Making genotyping cheaper and easier

背景捕捉任何给定物种的全部遗传变异的机会是至关重要的，因为这可以对个体进行准确的分类，并更准确地将因果变异与表型联系起来。现在有太多的工具和技术可以对变异类型进行差异分析，从单核苷酸多态到DNA碱基修饰。挑战在于开发更易于执行和分析的方法。目标本专业将致力于开发实验室和生物信息学技术，利用各种具有农学重要性的生物模型来捕捉遗传变异的全谱，这些生物模型需要开发专门的测试来研究非标准的遗传修饰。方法研究工作将被分成最多四个工作包(WPS)，每个工作包都有明确的交付内容。这些可能包括：WP1：SNP小组构建-努力找出一种使用单分子测序进行SNP评估的低成本方法WP2：EPI-使用单分子测序进行等位基因鉴定-使用脆壁疫霉作为表观变异的模型WP3：结构变异跟踪-使用特殊镰刀菌结构重排来识别动态基因组重排WP4：K-mer和基于签名的鉴定-使用单分子测序跟踪等位基因变异的无参考方法。这项工作的研究成果将有助于开发可用于育种、品种鉴定和分子诊断的新的基因分型技术。

BackgroundThe opportunity to capture the full spectrum of genetic variants in any given species is crucial, as this allows accurate classification of individuals and the more accurate linkage of causal variants to phenotypes. There are now a plethora of tools and techniques that allow differential profiling of variant types, from single nucleotide polymorphisms, to DNA base modifications. The challenge is to develop approaches that are easier to execute and analyse. ObjectivesThis studentship will aim to develop both laboratory and bioinformatics techniques to capture the full spectrum of genetic variants using a variety of biological models with modifications of agronomic importance that require the development of specific tests to study non-standard genetic modifications. ApproachesThe research work will be divided into upto four workpackages (WPs), each with clear deliverables. These may include:WP1: SNP panel construction- work to identify a low cost method for SNP evaluation using single molecule sequencing WP2: Epi-allele identification using single molecule sequencing- using Phytophthora fragariae as a model of epiallelic variationWP3: Structural variant tracking- using Fusarium formae specialis structural rearrangements to identify dynamic genomic rearrangementsWP4: k-mer and signature based identification- reference free approaches of tracking allelic variation using single molecule sequencing. Benefit to the industryThe research outcome from this work will enable the development of novel genotyping technologies that can be used in breeding, varietal characterization and molecular diagnostics.