The circadian clock is an endogenous timing mechanism which acts to synchronise internal processes with daily and seasonal cycles in light and temperature. In Arabidopsis, the components which comprise the circadian oscillator and output pathways are well defined. Photoperiod dependent flowering, metabolism, growth and defence signalling networks receive information regarding the timing of the day/night cycle from the circadian clock. Many circadian output pathways are targets for crop improvement, with variation at circadian loci selected for during domestication and breeding. Investigations into how the circadian clock controls agronomically important traits may identify novel targets for breeders looking to create new elite wheat cultivars. The first aim of this thesis was to identify naturally occurring variation in circadian clock genes across wheat cultivars important in modern breeding efforts. In Arabidopsis, LUX ARRYTHMO (LUX) and EARLY FLOWERING 3 (ELF3) are circadian clock genes which are co- expressed at dusk, forming a transcriptional repressor complex which restricts the expression of day phased circadian clock genes. Deletions, which may result in a null allele, were identified in LUX along with presence absence variation (PAV) for ELF3 across different wheat cultivars. Sequence analysis of ELF3 and LUX promoter regions identified enrichment of motifs associated with morning and evening phased expression respectively, supporting previous studies which indicate that the phasing of LUX and ELF3 expression is not conserved between Arabidopsis and wheat. I present further tools to investigate the diel turnover of LUX and ELF3 proteins. The second aim of this thesis was to study the effect of perturbation to the circadian clock on circadian output pathways. Predicted loss of function of the circadian clock gene GIGANTEA (TtGIab) results in circadian arrythmia in chlorophyll fluorescence parameters and late flowering in long and short day controlled environment conditions. No differences in flowering time were observed in the field. Perturbation to the circadian clock through loss of functional ELF3 (TtELF3ab) and TtGIab resulted in mismanagement of diel carbohydrate turnover. The implications for growth and biomass accumulation are discussed. This thesis demonstrates that the wheat flowering and carbohydrate turnover pathways are controlled by the circadian clock. Utilising variation at circadian loci may provide novel targets for breeders looking to manipulate these systems for improved crop performance.