School of BioSciences - Theses
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ItemThe influence of circadian clock variation on local adaptation in Arabidopsis and agronomic traits in wheat( 2023-11)Plants have evolved diverse mechanisms to cope with changes in their environment. Among the most important of these, the plant circadian clock adjusts physiology and development in response to daily and seasonal environmental rhythms. The cues perceived by plant circadian clocks are non-uniform across the biogeographical environment, and variation of circadian function is required between and within species. The overarching aim of this thesis was to identify how this functional clock variation arises in plants. Extant phenotypic variation in circadian rhythms across a naturally occurring species, Arabidopsis thaliana, and a cultivated species, bread wheat (Triticum aestivum), was quantified and compared. The respective contributions of this variation to local adaptation in Arabidopsis and agronomic traits in wheat were rigorously assessed. In Chapter 2, a transient luciferase imaging assay was used to measure circadian rhythms of 287 natural Arabidopsis accessions. Through genome-wide association mapping, three SNPs were identified in the evening-expressed clock gene EARLY FLOWERING 3 (ELF3) that were highly associated with variation in circadian period. Accessions harbouring these SNPs primarily occupy continental climates of Eastern Europe and Central Asia, and through physiological and population genetic analyses, evidence is provided that ELF3 has aided local adaptation to highly seasonal climates. The circadian rhythms of elite Australian wheat cultivars were measured using delayed leaf fluorescence in Chapter 3, and a large range in circadian period was detected. By leveraging existing and novel clock gene markers, specific combinations of clock gene alleles (chronotypes) were defined that are associated with circadian period. To test the importance of circadian rhythm variation to agricultural traits, the timing of leaf senescence and grain nutrition traits were measured across the same cultivars, and strong associations with circadian period were observed. A specific effect on timing of senescence and grain protein content was found for a widespread deletion in TaELF3-D1 using pairs of near-isogenic lines (NILs). To define the global transcriptional response of circadian rhythms to senescence, in Chapter 4 48-hour ‘circadian transcriptomes’ were generated in both mature and senescent flag leaves. This analysis revealed that the output of the clock expands and diversifies at senescence, and this response is associated with increasing rhythmicity of WRKY transcription factor expression. The average circadian period of transcripts shortens by 0.5 h in senescent tissue, akin to previous studies of circadian rhythms during ageing. Interestingly, the pace of circadian oscillator genes is largely unchanged. Instead, clock genes are enriched amongst transcripts that exhibit significant advancement of phase, which is perhaps a driver of the changing period of global gene expression. These findings demonstrate abundant phenotypic variation in the circadian clocks of naturally occurring and domesticated plant species. This variation is not only consequential for traits related to seasonal development (e.g. flowering or senescence); it can also have pleiotropic effects on traits like response to high temperature and nutrient use efficiency. Clock gene variation has been co-opted by the forces of natural and artificial selection and thus holds promise for the finetuning of agricultural traits in future changing environmental conditions.