Background

The chloroplast/plastid and the mitochondrion are the two major organelles in plant cells. These organelles co-operate to direct plant cell energy capture and storage of this energy in the form of sugars, starch, oils, protein and fibre - all of which are major agricultural products.

The metabolism of plant organelles underlies the growth and performance of a plant, including its ability to withstand environmental stresses. The Centre has previously shown that chloroplasts and mitochondria are environmental sensors that control growth. Environmental variables such as light, temperature, water and nutrient availability all interact with plant energy systems via signalling processes.

The complex and ancient ways in which organelle function and efficiency are influenced and respond to the environment form the foundation of how plants control conversion of energy to functionally useful forms.

Program aim

Maximise the efficiency of energy organelles by modelling the efficiency of metabolic strategies in plants, altering the biogenesis of energy organelles and co-opting the signalling processes that control the activity of energy organelles during environmental challenges and recovery.

• Modelling energy processes under varied conditions to choose optimal energy efficiency strategies.

  Choosing optimal energy efficiency strategies requires a holistic understanding of the costs of building and maintaining cellular machinery and metabolism, which in turn has required the development of integrative models at scales from single cells to whole plants and ecosystems. Examples of application of these models are the simulation and exploration of the genetic basis and metabolic consequences of hybrid vigour, and the examination of temperature responses of leaf energy metabolism over a range of spatial and temporal scales.

  Data for these models comes from measurements of respiration rates and energy costs associated with the major energy-consuming processes in plants, notably synthesis of proteins and cell wall components and transport processes including ion pumps and nutrient assimilation.

• Modifying energy organelle number, quality and function to improve energy processes in variable environments.

  The Centre has made great strides in understanding biogenesis of mitochondria and plastids, particularly in the coordination of organellar and nuclear gene expression. PEB is now using our understanding of the ‘switches’ that control energy organelle biogenesis and function to change metabolic outcomes in plant cells, through collaborative research with our partners.

  Combined with a number of established resources, including plant lines with altered organelle biogenesis and growth characteristics, this provides novel opportunities to measure and modify cellular costs and identify new signals of interest.

• Using the receptors and transducers of organelle signals to integrate changes across whole plants.

  PEB is using signal-protein bait/prey strategies and genetic screens to identify previously unknown steps and components in chloroplast and mitochondrial signalling pathways which contribute to environmental sensing by organelles. The Centre is now undertaking research to address whether organelle number or composition can be optimised by regulating signalling networks and whether this can, in turn, optimise plant performance.

  PEB researchers are investigating networks to define what evolutionary boundaries can be jumped and which networks can be rewired without compromising other aspects of energy efficiency.

Regulators of energy efficiency are not directly selected for by most current breeding strategies, meaning there is considerable potential for improvement. Future assisted-breeding of crops requires knowledge of networks of molecular targets that are yet to be discovered. PEB’s research will aid in identifying such targets and lead to enhanced plant energy efficiency for yield by focusing on improvements that can be stacked together for gains in crops.

Background

Across diverse and changing habitats of agriculture and ecosystems, crop and wild plant populations fine-tune and adapt their energy systems to survive and thrive. Natural genetic diversity underlies complex and adaptive traits responding to natural selection. The molecular basis of these traits can now be mined from plant genomes by unifying modern genomics technologies with precision phenotyping and sensitive environmental observation. This allows prediction traits and selection of individual plants or populations.

In addition to determining the genetic components underlying complex traits of an organism, it may be important to understand the epigenetic codes that govern where and when the genetic information is used. Epigenetic modifications that do not alter the genome sequence but that can regulate the readout of the underlying genetic information may be environmentally sensitive and/or heritable.

Knowledge of the underlying variation that governs complex plant functions will allow selection and engineering of plants for future variable environments to be done with far more precision.

Project aim

Identify genetic and epigenetic control of energy capture and use during plant growth by dissecting out how this controls phenomic variation in natural populations of plants using genome wide association studies, and through (epi)genome profiling in a variety of environments.

• Exploiting (epi)genetic variation to define the gene networks and gene variants that determine energy efficiency.

  The historical selection of plants for high yield in optimal environments has resulted in elite varieties that often do not possess the resilience found in natural populations. We can now tap into a wild molecular genebank of (epi)genetic solutions to challenging environments.

  The Centre is driving major advances in tools to precisely dissect out these (epi)genetic solutions from natural populations of plants. This will clarify the contribution of the (epi)genome to natural variation in plant energy systems and the molecular basis of how plants transform energy to grow and survive in changing and challenging environments.

• Uncovering the role of epigenetics through multigenerational responses to environments.

  It has been proposed that epigenetic modifications in plant genomes can change rapidly, in an apparently stochastic manner, and may transmit to subsequent generations of plants. There is also evidence that the plant epigenome undergoes specific changes in response to challenging environmental conditions.

  We have investigated the role of epigenetic plasticity in plant multigenerational responses to challenging environments. Understanding the extent to which multigenerational epigenomic variability influences genetic and phenotypic variation under challenging conditions will determine the extent to which control of these processes can generate stable and resilient plants in the future.

  We have discovered changes in the epigenome in response to a range of stress conditions. Detailed examination is indicating that these changes can, at least partially, be transmitted through mitosis transiently, but not passed onto subsequent generations.

• Developing new tools for precision manipulation of gene activity to engineer plant energy efficiency.

  To further study and manipulate genes and cellular signalling pathways the Centre aims to develop new approaches to modify gene activity in plants, ranging from targeted transcriptional manipulation to artificial gene circuits technologies. Novel approaches to precisely control gene expression with much greater sophistication will allow the design of advantageous plant functions.

  Furthermore, by studying gene expression at the single cell resolution, we have been able to discover and define previously unknown cell states and functionalities in plant tissues. From this, we can identify the genome regulatory processes that specialized cell functions, and integrate this understanding with our new gene activity regulation tools in order to precisely manipulate plant functions.

We are targeting phenotyping of dynamic plant responses to changing environments and conditions, with specific focus on light, temperature and drought cycles and nutrient-limitation. Our approaches will enable the design, breeding and selection of plants that with altered growth and carbon allocation under limiting and variable conditions of the future.