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

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.