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    Development of a SNP validation toolset for wheat

    Kong, Hoi Yee
    Abstract
    Recent advances in high-throughput technologies and the corresponding growth of the bioinformatics databases, a lot of bioinformatics tools have been constantly developed and published in journals for data-intensive genetic analysis. However, repoducibility has been one of the biggest challenges in delivering bioinformatics. Virtualisation is one of the most commonly used solutions by creating virtualised and isolated environments for running different bioinformatics tools. Containerisation, however, is a more recent, promising, scalable and reproducible approach for delivering bioinformatics. It allows running bioinformatics tools on preconfigured containerised environments, which is lightweight and can be easily updated and shared between researchers. This dissertation has evaluated a bioinformatics toolkit previously developed for genetic marker design in preconfigured containers. The objectives for this dissertation were (1) to improve marker design software to correctly handle melt prediction of amplicons with multiple SNPs, (2) using containerised environments to design and screen PCR assay to (a) validate candidate SNPs detected by GBS of barley H. bulbosum introgression line, (b) validate QTL markers of wheat identified by GWAS on chromosome 1A, and (c) convert SNPs from 90K SNP chip for the bread wheat A genome to HRM markers.... [Show full abstract]
    Keywords
    bioinformatics; high throughput sequencing analysis; reproducibility; virtualisation; single nucleotide polymorphism; marker assisted selection; cleaved amplified polymorphic sequence (CAPS); high resolution melting; wheat; containerisation
    Fields of Research
    080204 Mathematical Software; 060705 Plant Physiology; 070103 Agricultural Production Systems Simulation
    Date
    2015
    Type
    Dissertation
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    • Dissertations [445]
    • Department of Wine, Food and Molecular Biosciences [630]
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