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MSc and PhD Bursary Research Programme (2015) SOUTH AFRICAN SUGARCANE RESEARCH INSTITUTE The Institute As primary provider of agro-technical expertise to the South African sugar industry, the South African Sugarcane Research Institute (SASRI) delivers diverse research and development (R&D) outcomes to the industry, including: (a) pertinent and robust agricultural solutions, products and services; (b) novel and improved in-house technologies to enhance the scope and quality of service provision; and (c) innovations to support industry strategic initiatives, particularly those pertaining to sustainability. To support and promote innovation in these key R&D areas, SASRI hosts a dynamic post-graduate student and post-doctoral researcher programme in conjunction with several leading South African universities, including the University of KwaZulu-Natal, University of Pretoria, University of the Free State and Stellenbosch University. Information for 2015 Post-graduate Students Opportunity Discipline Reference Project Title Project Description MSc Plant 00VI01A Breeding Family selection for sugarcane yield and determination of selection Family selection provides the potential to improve gains for quantitative traits such as cane yield at early selection stages. Families can be replicated while individual genotypes cannot because of limited planting material as well as the large numbers involved at early stages. With family selection, superior clones will only be selected from the elite families where a greater chance of identifying superior genotypes exists. The data used for family selection can also be used to evaluate and identify superior parents for use in future crossing. Therefore, a greater understanding of the potential of family selection is important for unlocking the potential gains that can be achieved the early stages. The objectives of this study is to determine family effects and family gains for yield and quality traits, compare family and individual selection parameters, and evaluate effectiveness of parent evaluation among Midlands breeding programmes. MSc Plant 00VI01B Breeding Evaluating genotype by environmental interaction and its implications for the coastal short cycle regional programmes Genotype by environment interaction (GxE) is known to significantly influence variety development by confounding genetic values in trials. When GxE influence is known, it can be used to increase the efficiency of identifying superior genotypes for specific environments. GxE defines the expression of traits in different environments such as soil types, agroclimatic conditions and crop management as represented by trial sites. The coastal short cycle high yield potential is based at the SASRI Empangeni Research Station and the average yield potential is based at SASRI Gingindlovu Research Station. The advanced genotypes from these programmes are combined in advanced variety trials. The objectives of this study is to determine the existence and magnitudes of genotype by environment interaction, to evaluate the impact of combining genotypes from these programmes in the final stage testing, evaluate realised gains over time and determine potential strategies for optimising these programs to enhance the identification of superior genotypes. Competitive bursaries and on-site accommodation in student residences. Further information on the South African sugar industry, the South African Sugar Association and the SASRI R&D programme is available at www.sasa.org.za. South African Sugarcane Research Institute is a division of the South African Sugar Association Opportunity Discipline Reference Project Title Project Description PhD Plant Genetics/ Plant molecular biology 12VI06 Reassembly, annota- The aim of this project is to conduct phylogenomic analyses amongst Saccharum and related species based on whole chloroplast genomes. Specific objectives are: tion and phylogeny of •To assemble 42 chloroplast genomes sequenced by SASRI by mapping to an in-house assembled reference. Saccharum and related •To annotate by remapping the assembled chloroplast. species. •To identify and download eight whole genome sequences (three sugarcane varieties and five outgroups) from the NCBI database. •To conduct de novo assembly and annotation of chloroplast sequences from NCBI datasets. •To perform phylogenomic analyses on all the assembled chloroplast genomes. •To compare the benefit and accuracy of assembling whole genome vs isolated chloroplast sequence data. •To create chloroplast region barcode to identify minimum number of regions required to phylogenetically discriminate species and varieties. Skills Required: Knowledge of plant genetics, basic programming (Python, Perl), prior exposure to a Unix computing environment, basic knowledge of bioinformatics applications (BLAST, PHYLIP) MSc Plant Molecular Pathology/ Biology 14VI03 Mutation breeding for eldana resistance MSc Entomology 14CP06A Screening and development of entomopathogens as bio-insecticides for South African white grub species infesting sugarcane. White grubs (Coleoptera: Scarabaeidae) are species with one and two year life cycles. Their adults emerge and fly only in spring and early summer. The project is based in the KwaZulu-Natal Midlands sugarcane growing area and the successful student will be based at the Pietermaritzburg Campus of the University of KwaZulu-Natal. The project has four objectives: •To determine species composition of insect adults attracted to light traps set up for adult white grub trapping and monitoring; •To develop species specific lures (different light types, plant volatiles and /or sex pheromones), to use in traps designed to trap white grub adults; •To develop a species specific walk through trap to infect adult white grub species with a virulent Beauveria brongniartii formulation; •To follow transmission of the isolate from adults infected in walk through traps, to adults they mate with to soils where infected adults die. The project will run in conjunction with the field registration of the B. brongniartii isolate against white grub larvae project, and will thus involve working with a team of dedicated researchers. MSc Entomology 14CP06B Screening and development of entomopathogens as bio-insecticides for South African white grub species infesting sugarcane. A virulent isolate of Beauveria brongniartii causes epizootics in two white grub (Coleoptera: Scarabaeidae) species found in the KwaZulu-Natal Midlands North sugarcane growing area, and shows promise as a biological insecticide. In order to register this isolate as a product, it has to be tested in replicated field trials in this region. The successful student will be based at the Pietermaritzburg Campus of the University of KwaZulu-Natal. White grub species have life cycles of at least a year, thus the project could last for four years and has the following objectives (Objectives 1 and 2 apply to the first two years of the research): •To determine the most appropriate application technology for field trials •To test the infectivity of this isolate in laboratory bioassays against larvae and adults of other white grub species occurring in South African sugarcane to broaden the host range of the isolate, thus increasing its marketability. •To determine the most appropriate time to apply the formulation (spring, summer, autumn) •To submit results of the trials to the registrar for product registration. The project will be run in conjunction with the walk through trap development project, and will involve working with a team of dedicated researchers. The sugarcane stem borer Eldana saccharina is the single biggest constraint on production in South Africa causing an estimated R 900 million loss per annum. Associated with the borer are Fusarium fungal infections which are of benefit to the insect by improving its nutrition, and by suppressing the plants jasmonate induced defence mechanisms. The aim of this project is to generate sugarcane mutants which are resistant to defence suppressing Fusarium mycotoxins. Additionally the possibility of fixing a desirable epigenetic resistant state (priming) will be explored in vitro using cis-jasmone. Potential resistance will be induced through in vitro generation of epigenetic (primed) variation using a DNA methylation inhibitor plus cis-jasmone. An established sugarcane micro-propagation protocol will be used to screen for resistance to mycotoxins. Regenerated plants will be characterised for resistance in bioassays. Steps will be taken towards identifying changes in epigenetic DNA methylation and gene expression using molecular methodology. Expressions of Interest and Closing Date Interested prospective MSc and PhD students are invited to submit expressions of interest and full curriculum vitae for the several research opportunities that will be available from 2015 at the SASRI Mount Edgecombe campus in KwaZuluNatal. Applications are to be made via our online job portal accessible from our website at www.sasa.org.za (navigate to Careers @ SASA - Vacancies). Closing date is 17 November 2014. Please quote the Reference given in the table of opportunities for each study opportunity.