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.
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ItemThe effect of sub-optimal temperature on the cellular metabolism of wheat and Arabidopsis thaliana( 2020)Low or suboptimal temperature stress is one of the primary abiotic conditions limiting the growth and productivity of economic crops in many regions of the world. Wheat is one of the major crops in Australia, it is grown during winter to avoid hot summers and they flower in early spring. The sensitive flowering stage of wheat is therefore frequently exposed to spring frost. In Australia, the frequency of spring frosts during the flowering stage has increased significantly since 1960, and the reoccurrence of frost events led to an estimated $360 million of losses in the Australian wheat industry per annum. It is therefore important for breeders to minimize the loss via the development of more chilling/frost-tolerant wheat varieties, especially during their reproductive stages. Two approaches could be employed to achieve this goal. The first one is by employing metabolomics approaches to understand the underlying molecular mechanisms involved in cold responses of wheat upon cold stress. The second approach is via bioengineering of cold responsive genes into wheat to create chilling/frost-tolerant varieties. With this in mind, my PhD study was carried out with three main objectives. The first objective was to investigate and understand metabolic traits involved in the cold acclimation of two Australian wheat varieties with contrasting cold tolerance using targeted metabolomics and lipidomics approaches. The cold-sensitive variety used in this study was Wyalkatchem and the cold tolerant variety used was Young. The second objective of this study was to identify potential metabolite and lipid responsible for chilling tolerance in the two studied wheat varieties. The third objective was to evaluate the potential of REIL (Required for isotropic bud growth1 – like) protein as cold acclimation factor in Arabidopsis thaliana for potentially enhancing wheat cold tolerance. Chapter 1 consists of a review of the recent literature covering cold stress responses (physiologically and metabolically) of plants and how plants adopt to cold stress. It describes how metabolomics and lipidomics can be used as promising tools to decipher cold stress responses in wheat and discuss the role of cold-induced genes to increase cold tolerance in plants. The targeted protein in this study, REIL, as a new potential cold acclimation factor in Arabidopsis thaliana and wheat is also reviewed. To achieve the first and second objectives of this study, work described in Chapter 2 was conducted to investigate the cold acclimation of two Australian wheat varieties with contrasting cold tolerance using targeted metabolomics and lipidomics approaches. The selected cold-sensitive spring wheat variety used in this study was Wyalkatchem and the selected cold-tolerant spring wheat variety was Young. Samples of flag leaves and spikes at the young microspore stage were collected and analysed in this study. The results obtained provide us with a better understanding of the cold responses of wheat, and pointed out the potential of several sugars, amino acids, amines and glycerolipids to confer cold-tolerance to the Young variety. The outcomes gained from this study have been published in Cheong et al., (2019) for the study on flag leaves, and in Cheong et al., (2020) for the study on spikes. The outcomes also pointed out the profound potential of lipid species as biomarkers that can be explored to distinguish the two varieties. This further motivated us to expand the lipidomics study on the underground part of wheat, the roots (Chapter 3). There are limited cold stress studies on the lipidome of whole roots and to the best of our knowledge, no data are available on responses of specific root developmental zones. In Chapter 3, the lipid profiles of the spatial root zones derived from young seedlings of Wyalkatchem and Young grown at optimal, chilling and freezing temperatures were investigated. The outcomes indicate the involvement of not only glycerolipids in discriminating Young from Wyalkatchem, but sphingolipids are also involved in conferring cold-tolerance of Young. Next, to fulfil the third objective of this study, REIL, a protein that has been postulated to act as a potential cold acclimation factor in the mature leaves of Arabidopsis thaliana, was evaluated in roots in Chapter 4, followed by the evaluation of its potential in wheat in Chapter 5. REIL proteins have been postulated to be involved in late ribosomal biogenesis and affect the accumulation of 60S large subunits in the mature leaves of A. thaliana upon cold stress. To validate these roles in A. thaliana, a systematic analysis of roots grown at optimized and cold temperatures was conducted in Chapter 4. The outcomes substantiate the role of REIL proteins as a cold acclimation factor in Arabidopsis by being involved in ribosomal biogenesis during cold acclimation. In Chapter 5, three REIL homologs are found to be expressed in wheat. Evaluation of the REIL expressions in wheat subjected to cold stress through the re-analyses of published transcriptomics datasets show the potential cold and heat responsiveness of REILs. A real-time PCR analysis was then performed to evaluate the REIL expressions in Wyalkatchem and Young under cold stress, but no significant changes of expressions were observed in both varieties upon cold stress. It is then yet-to-be-known whether the cold acclimation function of REIL is conserved among dicots (A. thaliana) and monocots (wheat). Therefore, more in-depth investigation such as overexpression or silencing of the REIL expression in Australian spring wheat varieties is needed. The last chapter of this thesis (Chapter 6) summarizes the key results from each research chapter (Chapter 2 to 5) and also discusses the future directions and perspectives.