Associate Professor Chris Cazzonelli


Chris CazzonelliIn 2014 A/Prof Chris Cazzonelli was recruited by Western Sydney University (WSU) as a Senior Lecturer in Plant Molecular Biology. He completed his Bachelor of Science (Honours Class I) at the University of Queensland and won an Australian Postgraduate Award to study the regulation of mechanical stress events in plants receiving a PhD in plant molecular biology and plant genetic engineering from the University of Queensland in 2002. He subsequently won a prestigious United States Department of Agriculture (USDA) Postdoctoral Fellowship to investigate the molecular nature of gene activation, RNA gene silencing and remote sensing of plant stress events. In 2006, A/Prof Cazzonelli was recruited by the ARC Centre of Excellence in Plant Energy Biology at the Australian National University to investigate what regulates the production of health promoting carotenoid metabolites in plants. He was awarded the prestigious Goldacre Medal by the Australian Society of Plant Biologists in 2010. A/Prof Cazzonelli now leads the Environmental Epigenetics Laboratory within the Hawkesbury Institute for the Environment (HIE) at WSU.

Epigenetics laboratory We explore memory-forming processes controlling carotenoid biosynthesis and apocarotenoid signalling in response to altered light quality, mechanical stimulation, acoustic vibrations, elevated carbon dioxide, heatwaves, and drought stress. We study the entourage affect with other medicinal and nutritional plant secondary metabolites generated in plant energy organelles such as the chloroplast. We advance knowledge and Agri-Tech innovation in glasshouse protected cropping, horticultural tree genomics, and precision floral pollination technologies fast-forwarding improvements in crop yield, quality and produce nutrition value. Our research goal is to enhance the environmental sustainability of agricultural and horticultural production systems with follow-on benefits for human and animal health.


Environmental Epigenetic Laboratory Overview

Current Research Projects and Student Opportunities

Value Adding in Plants

The ultimate aim of the Environmental Epigenetics Laboratory is to understand how changes in the environment (e.g. rising temperatures, higher CO2 levels, drought and mechanical stress) influence regulatory mechanisms and metabolite accumulation in plants, processes that can facilitate memory, cellular acclimation, reproduction and plant adaptation.

Research projects span across disciplines, from genome to phenotype. Projects offer experience in a range of next generation sequencing, molecular, genetic, epigenetic, metabolic, transgenic, genetic engineering, phenomic and reporter gene technologies.

The goal is to develop new solutions that can improve plant performance and facilitate agricultural sustainability. Model plant species (Arabidopsis, tobacco and tomato) and agronomic important crops (e.g. cotton and peanut) will be used to answer fundamental scientific questions and address key hypotheses relating to cutting edge research topics.

Honours and PhD research projects are available for qualified, enthusiastic and talented postgraduate students. Mentored science research projects are also available to undergraduate students and summer scholars. Post-doctoral research candidates are also invited to contact me with regard to potential research projects and funding opportunities.

1. The Hunt for RNA Riboswitches that regulate plant metabolism and contribute to memory forming epigenetic events.

The Hunt for RNA Riboswitches that regulate plant metabolism and contribute to memory forming epigenetic events.

The Hunt for RNA Riboswitches that regulate plant metabolism and contribute to memory forming epigenetic events.

Bacteria and plants are natural chemical factories producing nutrient metabolites such as Vitamin B (e.g. thiamine) and antioxidant pigments (e.g. carotenoids). These metabolites are essential for human health, plant energy and facilitate cellular communications by controlling their own biosynthesis within energy organelles. They can do this by altering the packaging and structure of genetic material within the nucleus, which controls gene expression.

The structure of Ribonucleic Acid (RNA) can influence the molecular nature of gene expression by controlling transcription attenuation, translation initiation, mRNA splicing and mRNA processing. In bacteria, ancient RNA structural switches (called riboswitches) sense metabolite (ligand) concentrations and control gene expression or protein levels. They are widespread identified in bacteria, animals and one in plants.

This ARC funded project aims to; 1) identify RNA switches in plants that control secondary metabolism, and 2) demonstrate how changes in temperature alter RNA structure and gene regulation in Arabidopsis, and 3) link metabolite production to DNA memory forming processes that facilitate cellular adaptation.

2. The discovery of how phytochemical variation and environmental stress affects plant development and biotic interactions within the rhizosphere.

Carotenoid Pathway

Changing environmental conditions (rising temperatures and CO2 in combination with water availability) can affect the temporal and spatial variation of plant secondary metabolite profiles of pharmaceutically and nutritionally important plants. The accumulation of secondary metabolites in the rhizosphere (zone of soil surrounding plant roots) can affect microbial and mycorrhizal associations that promote nutrient uptake and essentially enhance plant growth.

Carotenoids for example are colourful pigments found in plants that are essential for human health. In plants, carotenoids are required for photosynthesis, photoprotection and the production of signaling molecules (e.g. hormones and volatiles) that promote chloroplast to nucleus communication, shoot branching, root-mycorrhizal symbiosis, parasitic weed germination and abiotic stress resistance (Cazzonelli and Pogson, Trends in Plant Science 2010; 15: 266-274).

We have shown that alterations in carotenogenesis and hence the synthesis of carotenoid-derived signaling molecules can perturb root and shoot development (Cazzonelli et al., Plant Cell 2009; 21,39-53: Van Norman, et al., PNAS 2014; In Press).

This project aims to; 1) investigate how perturbations in metabolite profiles influence root development, and 2) establish links between temperature change, development and the regulation of secondary metabolism, 3) assess gene expression and phytochemical profiles of genetic diverse plant populations growing under variable soil microenvironments, and 4) identify signaling molecules essential for promoting a healthy soil microenvironment and maintaining agricultural sustainability.

3. An epigenetic investigation into the phenomenon of thigomorphogenesis in plants?


Plants sense and respond to wind, rubbing, insect feeding, touching and mechanical stress by altering their phenotype, a phenomenon called thigmomorphogenesis. This is the physiological and morphological adaptation by a plant to environmental mechanical influences.

Changes can include less elongation, thicker stems, enhanced senescence, delayed flowering, altered leaf morphology, enhanced pest resistance and decreased susceptibility to various stresses. The altered growth responses associated with mechanical stress can decrease photosynthesis and are also coupled to increases in respiration.

Despite the widespread relevance of thigmomorphogenesis, the molecular nature that underlies plant mechanostimulus-induced morphological responses remains rather enigmatic and largely unknown. Recent evidence in our laboratory shows that chromatin modifications regulate mechanical induced gene expression.

The project will address the following questions; 1) what are the regulatory mechanisms controlling mechanical touch induced gene expression, 2) how do chromatin modifications target gene loci, 3) does mechanical-induced growth responses involve epigenetic memory formation, and 4) is thigomomorphogenesis a process of cellular acclimation or plant adaptation?

Lab Members

Lucky Paudel
Lucky Paudel
Lucky Paudel
Jwalit Nayak
Jwalit Nayak
Jwalit Nayak
Mahfuza Pervin
Mahfuza Pervin
Mahfuza Pervin
Mekala Manivannan
Mekala Manivannan
Mekala Manivannan
Husnain Butt
Husnain Butt
Husnain Butt
Kanti Ghimirey
Kanti Ghimirey
Avijit Biswas
Avijit Biswas
Avijit Biswas

Current Postgraduate Students

  • 2023 Kanti Ghimirey, MRes (Light-mediated Regulation of Health-Promoting Carotenoid Micronutrients and Photoprotection in Capsicum Cultivators)
  • 2023 Hasan, PhD (Plant molecular responses of capsicum to light-blocking and light-altering films)
  • 2023 Avijit Biswas, PhD (Linking mechanical stress to bioactive carotenoid signals that prime insect resistance in crops)
  • 2022 Husnain Butt, PhD (Regulation of carotenoid derived signals that drive Mycorrhizal interactions within the tomato rhizosphere)
  • 2022 Happy, PhD (Unravelling how mechanical and acoustic stimulation alter gene expression, pollination, fruit development and metabolism in plants
  • 2021 Mekala Manivannan, PhD (Functional Genomics in Almond Tress using Viral Induced Gene Regulation)
  • 2019 Lucky Paudel, PhD (Developing Virual Induced Gene Silencing Technology To Advance Functional Genomics And Breeding In Horticultural Tree Crops)
  • 2019 Jwalit Nayak, PhD (Discovering genetic and chemical switches that regulate carotenogenesis)
  • 2019 Mahfuza Pervin, PhD (Deciphering how mechanical stress can prime plant defenses and train a hardier crop plant)

Undergraduate Students

  • 2020 Cameron Pike (Transcriptome analysis and annotation of differentially expressed genes in etiolated Solanum lycopersicum seedlings)
  • 2019 Kanupriya Singhal (HIE Summer Scholar: Touching plants to prime defence against insect herbivory)
  • 2018 Aliki Jones (Science Research Projects, 300924: Discovering the dark side of carotenoids in plants)
  • 2017 Jessica Tyler (HIE Internship; Mechanical stress training primes plant defense responses)
  • 2017 Laura Lynch (HIE Summer Scholar: A forward genetics screen restores root development in an Arabidopsis carotenoid mutant)
  • 2016 Jordan Hollis (HIE Internship: Investigating cis-carotene accumulation during the de-etiolation of tomato seedlings)
  • 2016 Grace Scott (300910/Advanced Science Project C and 300913/Field Project 1; Biofortification of Tomato: Investigating novel roles for carotenoids in mutualistic mycorrhiza associations)
  • 2015 Wendy Ng (HIE Summer Scholar: Characterisation of an Arabidopsis carotenoid mutant with an altered root phenotype)
  • 2014 Inan Muhsin (UWS Science Research Project: Investigating carotenoid regulatory pathways using a suppressor mutant screen)

Past Postgraduate Students

  • 2023 Sidra Anwar; PhD (A carotenoid-derived signal controls root architecture in Arabidopsis; WSU-HIE)
  • 2020 Yagiz Alagoz; PhD (Feedback regulation of carotenoid biosynthesis by an apocarotenoid sensing RNA structural switch; WSU-HIE)
  • 2020 Eric Brenya; PhD (Elucidating thigmomorphogenesis: An epigenetic phenomenon of plant stress acclimation and transgenerational adaptation, WSU-HIE)
  • 2019 Pranjali Nayak, MRes (Elucidating a novel apocarotenoid signalling pathway controlling root development in plants; Western Sydney University)
  • 2019 Namraj Dhami; PhD (Environmental And Developmental Regulation Of Carotenoid Metabolism In Arabidopsis Leaves) - Western Sydney University
  • 2014 John Rivers; PhD (RNA secondary structure and its effect upon gene expression in plants; co-supervised with Prof. Barry Pogson, Australian National University)
  • 2012 Xin Hou; PhD (Hunting for genes that link cis-carotenes to chloroplast development; co-supervised with Prof. Barry Pogson, Australian National University)
  • 2013 Sophie Holland (Honours: The molecular nature of metabolic feedback regulation in plants)
  • 2012 Jacinta Watkins (Honours: cis-carotenes: Do they have regulatory roles in plants)
  • 2010 Alice Burgess (Honours: Investigating the role and function of the chromatin modifying protein, SDG8 in plant development)
  • 2009 Andrea Roberts (Honours: Characterisation of the histone methyltransferase SET DOMAIN GROUP 8, in Arabidopsis thaliana).
  • 2007 Melanie Carmody (Honours: Characterisation of the CRTISO Promoter).

Selected Publications

Book Chapters

Anwar S, Nayak J, Alagoz Y, Wojtalewicz D, Cazzonelli CI, (2022) 'Purification and use of carotenoid standards to quantify cis-trans geometrical carotenoid isomers in plant tissues', Methods in Enzymology: Carotenoids and Apocarotenoids. 670; pp 57-85

Biru FN, Cazzonelli CI, Elbaum R, Johnson SN, (2022) 'Contrasting impacts of herbivore induction and elevated atmospheric CO2 on silicon defences and consequences for subsequent herbivores', Entomologia Experimentalis et Applicata vol.170, no.8, pp 681-688

Chavan SG, Chen ZH, Ghannoum O, Cazzonelli CI, Tissue DT, (2022) 'Current technologies and target crops: A review on Australian protected cropping', MDPI Crops. 2; pp 172-185

Alagoz Y, Dhami N, Mitchel C and Cazzonelli, CI. (2020) cis/trans carotenoid extraction, purification, detection, quantification and profiling in plant tissues, in Plant and Food Carotenoids: Methods and Protocols, Methods in Molecular Biology, Ed. Manuel Rodríguez-Concepción and Ralf Welsch, Springer Science, Business Media New York, 2083:145-163.

Baranski R and Cazzonelli CI (2015) 'Carotenoid biosynthesis and regulation in plants'. In Carotenoids: Nutrition, Analysis and Technology (A. Kaczor and M. Baranska), pp 159-189, John Wiley & Sons, Ltd, Oxford

Cuttriss AJ, Cazzonelli CI, Wurtzel ET, Pogson BJ, (2011) 'Carotenoids', In Biosynthesis of Vitamins in Plants, Advances in Botanical Research, vol58. Ed. Rébeillé, F. and Douce, R. Elsevier, Amsterdam, The Netherlands, pp 1-36

Cazzonelli CI, Nisar N, Hussain D, Carmody M, Pogson BJ, (2010) 'Biosynthesis and Regulation of Carotenoids in Plants- micronutrients, vitamins and health benefits', In Plant Developmental Biology-Biotechnology Perspectives, vol.2, Ed. E.C. Pua and M.R. Davey Springer-Verlag Berlin Heidelberg, pp 117-137

Journal Articles

Babla MH, Donovan-Mak M, Cazzonelli CI, Tissue DT, Chen Z-H, (2023) 'Linking high light-induced cellular ionic and oxidative responses in leaves to fruit quality in tomato', Plant Growth Regulation, vol.101, no.1, pp 267-284

Chavan SG, He X, Maier C, Alagoz Y, Anwar S, Chen Z-H, Ghannoum O, Cazzonelli CI, Tissue DT, (2023) 'An energy-saving glasshouse film reduces seasonal, and cultivar dependent Capsicum yield due to light limited photosynthesis', Annals of Agricultural Sciences, vol.68, no.1, pp 21 - 35

Maier CR, Chavan SG, Klause N, Liang W, Cazzonelli CI, Ghannoum O, Chen Z-H, Tissue DT, (2023) 'Light blocking film in a glasshouse impacts Capsicum annuum L. yield differentially across planting season', Frontiers in Plant Science, vol.14, Article no.1277037

Brenya E, Pervin M, Chen Z, Tissue D, Johnson SN, Braam J, Cazzonelli CI, (2022) 'Mechanical stress acclimation in plants: Linking hormones and somatic memory to thigmomorphogenesis', Plant Cell and Environment, nol.45, no.4, pp 989-1010

Chavan SG, Chen ZH, Ghannoum O, Cazzonelli CI, Tissue DT (2022) 'Current technologies and target crops: A review on Australian protected cropping', MDPI Crops, vol.2, pp 172-185

Dhami N, Pogson B, Tissue DT, Cazzonelli CI, (2022) 'A Foliar Pigment-Based Bioassay for Interrogating Chloroplast Signalling Reveals that Chlorophyll Biosynthesis Requires Carotenoid Isomerisation', BMC Plant Methods, vol.18, Article 18

Dingley A, Anwar S, Kristiansen P, Warwick N, Wang C, Sindel B, Cazzonelli CI, (2022) 'Precision pollination strategies for advancing horticultural tomato cropping in Australia', MDPI Agronomy, vol.12, no.2, p 518

He X, Chavan SG, Hamoui Z, Maier C, Ghannoum O, Chen ZH, Tissue DT, Cazzonelli CI, (2022) 'Smart Glass Film Reduced Ascorbic Acid in Red and Orange Capsicum Fruit Cultivars without Impacting Shelf Life', Plants-Basel, vol.11, no.7, Article no.985

Hill RA, Wong-Bajracharya J, Anwar S, Coles D, Wang M, Lipzen A, Ng V, Grigoriev IV, Martin F, Anderson IC, Cazzonelli CI, Jeffries T, Plett KL, Plett JM, (2022) 'Abscisic acid supports colonization of Eucalyptus grandis roots by the mutualistic ectomycorrhizal fungus Pisolithus microcarpus', New Phytologist, vol.233, no.2, pp 966-982

Lin T, Goldsworthy M, Chavan S, Liang W, Maier C, Ghannoum O, Cazzonelli C, Tissue DT, Lan Y-C, Sethuvenkatraman S, Lin H, Jia B, Chen Z-H, (2022) 'A novel cover material improves cooling energy and fertigation efficiency for glasshouse eggplant production', Energy, vol.251, Article no.123871

Maier CR, Chen ZH, Cazzonelli CI, Tissue DT, Ghannoum O (2022) 'Precise Phenotyping for Improved Crop Quality and Management in Protected Cropping: A Review', MDPI Crops, vol.2, no.4, pp 336-350

Nayak JJ, Anwar S, Krishna P, Chen Z-H, Plett JM, Foo E, Cazzonelli CI, (2022) 'Tangerine tomato roots show increased accumulation of acyclic carotenoids, less abscisic acid, drought sensitivity, and impaired endomycorrhizal colonization', Plant Science, vol.321, Article no.111308

Paudel L, Kerr S, Prentis P, Tanurdzic M, Papanikolaou A, Plett J, Cazzonelli CI, (2022) 'Horticultural Innovation by Viral-Induced Gene Regulation of Carotenogenesis', Horticulture Research, vol.9, Article uhab008

Anwar S, Brenya E, Alagoz Y, Cazzonelli CI, (2021) 'Epigenetic control of carotenogenesis during plant development', Critical Reviews in Plant Sciences, vol.40, no.1, pp 23-48

Biru FN, Islam T, Cibils-Stewart X, Cazzonelli CI, Elbaum R, Johnson SN, (2021) 'Anti-herbivore silicon defences in a model grass are greatest under Miocene levels of atmospheric CO2', Global Change Biology, vol.27, no.12, pp 2959-2969

Dhami N, Cazzonelli CI, (2021) 'Short photoperiod attenuates CO2 fertilization effect on shoot biomass in Arabidopsis thaliana', Physiology and Molecular Biology of Plants, vol.27, pp 825–834

He X, Maier C, Chavan S, Chenchen Z, Alagoz Y, Cazzonelli CI, Ghannoum O, Tissue DT, Chen ZH, (2021) 'Light-altering Cover Materials and Sustainable Greenhouse Production of Vegetables: A Review', Plant Growth Regulation, vol.95, pp 1-17

Waterman JM, Cibils-Stewart X, Cazzonelli CI, Hartley SE, Johnson SN, (2021) 'Short-term exposure to silicon rapidly enhances plant resistance to herbivory', Ecology, vol.102, no.9, Article no.e03438

Waterman JM, Hall CR, Mikhael M, Cazzonelli CI, Hartley SE, Johnson SN, (2021) 'Short-term resistance that persists: Rapidly induced silicon anti-herbivore defence affects carbon-based plant defences', Functional Ecology, vol.35, no.1, pp 82-92

Zhao C, Chavan S, He X, Zhou M, Cazzonelli CI, Chen Z-H, Tissue DT, Ghannoum O, (2021) 'Smart glass impacts stomatal sensitivity of greenhouse Capsicum through altered light', Journal of Experimental Botany, vol.72, no.8, pp 3235–3248

Babla MH, Tissue DT, Cazzonelli CI, Chen Z-H, (2020) 'Effect of high light on canopy-level photosynthesis and leaf mesophyll ion flux in tomato', Planta, vol.252, no.5, Article no.80

Biru FN, Cazzonelli CI, Elbaum R, Johnson SN, (2020) 'Contrasting effects of Miocene and Anthropocene levels of atmospheric CO2 on silicon accumulation in a model grass', Biology letters, vol.16, no.11, p 20200608

Brenya E, Chen Z-H, Tissue D, Papanicolaou A, Cazzonelli CI, (2020) 'Prior exposure of Arabidopsis seedlings to mechanical stress heightens jasmonic acid-mediated defense against necrotrophic pathogens', BMC Plant Biology, vol.20, no.1, Article no.548

Cazzonelli CI, Hou X, Alagoz Y, Rivers J, Dhami N, Lee J, Marri S, Pogson BJ, (2020) 'A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development', ELife, vol.9, Article no.e45310

Chavan SG, Maier C, Alagoz Y, Filipe JC, Warren CR, Lin H, Jia BH, Loik ME, Cazzonelli CI, Chen ZHH, Ghannoum O, Tissue DT, (2020) 'Light-limited photosynthesis under energy-saving film decreases eggplant yield', Food and Energy Security, Article no.e245

Dhami N, Cazzonelli, CI, (2020) 'Environmental impacts on carotenoid metabolism in leaves', Plant Growth Regulation, vol.92, pp 455-477

Dhami N, Cazzonelli CI, (2020) 'Prolonged cold exposure to Arabidopsis juvenile seedlings extends vegetative growth and increases the number of shoot branches', Plant Signaling and Behavior, Article no.1789320

Dhami N, Drake JE, Tjoelker MG, Tissue DT, Cazzonelli CI, (2020) ' An extreme heatwave enhanced the xanthophyll de-epoxidation state in leaves of Eucalyptus trees grown in the field', Physiology and Molecular Biology of Plants, vol.26, no.2, pp 211-218

Waterman JM, Mann TJ, Cazzonelli CI, Hartley SE, Johnson SN, (2020) 'Microbes in Helicoverpa armigera oral secretions contribute to increased senescence around plant wounds', Ecological Entomology, vol.45, no.5, pp 1224-1229

Babla M, Cai S, Chen G, Tissue DT, Cazzonelli CI, Chen Z-H, (2019) 'Molecular Evolution and Interaction of Membrane Transport and Photoreception in Plants', Frontiers in Genetics, vol.10, Article no.956

Khan SS, Cazzonelli CI, Kurata H, Li CG, Badsha B, Munch G, Majid AMSA (2019). Advancing herbal medicine through metabolic pathway analysis in plants and animals for routine pharmacological assessments. Advances in Integrative Medicine, vol.6, no.1, pp S106-S107

Khan SS, Cazzonelli CI, Kurata H, Li CG, Badsha B, Munch G, Majid AMSA (2019). Advancing herbal medicine through metabolic pathway analysis in plants and animals for routine pharmacological assessments. Australian Herbal Insight, vol.2, no.1, pp 28-37

Waterman JM, Cazzonelli CI, Hartley SE, Johnson SN, (2019) 'Simulated Herbivory: The Key to Disentangling Plant Defence Responses', Trends in Ecology & Evolution, vol.34, no.5, pp 447-458

Alagoz Y, Nayak P, Dhami N, Cazzonelli CI, (2018) 'cis-carotene biosynthesis, evolution and regulation in plants: The emergence of novel signaling metabolites', Archives of Biochemistry and Biophysics, vol.654, pp 172-184

Dhami N, Tissue DT, Cazzonelli CI, (2018) 'Leaf-age dependent response of carotenoid accumulation to elevated CO2 in Arabidopsis', Archives of Biochemistry and Biophysics, vol.647, pp 67-75

Schaub P, Rodriguez-Franco M, Cazzonelli CI, Alvarez D, Wuest F, Welsch R, (2018) 'Establishment of an Arabidopsis callus system to study the interrelations of biosynthesis, degradation and accumulation of carotenoids', Plos One, vol.13, no.2, Article no.e0192158

Pornsiriwong W, Estavillo GM, Chan KX, Tee EE, Ganguly D, Crisp PA, Phua SY, Zhao CC, Qiu J, Park J, Yong MT, Nisar N, Yadav AK, Schwessinger B, Rathjen J, Cazzonelli CI, Wilson PB, Gilliham M, Chen ZH, Pogson BJ, (2017) 'A chloroplast retrograde signal, 3 '-phosphoadenosine 5 '-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination', Elife, vol.6, Article no.e23361

Zhang B, Aken OV, Thatcher L, Clercq ID, Duncan O, Law SR, Murcha MW, van der Merwe M, Seifi HS, Carrie C, Cazzonelli CI, Radomiljac J, Höfte M, Singh KB, Breusegem FV, Whelan J, (2014) 'The mitochondrial outer membrane AAA ATPase AtOM66 affects cell death and pathogen resistance in Arabidopsis thaliana', Plant Journal, (in press)

Avendano-Vazquez AO, Cordoba E, Llamas E, San Roman C, Nisar N, De la Torre S, Ramos-Vega M, Gutierrez-Nava MD, Cazzonelli CI, Pogson BJ, Leon P, (2014) 'An Uncharacterized Apocarotenoid-Derived Signal Generated in zeta-Carotene Desaturase Mutants Regulates Leaf Development and the Expression of Chloroplast and Nuclear Genes in Arabidopsis', Plant Cell, vol.26, no.6, pp 2524-2537

Cazzonelli CI, Nisar N, Roberts AC, Murray KD, Borevitz JO, Pogson BJ, (2014) 'A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation', Frontiers in Plant Science, vol.5, Article no.533

Nisar N, Cuttriss AJ, Pogson BJ, Cazzonelli CI, (2014) 'The promoter of the Arabidopsis PIN6 auxin transporter enabled strong expression in the vasculature of roots, leaves, floral stems and reproductive organs' (opens in a new window), Plant Signaling & Behavior,vol.9, no.1, e27898

Van Norman JM, Zhang J, Cazzonelli CI, Pogson BJ, Harrison PJ, Bugg TD, Chan KX, Thompson AJ, Benfey PN, (2014) 'Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative' (opens in a new window), Proceedings ot the National Academy of Sciences of the USA, vol.111, no.13, pp E1300-E1309

Cazzonelli CI, Vanstraelen M, Simon S, Yin K, Carron-Arthur A, Mathesius U, Cuttriss AJ, Tarle G, Searle I, Masle J, Benkova E, Friml J, Pogson BJ, (2013) 'Role Of The Arabidopsis PIN6 Auxin Transporter In Auxin Homeostasis And Auxin-Mediated Development' (opens in a new window), PLoS One, vol.8, no.7, article no.e70069

Velten J, Cakir C, Youn E, Chen J, Cazzonelli CI, (2012) 'Transgene Silencing and Transgene-derived siRNA Production in Tobacco Plants Homozygous for an Introduced AtMYB90 Construct' (opens in a new window), PLoS One, vol.7, no.2, article no.e30141

Cazzonelli CI, (2011) 'Carotenoids in Nature: insights from plants and beyond' (opens in a new window), Functional Plant Biology, vol.38, pp 833–847

Cazzonelli CI, Pogson BJ, (2010) 'Source and Sink: regulation of carotenoid composition in plants', Trends in Plant Science, vol.15, no.5, pp 266-274

Cazzonelli CI, Roberts A, Carmody M, Pogson BJ, (2010) 'Transcriptional Control of SET DOMAIN GROUP8 and CAROTENOID ISOMERASE during Arabidopsis Development' (opens in a new window), Molecular Plant, vol.3, no.1, pp 174-191

Velten J, Chakir C, Cazzonelli CI, (2010) 'A spontaneous dominant-negative mutation within a 35S::AtMYB90 transgene inhibits flower pigment production in tobacco' (opens in a new window), PLoS One, vol.5, no.3, article no. e9917

Wever W, McCallum EJ, Chakravorty D, Cazzonelli CI, Botella JR, (2010) 'The 5 ′ untranslated region of the VR-ACS1 mRNA acts as a strong translational enhancer in plants' (opens in a new window), Transgenic Research, vol.19, no.4, pp 667-674

Cazzonelli CI, Cuttriss AJ, Cossetto SB, Pye W, Crisp P, Whelan J, Finnegan J, Turnbull C, Pogson BJ, (2009) 'Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8' (opens in a new window), Plant Cell, vol.21, no.1, pp 39-53

Cazzonelli CI, Millar T, Finnegan J, Pogson BJ, (2009) 'Promoting gene expression in plants by permissive histone lysine methylation' (opens in a new window), Plant Signaling & Behavior, vol.4, no.6, pp 484-488

Cazzonelli CI, Yin K, Pogson BJ, (2009) 'Potential implications for epigenetic regulation of carotenoid biosynthesis during root and shoot development' (opens in a new window), Plant Signaling & Behavior, vol.4, no.4, pp 339-341

Howitt CA, Cavanagh C, Bowerman AF, Cazzonelli CI, Rampling L, Mimica JL, Pogson BJ, (2009) 'Alternative splicing, activation of cryptic exons and amino acid substitutions in carotenoid biosynthetic genes are associated with lutein accumulation in wheat endosperm' (opens in a new window), Functional and Integrative Genomics, vol.9, pp 363-373

Cazzonelli CI, Velten JP, (2008) 'In vivo characterisation of plant promoter element interaction using synthetic promoters' (opens in a new window), Transgenic Research, vol.17, pp 437–457

Cazzonelli CI, Velten JP, (2006) 'An in vivo luciferase-based transient assay system using Agrobacteria-infiltrated tobacco leaves: implications for post-transcriptional gene silencing' (opens in a new window), Planta, vol.224, pp 582-597

Cazzonelli CI, Burke J, Velten JP, (2005) 'Functional characterization of the geminiviral conserved late element (CLE) in uninfected tobacco', Plant Molecular Biology, vol.58, no.4), pp 465-481

Cazzonelli CI, McCallum E, Lee, R, Botella JR, (2005) 'Characterisation of a strong, constitutive mung bean (Vigna radiata L.) promoter with a complex mode of regulation in planta', Transgenic Research, vol.14, pp 941-967

Schaub P, Rodriguez-Franco M, Cazzonelli CI, Alvarez D, Wust F, Welsch R (2018). Establishment of an Arabidopsis callus system to study the interrelations of biosynthesis, degradation and accumulation of carotenoids. PLoS ONE 13(2): e0192158. (opens in a new window)

Velten JP, Morey K, Cazzonelli CI, (2005) 'Plant viral intergenic DNA sequence repeats with transcriptional enhancing activity', Virology Journal, vol.2, no.1, p 16


Cazzonelli CI and Botella JR (1998). Patent Application No. PP5572/98 "A Novel Plant Promoter and Uses Therefor" The present invention provides a plant promoter capable of induction by physical and/or environmental stimuli in cells in which the promoter is indigenous and, in the absence of any negative regulatory mechanism, is capable of constitutive expression in cells in which the promoter is non-indigenous.

The invention is further directed to derivatives of the subject promoter including modular forms of the promoter which are, for example, inducible by different physical and environmental stimuli or which are constitutively expressed. The promoter of the present invention has a range of uses including directing expression of genes conferring useful traits on plants. UniQuest Pty Limited, University of Queensland, Brisbane, Australia

Grants / Current Projects

  • 2023-2028 Future Food Systems Cooperative Research Centre ($2,992,758). Automated crop monitoring for protected cropping systems.  O Ghannoum, DT Tissue, R Sharwood, CI Cazzonelli, Z Chen
  • 2022-2027 Future Food Systems Cooperative Research Centre, Horticulture Innovation Australia, RMIT University, Innofocus Photonics Technology ($3,562,472). National Vegetable Protected Cropping Centre - Glasshouse films to reduce energy use and increase resource use efficiency. DT Tissue, O Ghannoum, CI Cazzonelli, R. Sharwood, Z Chen, Y Lan
  • 2021-2022 Future Food Systems Cooperative Research Centre (P2-013; $240,000). Smart Glass film impacts on energy use and productivity in greenhouse lettuce. DT Tissue, Z Chen, CI Cazzonelli, O Ghannoum, R Sharwood
  • 2021 Advancing an acoustic-induced pollination solution for protected cropping (CRC in Future Food Systems and Perfection Fresh; $59,632)
  • 2020-2029 Cooperative Research Centre in Future Food Systems ($35 million)
  • 2018-2022 Hort Innovation (AS1700; $3,785,714) - National Tree Genomics Program - Genotype Prediction Toolbox. Dr Chris Cazzonelli, DR Jonathon Plett and Dr Alexie Papanikolaou)
  • 2017-2020 Horticulture Innovation Australia Grant (VG16070: $799,071) Research and Operations to Trial Innovation Glass and Photovoltaic technologies in Protected Cropping. David Tissue, Zhonghua Chen, Chris Cazzonelli, Oula Ghannoum, Ian Anderson, Nisha Rakhesh & David Thompson
  • 2013-ARC Discovery Grant (DP130102593; $375,000). The Hunt for RNA Riboswitches and Genetic Sensors of Metabolic Flux in Plants. Cazzonelli CI (Lead Investigator), Pogson BJ, Aharoni, A.
  • 2008-ARC Linkage Infrastructure, Equipment and Facilities ($550,000). A massively parallel genome analysis facility for the ACT region (LE0989589).

Areas Of Research

  • Molecular biology
  • genomics
  • epigenetics
  • RNA regulation
  • riboswitches
  • secondary metabolism
  • carotenoids
  • anthocyanin
  • chlorophyll
  • plant energy biology
  • organelle signalling
  • cellular communication
  • genetic engineering
  • crop biofortication
  • environmental stress regulation
  • plant acclimation and adaptation
  • Curcumin
  • Thermoswitch
  • Tomato
  • Arabidopsis
  • Turmeric

To discuss opportunities within the Epigenetics and Plant Molecular Biology field, please contact me on (02) 4570 1752 or by email on


The EELaboratory continues to grow in 2023 as we unravel genetic as well as metabolic signals enabling foliar photoprotection, bud dormancy, flowering, floral pollination and fruit nutrition as core traits for advancing next generation horticultural protected and orchard cropping.

EEL Celebration 2022
EELab celebration time 2022

The EElab had a going away BBQ for Namraj Dhami at Hanna Park in North Richmond

2018 Jessica Tyler (HIE Summer Scholar: Mechanical stress training primes plant defense responses).

The EElab enjoyed their 2017 Christmas party and BBQ at the McMahon Park in Kurrajong.

Undergraduate student, Ms Jessica Tyler recently completed her WSU-HIE Research Internship within the EELab in Autumn of 2017. She and her supervisor Mr Eric Brenya discovered new insights into how mechanical stress can alter defences to different plant pathogens.

EElab members enjoyed their 2016 Christmas party at The Blue Mountains Botanic Garden at Mount Tomah.

Ms Laura Lynch undertook a Summer Scholarship with the EELab under supervision of PhD student Yagiz Alagoz. Together they explored how feedback regulation of carotenoid secondary metabolism might be regulated by an RNA regulatory switch using molecular tools to quantify luminescence in transgenic plants expressing synthetic riboregulators.

The EEL team enjoys the nature of spring and welcomes PhD candidate Yagiz Alagoz as well as HIE internship awardee Jordan Hollis (left to right: Jordan Hollis, Dr Rishi Aryal, Mr Eric Brenya, Mr Namraj Dhami, Mr Yagiz Alagoz and Dr Chris Cazzonelli).

Epigenetics in Nature: EELab First Christmas Party 2015 with Rishi Aryal, Namraj Dhami, Eric Brenya and Chris Cazzonelli at a secret location in the Kurrajong Heights

The EEL team continues to grow and welcomes new PhD candidate Namraj Dhami and HIE internship awardee Tracey Azzopardi (left to right: Ms Tracey Azzopardi, Dr Rishi Aryal, Mr Namraj Dhami and Dr Chris Cazzonelli).

2022 PhD students, Lucky Paudel and Mekala Manivannan won first and second place, respectively at the WSU - Hawkesbury Institute for the Environment Higher Degree Forum Conference

2022 Mahfuza Pervin wins Australian Society of Plant Scientists (ASPS) prize for her poster titled: Prolonged mechanical stress events have contra-regulatory effects on carotenoid and ABA biosynthesis in Arabidopsis rosette leaves at ComBio2022.

2021 Nayak J. Best talk in the session: Carotenoid Biosynthesis & Biotechnology” at the 2nd Virtual International Conference on Carotenoids

HDR student Yagiz Alagoz for winning best poster presentation award at the prestigious 9th Gordon Research Conference on Carotenoids


2017 Grace Scott; NSW Chris Russell Medal of Excellence for undergraduate research on the regulation of carotenoid micronutrients in plants

2010 Dr Chris Cazzonelli; Australian Society of Plant Scientists Peter Goldacre Medal for outstanding contribution to Plant Science

Awards & Recognition

» 2010 Peter Goldacre Medal from the Australian Society of Plant Scientists (awarded yearly to an early career researcher for their outstanding contribution to Plant Science within 10 years of their PhD)

» 2003-05 Outstanding Performance Certificates of Merit (United States Department of Agriculture)

» 2001-03 USDA-ARS Post-Doctoral Fellowship

» 1996-99 Australian Postgraduate Award

Epigenetics Research

Eucalyptus Leaf