Identification of transcripts regulated by wheat circadian clock genes.

The fundamental role of the plant circadian clock (CC) is to optimize cellular processes with respect to external conditions. The number of genes for core CC regulators in plants is limited and seven single/low copy genes are known in wheat. We are using an integrative approach of accelerated evolution through genome editing and conventional breeding to modulate the CC by focusing on three core CC genes: LHY/CCA1, PRR5/95 and TOC1/PRR9 to improve wheat resilience to changing climatic conditions. These genes have an essential role in photoperiodic sensitivity and are also involved in plant development and regulatory processes, including nitrogen and phosphate accumulation (LHY), CO2 fixation and biomass yield (LHY), regulation of flowering (LHY, PRR55 and TOC1), abiotic stress response such as drought and cold (PRR5 and TOC1). Most genes displaying circadian rhythms are controlled by the core CC regulators. We have used qPCR and RNA-Seq to assess the oscillation of these core CC genes over a 24 h period. Our results on maximum expression confirm in silico analyses and annotation that LHY, PRR5 and TOC1 peak in the morning, midday and evening, respectively. Cluster analyses of RNA-Seq results have revealed which transcripts from hexaploid bread wheat are regulated in a similar fashion to the three CC regulators. Gene ontology of the differentially expressed sequences reveals clues to what metabolism is at play and how expression level of these three CC core genes influence different metabolic pathways. We have gained insights into which metabolic pathways are affected and this will help guide our genome editing efforts. Targeting of the three CC core genes in which all three homeoelogous sequences have been identified provides a means towards improving wheat resilience in a changing climate while at the same time maintaining productivity.