Chromatin and recombination landscapes in the hexaploid wheat genome.

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Meiotic recombination creates genetic diversity in the progeny of sexually reproducing species.For example, reciprocal exchange between homologous chromosomes (known as crossover)creates novel combinations of genetic variation. The variation-generating processes actingduring meiosis remain a major tool for crop improvement, whereby useful characteristics fromdifferent backgrounds can be combined.Bread wheat is a major crop in the UK and globally, where meiotic recombination duringbreeding remains an essential tool for variety improvement. However, the wheat genome isextremely large (17 gigabases) and shows highly skewed recombination distributions, with mostcrossovers occurring in the distal regions of the chromosomes. This severely limits the ability ofbreeders to utilise variation located in the central regions of the chromosomes. Therefore,developing tools and technologies to control recombination in wheat has direct relevance forfood security.In this project the student will use chromatin immunoprecipitation (ChIP) followed by highthroughput sequencing to profile the distribution of euchromatic and heterochromatic chromatinmodifications throughout the wheat genome. These distributions will be related to highresolutiongenetic maps generated by KWS and genotypes that differ in their genetic maplengths. These experiments will be conducted in backgrounds of interest to KWS and thestudent will identify chromatin patterns that correlate with altered frequencies and patterns ofrecombination. The recent public release of a high quality reference genome assembly for wheatmakes this project feasible and timely.New reverse genetic resources (e.g. TILLING, CRISPR-Cas9) are available that allow genes ofinterest to be disrupted in bread wheat. To functionally investigate the role of chromatin onrecombination the student will isolate mutations in epigenetic regulators. These mutants will beprofiled using ChIP-seq in order to characterise how chromatin is altered genome-wide. Finally,these mutants will be used to measure effects on number and distribution of recombinationevents during meiosis.This project will provide the student with advanced training in wheat genetics and genomics.They will generate data of basic importance for understanding wheat genome function andevolution. They will gain experience in wheat genetics relevant to both academic and industrialscientific contexts.