Development of a SNP validation toolset for wheat

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.