Identification of epigenetic mechanisms controlling gene expression in double haploid Brassica.

随着全球变暖和气候变化的影响变得更加严重，人们对这些问题对全球粮食安全和生境保护的影响的担忧大大增加。因此，提高植物育种技术的效率至关重要。基因组学的最新发现使得更有效的育种策略的发展成为可能，从而导致新品种的开发和改进。然而，直到最近，在植物育种计划中使用遗传和表观遗传技术一直严重不足。先前的研究为芸苔属双单倍体中控制基因表达的遗传和表观遗传机制提供了很好的见解。虽然双单倍体中的基因表达动态可能是由DNA甲基化的变化引起的，但精确的分子机制仍然未知。我的博士项目将专注于确定控制双单倍体基因表达的机制，并确定它们对理想性状稳定性的贡献。为了实现这一目标，我将首先使用染色体构象捕获来识别双单倍体基因组中染色质空间组织的变化。这种分析将使我能够建立预测模型，解释近端和远端基因座之间的相互作用。为了确定这些相互作用的重要性，我将使用ChIP-seq来量化这些相互作用在染色质景观中的重要性，并最终在基因调控中。总的来说，这些目标将提供双单倍体育种对染色质相互作用和表型性状稳定性的影响的第一个观点。这些知识也将为染色体合并在基因组调控中的作用提供更深入的了解，并有助于开发更有效的植物育种计划。

With the effects of global warming and climate change becoming much more severe, fears of the effects of these issues on global food security and habitat conservation have greatly increased. As a result, it is of vital importance to improve the efficiency of plant breeding techniques. Recent discoveries in genomics have allowed for the development of more efficient breeding strategies leading to the development and improvement of new cultivars. However, until recently the use of genetic and epigenetic techniques in plant breeding programs has been critically under used. A previous study provided great insights into the genetic and epigenetic mechanisms controlling gene expression in Brassica double haploids. While gene expression dynamics in double haploids may be caused by changes in DNA methylation, the precise molecular mechanisms remain unknown. My PhD project will focus on identifying the mechanism(s) that control gene expression in double haploids and determine their contribution on the stability of desirable traits. To address this aim, I will first use chromosome conformation capture to identify changes in the spatial organisation of chromatin in double haploid genomes. This analysis will allow me to build predictive models that may explain the interactions between proximal and distal genomic loci. To determine the significance of these interactions, I will use ChIP-seq to quantify the significance of these interactions the chromatin landscape and ultimately in gene regulation. Collectively, these objectives will provide a first view of the impact of double haploid breeding on chromatin interactions and the stability of phenotypic traits. This knowledge will also provide a deeper insight into the effects of chromosome mergers in genome regulation and aid the development of more efficient breeding programmes in plants.