Dr Peter Crisp
Dr

Peter Crisp

Email: 
Phone: 
+61 7 336 52141

Background

Dr Peter Crisp is an expert in crop genomics, epigenomics and molecular genetics. He leads a research group in the School of Agriculture and Food Science. His research group seeks to understand the contribution of epigenetics to heritable phenotypic variation in crop plants, focusing on cereals including barley, sorghum, wheat and maize. This includes the development of methods to harness epigenetic variation for crop improvement; understanding the role of epigenetics in stress responses and using innovative epigenomic approaches to distill large genomes down to the relatively small fraction of regions that are functionally important for trait variation. Research in the Crisp Lab spans both wet lab and computational biology providing a powerful platform to integrate genetic, genomic and biotechnological approaches.

Check out the CrispLab website here

Follow Dr Crisp on Twitter: @pete_crisp

Availability

Dr Peter Crisp is:
Available for supervision

Fields of research

Agricultural biotechnology Agricultural molecular engineering of nucleic acids and proteins Agricultural, Veterinary and Food Sciences Biological Sciences Crop and pasture production Epigenetics (incl. genome methylation and epigenomics) Genetics Plant biology

Qualifications

  • Doctor of Philosophy, Australian National University

Research impacts

Read about Dr Crisp’s work on plant stress memory and epigenetics in New Scientist here

Search Professor Peter Crisp’s works on UQ eSpace

45 works between 2009 and 2024
All (45) Journal Article (42) Book Chapter (2) Other Outputs (1)

1 - 20 of 45 works

2024

Journal Article

Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation

Smith, Aaron B., Ganguly, Diep R., Moore, Marten, Bowerman, Andrew F., Janapala, Yoshika, Shirokikh, Nikolay E., Pogson, Barry J. and Crisp, Peter A. (2024). Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. The Plant Journal, 117 (3), 818-839. doi: 10.1111/tpj.16531

Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation

2023

Journal Article

Genetic mapping, candidate gene identification and marker validation for host plant resistance to the race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis

Chen, Andrew, Sun, Jiaman, Viljoen, Altus, Mostert, Diane, Xie, Yucong, Mangila, Leroy, Bothma, Sheryl, Lyons, Rebecca, Hřibová, Eva, Christelová, Pavla, Uwimana, Brigitte, Amah, Delphine, Pearce, Stephen, Chen, Ning, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav, Crisp, Peter, Brown, Allan F., Martin, Guillaume, Yahiaoui, Nabila, D’Hont, Angelique, Coin, Lachlan, Swennen, Rony and Aitken, Elizabeth A. B. (2023). Genetic mapping, candidate gene identification and marker validation for host plant resistance to the race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis. Pathogens, 12 (6) 820, 820. doi: 10.3390/pathogens12060820

Genetic mapping, candidate gene identification and marker validation for host plant resistance to the race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis

2022

Journal Article

Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants

Weiss, Trevor, Crisp, Peter A., Rai, Krishan M., Song, Meredith, Springer, Nathan M. and Zhang, Feng (2022). Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants. Plant Physiology, 190 (2), 1153-1164. doi: 10.1093/plphys/kiac285

Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants

2022

Journal Article

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

Wrightsman, Travis, Marand, Alexandre P., Crisp, Peter A., Springer, Nathan M. and Buckler, Edward S. (2022). Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. The Plant Genome, 15 (3) e20249, 1-13. doi: 10.1002/tpg2.20249

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

2022

Journal Article

Identifying transcription factor-DNA interactions using machine learning

Bang, Sohyun, Galli, Mary, Crisp, Peter A., Gallavotti, Andrea and Schmitz, Robert J. (2022). Identifying transcription factor-DNA interactions using machine learning. In Silico Plants, 4 (2) diac014, 1-15. doi: 10.1093/insilicoplants/diac014

Identifying transcription factor-DNA interactions using machine learning

2022

Journal Article

Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis

Li, Lei, Duncan, Owen, Ganguly, Diep R., Lee, Chun Pong, Crisp, Peter A., Wijerathna-Yapa, Akila, Salih, Karzan, Trösch, Josua, Pogson, Barry J. and Millar, A. Harvey (2022). Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis. Proceedings of the National Academy of Sciences, 119 (20) e2121362119, 1-11. doi: 10.1073/pnas.2121362119

Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis

2022

Journal Article

Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants

Read, Andrew, Weiss, Trevor, Crisp, Peter A, Liang, Zhikai, Noshay, Jaclyn, Menard, Claire C, Wang, Chunfang, Song, Meredith, Hirsch, Candice N, Springer, Nathan M and Zhang, Feng (2022). Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants. The Plant Journal, 111 (1), 103-116. doi: 10.1111/tpj.15781

Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants

2022

Journal Article

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

Vafadarshamasbi, Ulduz, Mace, Emma, Jordan, David and Crisp, Peter A. (2022). Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits. Biochemical Society Transactions, 50 (1), 583-596. doi: 10.1042/bst20210908

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

2022

Journal Article

Harnessing genetic variation at regulatory regions to fine-tune traits for climate resilient crops

Ganguly, Diep R., Hickey, Lee T. and Crisp, Peter A. (2022). Harnessing genetic variation at regulatory regions to fine-tune traits for climate resilient crops. Molecular Plant, 15 (2), 222-224. doi: 10.1016/j.molp.2021.12.011

Harnessing genetic variation at regulatory regions to fine-tune traits for climate resilient crops

2022

Journal Article

Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future

Crisp, Peter A., Bhatnagar-Mathur, Pooja, Hundleby, Penny, Godwin, Ian D., Waterhouse, Peter M. and Hickey, Lee T. (2022). Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future. Current Opinion in Biotechnology, 73, 88-94. doi: 10.1016/j.copbio.2021.07.008

Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future

2022

Journal Article

Epigenome guided crop improvement: current progress and future opportunities

Zhang, Yan, Andrews, Haylie, Eglitis-Sexton, Judith, Godwin, Ian, Tanurdžić, Miloš and Crisp, Peter A. (2022). Epigenome guided crop improvement: current progress and future opportunities. Emerging Topics in Life Sciences, 6 (2), 141-151. doi: 10.1042/etls20210258

Epigenome guided crop improvement: current progress and future opportunities

2022

Journal Article

Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information

Zhou, Peng, Enders, Tara A., Myers, Zachary A., Magnusson, Erika, Crisp, Peter A., Noshay, Jaclyn M., Gomez-Cano, Fabio, Liang, Zhikai, Grotewold, Erich, Greenham, Kathleen and Springer, Nathan M. (2022). Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information. The Plant Cell, 34 (1), 514-534. doi: 10.1093/plcell/koab267

Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information

2021

Other Outputs

Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis

Li, Lei, Duncan, Owen, Ganguly, Diep R., Lee, Chun Pong, Crisp, Peter A., Wijerathna-Yapa, Akila, Salih, Karzan, Trösch, Josua, Pogson, Barry J. and Millar, A. Harvey (2021). Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis.

Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis

2021

Journal Article

Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes

Noshay, Jaclyn M., Liang, Zhikai, Zhou, Peng, Crisp, Peter A., Marand, Alexandre P., Hirsch, Candice N., Schmitz, Robert J. and Springer, Nathan M. (2021). Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3: Genes, Genomes, Genetics, 11 (8) jkab190. doi: 10.1093/g3journal/jkab190

Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes

2021

Journal Article

Science forum: a community-led initiative for training in reproducible research

Auer, Susann, Haelterman, Nele A., Weissgerber, Tracey L., Erlich, Jeffrey C., Susilaradeya, Damar, Julkowska, Magdalena, Gazda, Małgorzata Anna, Schwessinger, Benjamin, Jadavji, Nafisa M., Abitua, Angela, Niraulu, Anzela, Shahb, Aparna, Clyburne-Sherinb, April, Guiquel, Benoit, Alicea, Bradly, Lamanna, Caroline, Ganguly, Diep, Perkins, Eric, Jambor, Helena, Li, Ian Man Ho, Tsang, Jennifer, Kamens, Joanne, Teytelman, Lenny, Paul, Mariella, Cronin, Michelle, Schmelling, Nicolas, Crisp, Peter, Kutum, Rintu, Phuyal, Santosh ... Bachle, Susanna (2021). Science forum: a community-led initiative for training in reproducible research. eLife, 10 e64719. doi: 10.7554/eLife.64719

Science forum: a community-led initiative for training in reproducible research

2021

Journal Article

Current status and prospects of plant genome editing in Australia

Zhang, Yan, Restall, Jemma, Crisp, Peter, Godwin, Ian and Liu, Guoquan (2021). Current status and prospects of plant genome editing in Australia. In Vitro Cellular & Developmental Biology - Plant, 57 (4), 1-10. doi: 10.1007/s11627-021-10188-y

Current status and prospects of plant genome editing in Australia

2021

Journal Article

Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

Liang, Zhikai, Anderson, Sarah N., Noshay, Jaclyn M., Crisp, Peter A., Enders, Tara A. and Springer, Nathan M. (2021). Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize. Plant Physiology, 186 (1), 1-14. doi: 10.1093/plphys/kiab073

Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

2021

Journal Article

Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons

Noshay, Jaclyn M., Marand, Alexandre P., Anderson, Sarah N., Zhou, Peng, Mejia Guerra, Maria Katherine, Lu, Zefu, O’Connor, Christine H., Crisp, Peter A., Hirsch, Candice N., Schmitz, Robert J. and Springer, Nathan M. (2021). Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Genetics, 217 (1) iyaa003, 1-13. doi: 10.1093/genetics/iyaa003

Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons

2020

Journal Article

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

Crisp, Peter A., Marand, Alexandre P., Noshay, Jaclyn M., Zhou, Peng, Lu, Zefu, Schmitz, Robert J. and Springer, Nathan M. (2020). Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proceedings of the National Academy of Sciences, 117 (38), 202010250-24000. doi: 10.1073/pnas.2010250117

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

2020

Journal Article

Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis

Weiss, Trevor, Wang, Chunfang, Kang, Xiaojun, Zhao, Hui, Elena Gamo, Maria, Starker, Colby G., Crisp, Peter A., Zhou, Peng, Springer, Nathan M., Voytas, Daniel F. and Zhang, Feng (2020). Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis. Plant Journal, 104 (3) tpj.14949, 828-838. doi: 10.1111/tpj.14949

Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis

Current funding

  • 2024 - 2029
    ARC Training Centre in Predictive Breeding for Agricultural Futures
    ARC Industrial Transformation Training Centres
    Open grant
  • 2024 - 2028
    Program 2 - Resistance Sources: Using 'FastStack' to develop effective durable net blotch resistance gene stacks
    Grains Research & Development Corporation
    Open grant
  • 2023 - 2024
    EpiGrape: Exploring intra-varietal variation in grapevine using epigenetics
    Universities Australia - Germany Joint Research Co-operation Scheme
    Open grant

Past funding

  • 2021 - 2022
    An epigenetic blueprint for Queensland¿s sorghum crop of the future
    UQ Knowledge Exchange & Translation Fund
    Open grant
  • 2020 - 2023
    Discovering hidden control elements for crop improvement
    ARC Discovery Early Career Researcher Award
    Open grant

Availability

Dr Peter Crisp is:
Available for supervision

Before you email them, read our advice on how to contact a supervisor.

Available projects

  • Uncovering the contribution of epigenetics to heritable phenotypic variation in crops using (epi)genomics and large data

    New bioinformatic approaches for epigenomic analysis and epiGWAS in crops

    A bioinformatics oriented RHD project is available to study epigenomic variation and inheritance in crops including maize, sorghum and barley. This project will involve the development of new bioinformatic strategies to analyse novel types of epigenomic data we have developed in the lab. This project will address fundamental questions at the core of the field of epigenetics; and will have outcomes that are important for modern plant breeding and agriculture. The project can be largely bioinformatics or encompass a blend of wet lab (biotech and molecular biology) and computational work. Some prior bioinformatics experience is an advantage, although not essential if you are enthusiastic about learning bioinformatics.

  • Other projects available - get in touch!

    Projects can also be designed on new topics where our interests overlap and are happy to chat.

    • We are particularly interested in new projects in the areas of (epi)genomics and bioinformatics

    Other areas include:

    • Crop genomics and epigenomics
    • Biotechnology and CRISPR (sorghum and barley)
    • Bioinformatics focused on epigenomic analysis and DNA methylation
    • Enhancers and chromatin modifications

Supervision history

Current supervision

Completed supervision

Enquiries

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