and dead leaf numbers per stalk. It was fairly accurate in predicting green leaf numbers per plant, stalk population and intercepted PAR but was poor in predicting LA!. Version 2 has proved to be a substantial improvement over version 1 in predicting stalk population. Generally, the version 2 model overestimated tiller heights early and underestimated later, overestimated the tiller population and LAI after peak, underestimated green leaf numbers per stalk for varieties ZN6, ZN7 and N14 and overestimated dead leaf numbers per stalk and intercepted PAR. The version 2 model predicted a constant green leaf numbers per plant and LAI from peak to harvest while observed data showed that green leaf numbers per stalk and LAI decreased towards harvest. Version 2 model predicted the tiller population of NC0376 closely but underestimated tiller senescence in N14 and also underestimated final tiller population in varieties ZN6 and ZN7. Future model refinements may need to focus on the prediction of the sigmoid pattern of tiller heights. The model may need to be calibrated to predict the green leaf numbers per stalk accurately, which should possibly improve the prediction of LAI that in turn could improve the prediction of intercepted PAR. The improvement in the timing and rate of tiller senescence should improve the prediction of tiller population particularly in varieties ZN6, ZN7 and N14. The study showed that the broken stick method IS superior in explaining leaf and tiller population development compared to using polynomial equations. The development of variety parameters helped improve the prediction of variety differences in canopy growth and development. A major weakness of most crop models is modelling variety differences in canopy growth and development. The inability of crop models to predict variety differences has limited their use in plant breeding. This study has resulted in an improved version of CANEGRO version 1 that is an initial attempt at modelling variety differences of sugarcane. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2003.

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