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 is a Group Leader and Senior Lecturer in the School of Agriculture and Food Sustainability at The University of Queensland. Peter’s research program is focused on crop functional genomics, epigenetics and biotechnology, and has significantly advanced our understanding of the contribution of epigenetics to heritable phenotypic variation in plants.

His group has invented groundbreaking technologies for harnessing (epi)genetic variation and their discoveries have led to exciting new avenues for decoding genomes and for the rational engineering of gene regulation for trait improvement in plants. Having benefited immensely from brilliant mentors, Peter is passionate about training. He leads a budding group of talented students and researchers and is a Chief Investigator in the ARC Training Centre in Predictive Breeding and the International Research Training Group for Accelerating Crop Genetic Gain. Peter is also an affiliate of the Queensland Alliance for Agriculture and Food Innovation and the ARC Centre of Excellence for Plant Success in Nature and Agriculture. 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 environmental 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.

Peter is a former recipient of an ARC DECRA Fellowship and a UQ Amplify Fellowship and an ASPS Goldacre awardee.

Check out the CrispLab website here

Follow Dr Crisp on Bluesky: @pete-crisp.bsky.social, and 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

48 works between 2009 and 2025
All (48) Journal Article (44) Book Chapter (2) Other Outputs (2)

21 - 40 of 48 works

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

2020

Journal Article

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

Zhou, Peng, Li, Zhi, Magnusson, Erika, Gomez Cano, Fabio, Crisp, Peter A., Noshay, Jaclyn M., Grotewold, Erich, Hirsch, Candice N., Briggs, Steven P. and Springer, Nathan M. (2020). Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions. The Plant Cell, 32 (5), 1377-1396. doi: 10.1105/tpc.20.00080

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

2020

Journal Article

Epigenetic regulation of ABA-induced transcriptional responses in maize

Vendramin, Stefania, Huang, Ji, Crisp, Peter A., Madzima, Thelma F. and McGinnis, Karen M. (2020). Epigenetic regulation of ABA-induced transcriptional responses in maize. G3: Genes, Genomes, Genetics, 10 (5), 1727-1743. doi: 10.1534/g3.119.400993

Epigenetic regulation of ABA-induced transcriptional responses in maize

2020

Journal Article

Molecular and physiological responses during thermal acclimation of leaf photosynthesis and respiration in rice

Rashid, Fatimah Azzahra Ahmad, Crisp, Peter A., Zhang, You, Berkowitz, Oliver, Pogson, Barry J., Day, David A., Masle, Josette, Dewar, Roderick C., Whelan, James, Atkin, Owen K. and Scafaro, Andrew P. (2020). Molecular and physiological responses during thermal acclimation of leaf photosynthesis and respiration in rice. Plant Cell and Environment, 43 (3), 594-610. doi: 10.1111/pce.13706

Molecular and physiological responses during thermal acclimation of leaf photosynthesis and respiration in rice

2020

Journal Article

Variation and inheritance of small RNAs in maize inbreds and F1 hybrids

Crisp, Peter A., Hammond, Reza, Zhou, Peng, Vaillancourt, Brieanne, Lipzen, Anna, Daum, Chris, Barry, Kerrie, de Leon, Natalia, Buell, C Robin, Kaeppler, Shawn M., Meyers, Blake C., Hirsch, Candice N. and Springer, Nathan M. (2020). Variation and inheritance of small RNAs in maize inbreds and F1 hybrids. Plant Physiology, 182 (1), 318-331. doi: 10.1104/pp.19.00817

Variation and inheritance of small RNAs in maize inbreds and F1 hybrids

2019

Journal Article

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

Xu, Jing, Chen, Guo, Hermanson, Peter J., Xu, Qiang, Sun, Changshuo, Chen, Wenqing, Kan, Qiuxin, Li, Minqi, Crisp, Peter A., Yan, Jianbing, Li, Lin, Springer, Nathan M. and Li, Qing (2019). Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize. Genome Biology, 20 (1) 243. doi: 10.1186/s13059-019-1859-0

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

2019

Journal Article

Monitoring the interplay between transposable element families and DNA methylation in maize

Noshay, Jaclyn M., Anderson, Sarah N., Zhou, Peng, Ji, Lexiang, Ricci, William, Lu, Zefu, Stitzer, Michelle C., Crisp, Peter A., Hirsch, Candice N., Zhang, Xiaoyu, Schmitz, Robert J. and Springer, Nathan M. (2019). Monitoring the interplay between transposable element families and DNA methylation in maize. PLOS Genetics, 15 (9) e1008291, e1008291. doi: 10.1371/journal.pgen.1008291

Monitoring the interplay between transposable element families and DNA methylation in maize

2019

Journal Article

Opportunities to Use DNA methylation to distil functional elements in large crop genomes

Crisp, Peter A., Noshay, Jaclyn M., Anderson, Sarah N. and Springer, Nathan M. (2019). Opportunities to Use DNA methylation to distil functional elements in large crop genomes. Molecular Plant, 12 (3), 282-284. doi: 10.1016/j.molp.2019.02.006

Opportunities to Use DNA methylation to distil functional elements in large crop genomes

2019

Journal Article

Hybrid decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize

Xue, Wei, Anderson, Sarah N., Wang, Xufeng, Yang, Liyan, Crisp, Peter A., Li, Qing, Noshay, Jaclyn, Albert, Patrice S., Birchler, James A., Bilinski, Paul, Stitzer, Michelle C., Ross-Ibarra, Jeffrey, Flint-Garcia, Sherry, Chen, Xuemei, Springer, Nathan M. and Doebley, John F. (2019). Hybrid decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize. Genetics, 213 (1), 143-160. doi: 10.1534/genetics.119.302378

Hybrid decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize

2018

Journal Article

RNA polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling

Crisp, Peter A., Smith, Aaron B., Ganguly, Diep R., Murray, Kevin D., Eichten, Steven R., Millar, Anthony A. and Pogson, Barry J. (2018). RNA polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling. Plant Physiology, 178 (4), 1614-1630. doi: 10.1104/pp.18.00758

RNA polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling

2018

Journal Article

Heritable epigenomic changes to the maize methylome resulting from tissue culture

Han, Zhaoxue, Crisp, Peter A., Stelpflug, Scott, Kaeppler, Shawn M., Li, Qing and Springer, Nathan M. (2018). Heritable epigenomic changes to the maize methylome resulting from tissue culture. Genetics, 209 (4), 983-995. doi: 10.1534/genetics.118.300987

Heritable epigenomic changes to the maize methylome resulting from tissue culture

2018

Journal Article

Maintenance of pre-existing DNA methylation states through recurring excess-light stress

Ganguly, Diep R., Crisp, Peter A., Eichten, Steven R. and Pogson, Barry J. (2018). Maintenance of pre-existing DNA methylation states through recurring excess-light stress. Plant Cell and Environment, 41 (7), 1657-1672. doi: 10.1111/pce.13324

Maintenance of pre-existing DNA methylation states through recurring excess-light stress

2018

Book Chapter

The maize methylome

Noshay, Jaclyn M., Crisp, Peter A. and Springer, Nathan M. (2018). The maize methylome. The Maize Genome. (pp. 81-96) edited by Jeffrey Bennetzen, Sherry Flint-Garcia, Candice Hirsch and Roberto Tuberosa. Cham, Switzerland: Springer. doi: 10.1007/978-3-319-97427-9_6

The maize methylome

2017

Journal Article

The arabidopsis DNA methylome is stable under transgenerational drought stress

Ganguly, Diep R., Crisp, Peter A., Eichten, Steven R. and Pogson, Barry J. (2017). The arabidopsis DNA methylome is stable under transgenerational drought stress. Plant Physiology, 175 (4), 1893-1912. doi: 10.1104/pp.17.00744

The arabidopsis DNA methylome is stable under transgenerational drought stress

2017

Journal Article

Rapid recovery gene downregulation during excess-light stress and recovery in arabidopsis

Crisp, Peter A., Ganguly, Diep R., Smith, Aaron B., Murray, Kevin D., Estavillo, Gonzalo M., Searle, Iain, Ford, Ethan, Bogdanović, Ozren, Lister, Ryan, Borevitz, Justin O., Eichten, Steven R. and Pogson, Barry J. (2017). Rapid recovery gene downregulation during excess-light stress and recovery in arabidopsis. Plant Cell, 29 (8), 1836-1863. doi: 10.1105/tpc.16.00828

Rapid recovery gene downregulation during excess-light stress and recovery in arabidopsis

2017

Journal Article

A chloroplast retrograde signal, 3’phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination

Pornsiriwong, Wannarat, Estavillo, Gonzalo M., Chan, Kai Xun, Tee, Estee E., Ganguly, Diep, Crisp, Peter A., Phua, Su Yin, Zhao, Chenchen, Qiu, Jiaen, Park, Jiyoung, Yong, Miing Tiem, Nisar, Nazia, Yadav, Arun Kumar, Schwessinger, Benjamin, Rathjen, John, Cazzonelli, Christopher I., Wilson, Philippa B., Gilliham, Matthew, Chen, Zhong-Hua and Pogson, Barry J. (2017). A chloroplast retrograde signal, 3’phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination. eLife, 6 e23361, e23361. doi: 10.7554/eLife.23361

A chloroplast retrograde signal, 3’phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination

2016

Journal Article

Uncoupling high light responses from singlet oxygen retrograde signaling and spatial-temporal systemic acquired acclimation

Carmody, Melanie, Crisp, Peter A., d’Alessandro, Stefano, Ganguly, Diep, Gordon, Matthew, Havaux, Michel, Albrecht-Borth, Verónica and Pogson, Barry J. (2016). Uncoupling high light responses from singlet oxygen retrograde signaling and spatial-temporal systemic acquired acclimation. Plant Physiology, 171 (3), 1734-1749. doi: 10.1104/pp.16.00404

Uncoupling high light responses from singlet oxygen retrograde signaling and spatial-temporal systemic acquired acclimation

2016

Journal Article

Reconsidering plant memory: intersections between stress recovery, RNA turnover, and epigenetics

Crisp, Peter A., Ganguly, Diep, Eichten, Steven R., Borevitz, Justin O. and Pogson, Barry J. (2016). Reconsidering plant memory: intersections between stress recovery, RNA turnover, and epigenetics. Science Advances, 2 (2) e1501340, e1501340. doi: 10.1126/sciadv.1501340

Reconsidering plant memory: intersections between stress recovery, RNA turnover, and epigenetics

Current funding

  • 2025 - 2027
    Unlocking crop epigenomics to uncover and engineer hidden diversity
    ARC Discovery Projects
    Open grant
  • 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

Past funding

  • 2023 - 2024
    EpiGrape: Exploring intra-varietal variation in grapevine using epigenetics
    Universities Australia - Germany Joint Research Co-operation Scheme
    Open grant
  • 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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communications@uq.edu.au