Theses

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Included in the Research Theses collection are Masters, PHD and Professional Doctorate theses.
Masters and PHDs by coursework theses are included in the Honours and Coursework Theses collection. Some schools may choose to include Honours theses which make a significant contribution to knowledge.
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Browsing Theses by Advisors "Able, Jason"

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    Genome-wide characterisation of microRNAs and their target genes in different durum wheat genotypes under water limiting conditions
    (2016) Liu, Haipei; Able, Jason; Able, Amanda; Searle, Iain; Mather, Diane; School of Agriculture, Food and Wine
    Durum wheat (Triticum turgidum L. ssp. durum) is a tetraploid wheat species grown primarily in the North American Great Plains, Mediterranean Europe, Northern Africa, Mexico and Australia. An important limiting factor for durum production in Mediterranean environments like South Australia is water deficit immediately prior to and during anthesis, adversely affecting durum productivity and quality. Investigating water deficit response mechanisms and genotypic differences within a crop species is an important strategy for understanding the basis of water-deficit stress response and for selection of elite genotypes with improved stress tolerance. In plants, microRNAs (miRNAs), which are a class of small non coding RNAs, have been identified as important regulators of plant development and abiotic stress responses. While the miRNA transcriptome under water limiting conditions has been investigated in many crop species, it is poorly characterised in durum wheat. In this study, glasshouse experiments over two years evaluated 20 durum wheat genotypes for their variation in various morphological, physiological and yield responses to pre-anthesis water-deficit stress. Four Australian durum varieties with contrasting stress sensitivities were identified. High-throughput Illumina sequencing of 96 small RNA libraries constructed from the flag leaf and head tissues of these four genotypes detected 110 conserved miRNAs and 159 novel candidate miRNA hairpins. Statistical analysis of sequencing reads revealed the differential expression profiles of durum miRNAs associated with water-deficit stress treatment, tissue type and genotype. Most importantly, several conserved and novel miRNAs showed inverted regulatory profiles between the stress tolerant and sensitive varieties. Subsequent genome-wide in silico analysis identified 2055 putative targets for conserved durum miRNAs, and 131 targets for four novel durum miRNAs possibly contributing to genotypic stress tolerance. Predicted mRNA targets of the stress responsive miRNAs encode various transcription factors, binding proteins, and functional enzymes, which play vital roles in multiple biological pathways such as hormone signalling and metabolic processes, suggesting the extensive involvement of miRNA-target regulatory modules in water-deficit stress adaptation. Quantitative PCR profiling further characterised 50 target genes and 12 miRNAs with stress responsive and/or genotype-dependent expression profiles. A 5′ RLM-RACE approach subsequently validated the regulation of nine targets by water-deficit stress responsive miRNAs, providing the first experimental evidence that target mRNAs are genuinely cleaved by miRNAs in durum wheat. Characterisation of the individual miR160/Auxin Response Factors regulatory module further revealed their expression profile over different time points during water-deficit stress. The present study provides a comprehensive and comparative description of the miRNA transcriptome and their targets in durum wheat varieties with contrasting waterdeficit stress tolerance, providing new insights into the functional roles of miRNA-guided RNAi mechanisms. Results derived from this work could contribute to future research on the characterisation of individual miRNA regulatory modules and their specific biological functions, exploiting the potential of Triticum turgidum miRNA in developing RNAiimproved crops with stress tolerance.
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    ItemOpen Access
    Improving the Adaptation of Wheat (Triticum aestivum) to Heat Stress Conditions
    (2022) Telfer, Paul Robert; Kuchel, Haydn; Able, Jason; Edwards, James; School of Agriculture, Food and Wine
    Heat stress is a significant abiotic stress limiting crop production in many regions globally, including in the Mediterranean-type environments of southern Australia. Various approaches have been used to understand the negative impacts of heat stress conditions on plant function and crop productivity, with several loci identified with proposed benefits for adaptation to heat stress conditions. However, there has been little uptake of targeted selection for heat stress traits or loci by breeding programs. This study used a combination of controlled environment evaluation targeting heat stress conditions during grain filling (three consecutive days of 36°C with a wind speed of 40 km h-1 starting 10 days post anthesis), and evaluation over multiple representative field environments. Field environments were targeted to achieve a range of heat stress conditions during the sensitive anthesis and grain filling developmental stages and were conducted within the South Australian cereal producing region, with temperature co-variates used to quantify the level of stress in each environment. A series of experiments evaluated relevant Australian varieties and advanced breeding lines to evaluate the level of adaptation to heat stress conditions currently available in adapted germplasm. This allowed the impacts of heat stress on grain yield, and the role of heat stress during anthesis and grain filling on variety performance to be evaluated. In a second component of the study, seven doubled haploid mapping populations were evaluated to identify QTL for adaptation to heat stress conditions. The QTL analysis was conducted to identify performance (QTL with stable performance regardless of heat stress treatment, or across a range of stress conditions in the field), and to identify responsiveness (QTL with a favourable response to heat stress treatments in a controlled environment, or a favourable response to increasingly stressful conditions experienced in the field), with numerous QTL identified in both controlled environment and field conditions. The QTL identified provides opportunities for breeders to target improved adaptation to heat stress conditions through two mechanisms: performance QTL for stable and elite adaptation across all environments, and responsiveness for specific adaptation allowing selection of a favourable response to stressed conditions. This study proposes that assessing adaptation to heat stress conditions as the combination of performance and responsiveness is an improved definition and framework to assess tolerance to heat stress conditions, and is of greater relevance to breeders’ selection objectives.