Dr Peter Crisp
UQ Amplify Researcher
School of Agriculture and Food Sustainability
+61 7 336 52141
Researcher biography
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
Book Chapters
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
Bainbridge, Katherine, Bennett, Tom, Crisp, Peter, Leyser, Ottoline and Turnbull, Colin (2014). Grafting in Arabidopsis. Arabidopsis Protocols. (pp. 155-163) edited by SanchezSerrano, JJ and Salinas, J. New York, NY, United States: Humana Press. doi: 10.1007/978-1-62703-580-4_7
Journal Articles
Smith, Aaron B., Ganguly, Diep R., Moore, Marten, Bowerman, Andrew F., Janapala, Yoshika, Shirokikh, Nikolay E., Pogson, Barry J. and Crisp, Peter A. (2023). 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Chan, Kai Xun, Phua, Su Yin, Crisp, Peter, McQuinn, Ryan and Pogson, Barry J. (2016). Learning the languages of the chloroplast: retrograde signaling and beyond. Annual Review of Plant Biology, 67 (1), 25-53. doi: 10.1146/annurev-arplant-043015-111854
Ganguly, Diep, Crisp, Peter, Harter, Klaus, Pogson, Barry J. and Albrecht-Borth, Veronica (2015). Genetic suppression of plant development and chloroplast biogenesis via the Snowy Cotyledon 3 and Phytochrome B pathways. Functional Plant Biology, 42 (7), 676-686. doi: 10.1071/fp15026
Jung, Hou-Sung, Crisp, Peter A., Estavillo, Gonzalo M., Cole, Benjamin, Hong, Fangxin, Mockler, Todd C., Pogson, Barry J. and Chory, Joanne (2013). Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light. Proceedings of the National Academy of Sciences of the United States of America, 110 (35), 14474-14479. doi: 10.1073/pnas.1311632110
Estavillo, Gonzalo M., Crisp, Peter A., Pornsiriwong, Wannarat, Wirtz, Markus, Collinge, Derek, Carrie, Chris, Giraud, Estelle, Whelan, James, David, Pascale, Javot, Helene, Brearley, Charles, Hell, Ruediger, Marin, Elena and Pogson, Barry J. (2011). Evidence for a SAL1-PAP chloroplast retrograde pathway that functions in drought and high light signaling in Arabidopsis. Plant Cell, 23 (11), 3992-4012. doi: 10.1105/tpc.111.091033
Hirsch, Judith, Misson, Julie, Crisp, Peter A., David, Pascale, Bayle, Vincent, Estavillo, Gonzalo M., Javot, Helene, Chiarenza, Serge, Mallory, Allison C., Maizel, Alexis, Declerck, Marie, Pogson, Barry J., Vaucheret, Herve, Crespi, Martin, Desnos, Thierry, Thibaud, Marie-Christine, Nussaume, Laurent and Marin, Elena (2011). A novel fry1 allele reveals the existence of a mutant phenotype unrelated to 5 '-> 3 ' exoribonuclease (XRN) activities in Arabidopsis thaliana roots. PloS One, 6 (2) e16724, e16724. doi: 10.1371/journal.pone.0016724
Chan, Kai Xun, Crisp, Peter Alexander, Estavillo, Gonzalo Martin and Pogson, Barry James (2010). Chloroplast-to-nucleus communication: current knowledge, experimental strategies and relationship to drought stress signaling. Plant Signaling and Behavior, 5 (12), 1575-1582. doi: 10.4161/psb.5.12.13758
Cazzonelli, Christopher I., Cuttriss, Abby J., Cossetto, Susan B., Pye, William, Crisp, Peter, Whelan, Jim, Finnegan, E. Jean, Turnbull, Colin and Pogson, Barry J. (2009). Regulation of carotenoid composition and shoot branching in arabidopsis by a chromatin modifying histone methyltransferase, SDG8. Plant Cell, 21 (1), 39-53. doi: 10.1105/tpc.108.063131