Lab.Head, Dir. Centre of Grains for Health
School of Biological Sciences
Faculty of Sciences
Eligible to supervise Masters and PhD - email supervisor to discuss availability.
- My Research
- Grants and Funding
- Professional Activities
Epigenetic and post-transcriptional gene regluation
Our research in plant and animal epigenetics and RNA modifications has been driven by a strong interest in understanding and elucidating the molecular mechanisms of how plants and animals adapt to environmental signalling and how speciation barriers evolve in plants. We use a combination of next-generation sequencing, bioinformatics and synthetic biology to describe and elucidate the function of these epigenetic components.
Epigenetics, broadly defined, refers to all genetic information not encoded in the DNA sequence, with the best-understood consequence of epigenetic modifications being the regulation of gene expression. Although gene transcription and protein synthesis is required for plant development, the full repertoire of epigenetic mechanisms underpinning biological adaptation and speciation barriers remain equivocal.
The majority of the genome is pervasively transcribed such that more than 90% of transcriptional activity is related to the production of various long non-coding RNAs (lncRNA), which possess no or limited protein-coding capacity. Expansion of these transcriptionally active non-coding sequences in plant and animal genomes appears to have occurred primarily in higher multicellular organisms. We have identified thousands of novel lncRNAs transcribed in plants.
Furthermore, we have demonstrated RNA modifications, for example 5-methylcytosine (m5C) play an important role in extending the transcriptional space. Thus, both RNA modifications and lncRNAs represent attractive candidates for achieving context- and stimulus-specific epigenetic regulation of gene expression.
Honours, Masters, PhD and postdoctoral synthetic biology and biotechnology projects in epigenetics and bioinformatics are available. Email me at, email@example.com, for further information.
Sustainable crops for arid Australia
Australia is a hot, dry country and often water limits crop yields. We are developing Common Vetch, Vicia sativa, as a high protein, drought tolerant legume for arid Australia. We are accelerating common vetch improvement by; developing extensive genomic resources using a combination of second and third generation sequencing and bioinformatics, combining these large datasets with phenotyping information, and then using next generation breeding technologies (NBT), like CRISPR genome editing. We are working closely with the National Vetch Breeding program at SARDI (Waite campus) to further develop vetch.
Honours, Masters, PhD and postdoctoral CRISPR and biotechnology projects in are available. Email me at, firstname.lastname@example.org, for further information.
We are interested in how plants promote outcrossing to increase population fitness. We are using the model crop Brassica rapa to solve the molecular basis of an outcrossing mechanism. Conversely, these outcrossing mechanisms can decrease seed and crop yields and we are working with industrial partners to determine if we can increase crops yields.
Honours, Masters, PhD and postdoctoral ecology and industry projects in are available. Email me at, email@example.com, for further information.
Interested in joining our laboratory as an undergraduate placement student or postgraduate student? What to join our mentor programme? Ready to excel and be challenged with fascinating biological questions? Please don't hesitate to email me- firstname.lastname@example.org.
Our group's publications are available here.
Date Position Institution name 2018 Senior Lecturer University of Adelaide 2014 - 2018 ARC Future Fellow University of Adelaide 2009 - 2014 ARC QEII Fellow Australian National University
Language Competency German Can speak and understand spoken
Date Institution name Country Title 2004 University of Queensland Australia PhD 1996 University of Queensland Australia B Ag Sci Hons
Date Title Institution Country 2007 - 2009 Wellcome Trust VIP Fellow University of Cambridge United Kingdom 2006 - 2007 Marie Curie Postdoctoral Fellow The Sainsbury Laboratory United Kingdom 2002 - 2006 Max Planck Postdoctoral Fellow Max Planck Institute for Plant Breeding Research Germany
Year Citation 2021 Lim, S. M., Choo, J. M., Li, H., O'Rielly, R., Carragher, J., Rogers, G. B., . . . Muhlhausler, B. (2021). A High Amylose Wheat Diet Improves Gastrointestinal Health Parameters and Gut Microbiota in Male and Female Mice.. Foods (Basel, Switzerland), 10(2), 220.
2020 Xi, H., Ryder, M., & Searle, I. (2020). Complete genome sequence of Allorhizobium vitis strain K306, the causal agent of grapevine crown gall. Microbiologial Resource Annoucements, 9(29), e00565-20-1-e00565-20-3.
2020 Nguyen, V., Riley, S., Nagel, S., Fisk, I., & Searle, I. R. (2020). Common vetch: a drought tolerant, high protein neglected leguminous crop with potential as a sustainable food source. Frontiers in Plant Science, 11, 818-1-818-7.
2020 Xiao, L., Jiang, S., Huang, P., Chen, F., Wang, X., Cheng, Z., . . . Zhang, X. -M. (2020). Two Nucleoporin98 homologous genes jointly participate in the regulation of starch degradation to repress senescence in Arabidopsis. BMC Plant Biology, 20(1), 292-1-292-15.
DOI Scopus1 WoS1
2020 Sinha, P., Singh, V. K., Saxena, R. K., Kale, S. M., Li, Y., Garg, V., . . . Varshney, R. K. (2020). Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea.. Plant biotechnology journal, 18(8), 1697-1710.
DOI Scopus1 WoS2 Europe PMC1
2019 Guo, Q., Ng, P. Q., Shi, S., Fan, D., Li, J., Zhao, J., . . . Searle, I. R. (2019). Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth. PLoS ONE, 14(11), 1-26.
DOI Scopus1 Europe PMC1
2019 David, R., Kortschak, R. D., & Searle, I. (2019). The root hair defective phenotype of Arabidopsis thaliana Pol IV subunit mutant nrpd1a-3 is associated with a deletion in RHD6. microPublication Biology, 2019, 1-4.
2019 Lim, S. M., Page, A. J., Li, H., Carragher, J., Searle, I., Robertson, S., & Muhlhausler, B. (2019). Sexually Dimorphic Response of Increasing Dietary Intake of High Amylose Wheat on Metabolic and Reproductive Outcomes in Male and Female Mice.. Nutrients, 12(1), 14 pages.
2018 Wang, D., Gu, J., David, R., Wang, Z., Yang, S., Searle, I., . . . Timmis, J. (2018). Experimental reconstruction of double-stranded break repair-mediated plastid DNA insertion into the tobacco nucleus. The Plant Journal, 93(2), 227-234.
DOI Scopus2 WoS2 Europe PMC2
2017 David, R., Burgess, A., Parker, B., Li, J., Pulsford, K., Sibbritt, T., . . . Searle, I. (2017). Transcriptome-wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and non-coding RNAs. The Plant cell, 29(3), 16.00751-1-16.0075-30.
DOI Scopus70 WoS63 Europe PMC40
2017 Liu, L., Jiang, Y., Zhang, X., Wang, X., Wang, Y., Han, Y., . . . Chen, F. (2017). Two SUMO proteases SUMO PROTEASE RELATED TO FERTILITY1 and 2 are required for fertility in arabidopsis. Plant Physiology, 175(4), 1703-1719.
DOI Scopus21 WoS21 Europe PMC12
2017 Wang, D., Qu, Z., Yang, L., Zhang, Q., Liu, Z., Do, T., . . . Zhu, J. (2017). Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants. Plant Journal, 90(1), 133-146.
DOI Scopus46 WoS45 Europe PMC23
2017 Crisp, P., Ganguly, D., Smith, A., Murray, K., Estavillo, G., Searle, I., . . . Pogson, B. (2017). Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis. The Plant Cell, 29(8), 1836-1863.
DOI Scopus28 WoS27 Europe PMC18
2016 Ashby, R., Forêt, S., Searle, I., & Maleszka, R. (2016). MicroRNAs in Honey Bee Caste Determination. Scientific Reports, 6(1), 15 pages.
DOI Scopus52 WoS52 Europe PMC26
2016 Chen, M., Xu, J., Devis, D., Shi, J., Ren, K., Searle, I., & Zhang, D. (2016). Origin and functional prediction of pollen allergens in plants. Plant Physiology, 172(1), 341-357.
DOI Scopus16 WoS15 Europe PMC6
2016 Burgess, A., David, R., & Searle, I. (2016). Deciphering the epitranscriptome: a green perspective. Journal of Integrative Plant Biology, 58(10), 822-835.
DOI Scopus20 WoS21 Europe PMC11
2015 Burgess, A., David, R., & Searle, I. (2015). Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae. BMC Plant Biology, 15(1), 199-1-199-17.
DOI Scopus52 WoS49 Europe PMC32
2015 Liu, H., Searle, I., Mather, D., Able, A., & Able, J. (2015). Morphological, physiological and yield responses of durum wheat to pre-anthesis water-deficit stress are genotype-dependent. Crop and Pasture Science, 66(10), 1024-1038.
DOI Scopus25 WoS22
2015 Liu, H., Searle, I., Watson-Haigh, N., Baumann, U., Mather, D., Able, A., & Able, J. (2015). Genome-wide identification of microRNAs in leaves and the developing head of four durum genotypes during water deficit stress. PLoS One, 10(11), e0142799-1-e0142799-30.
DOI Scopus29 WoS28 Europe PMC18
2013 Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron-Arthur, A., Nisar, N., . . . Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One, 8(7), 1-14.
DOI Scopus38 WoS37 Europe PMC22
2012 Campoli, C., Drosse, B., Searle, I., Coupland, G., & von Korff, M. (2012). Functional characterisation of HvCO1, the barley (Hordeum vulgare) flowering time ortholog of CONSTANS. The Plant Journal, 69(5), 868-880.
DOI Scopus97 WoS87 Europe PMC64
2011 Castro Marín, I., Loef, I., Bartetzko, L., Searle, I., Coupland, G., Stitt, M., & Osuna, D. (2011). Nitrate regulates floral induction in Arabidopsis, acting independently of light, gibberellin and autonomous pathways. Planta, 233(3), 539-552.
DOI Scopus95 WoS87 Europe PMC53
2011 Indrasumunar, A., Searle, I., Lin, M., Kereszt, A., Men, A., Carroll, B., & Gresshoff, P. (2011). Nodulation factor receptor kinase 1α controls nodule organ number in soybean (Glycine max L. Merr). The Plant Journal, 65(1), 39-50.
DOI Scopus75 WoS70 Europe PMC56
2011 Burgess, A., & Searle, I. (2011). The clock primes defense at dawn. Immunology and Cell Biology, 89(6), 661-662.
DOI Scopus4 WoS4 Europe PMC3
2011 Gursanscky, N., Searle, I., & Carroll, B. (2011). Mobile microRNAs hit the target. Traffic, 12(11), 1475-1482.
DOI Scopus11 WoS11 Europe PMC6
2010 Searle, I. R., Pontes, O., Melnyk, C. W., Smith, L. M., & Baulcombe, D. C. (2010). JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes and Development, 24(10), 986-991.
DOI Scopus81 WoS77 Europe PMC56
2010 Indrasumunar, A., Kereszt, A., Searle, I., Miyagi, M., Li, D., Nguyen, C., . . . Gresshoff, P. (2010). Inactivation of duplicated nod factor receptor 5 (NFR5) genes in recessive loss-of-function non-nodulation mutants of allotetraploid soybean (Glycine max L. Merr.). Plant and Cell Physiology, 51(2), 201-214.
DOI Scopus76 WoS73 Europe PMC51
2009 Huang, L., Jones, A. M. E., Searle, I., Patel, K., Vogler, H., Hubner, N. C., & Baulcombe, D. C. (2009). An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nature Structural and Molecular Biology, 16(1), 91-93.
DOI Scopus99 WoS90 Europe PMC81
2007 Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, I., . . . Coupland, G. (2007). FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science, 316(5827), 1030-1033.
DOI Scopus1287 WoS1226 Europe PMC875
2007 Smith, L. M., Pontes, O., Searle, I., Yelina, N., Yousafzai, F. K., Herr, A. J., . . . Baulcombe, D. C. (2007). An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell, 19(5), 1507-1521.
DOI Scopus191 WoS181 Europe PMC158
2006 Searle, I., He, Y., Turck, F., Vincent, C., Fornara, F., Kröber, S., . . . Coupland, G. (2006). The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes and Development, 20(7), 898-912.
DOI Scopus513 WoS492 Europe PMC380
2006 Corbesier, L., Vincent, C., Searle, I., Fomara, F., & Coupland, G. (2006). Analysis of the expression pattern of FT protein during flowering. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY, 143(4), S166. 2005 Berendzen, K., Searle, I., Ravenscroft, D., Koncz, C., Batschauer, A., Coupland, G., . . . Ülker, B. (2005). A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta. Plant Methods, 1(1), 15 pages.
DOI Scopus51 WoS49 Europe PMC29
2004 Searle, I., & Coupland, G. (2004). Induction of flowering by seasonal changes in photoperiod. EMBO Journal, 23(6), 1217-1222.
DOI Scopus202 WoS188 Europe PMC126
2003 Searle, I., Men, A., Laniya, T., Buzas, D., Iturbe-Ormaetxe, I., Carroll, B., & Gresshoff, P. (2003). Long-distance signaling in nodulation directed by a CLAVATA1-like receptor kinase. Science, 299(5603), 109-112.
DOI Scopus367 WoS350 Europe PMC243
2003 Waldron, J., Peace, C. P., Searle, I. R., Furtado, A., Wade, N., Findlay, I., . . . Carroll, B. J. (2003). Randomly Amplified DNA Fingerprinting: A culmination of DNA marker technologies based on arbitrarily-primed PCR amplification. Journal of Biomedicine and Biotechnology, 2(3), 141-150.
DOI Scopus21 Europe PMC13
2002 May, K., Whisson, S., Zwart, R., Searle, I., Irwin, J., Maclean, D., . . . Drenth, A. (2002). Inheritance and mapping of 11 avirulence genes in Phytophthora sojae. Fungal Genetics and Biology, 37(1), 1-12.
DOI Scopus51 WoS44 Europe PMC37
2002 Waldron, J., Peace, C., Searle, I., Furtado, A., Wade, N., Findlay, I., . . . Carroll, B. (2002). Randomly amplified DNA fingerprinting: A culmination of DNA marker technologies based on arbitrarily-primed PCR amplification. Journal of Biomedicine and Biotechnology, 2002(3), 141-150.
1999 Schenk, G., Ge, Y., Carrington, L. E., Wynne, C. J., Searle, I. R., Carroll, B. J., . . . De Jersey, J. (1999). Binuclear metal centers in plant purple acid phosphatases: Fe-Zn in sweet potato and Fe-Zn in soybean. Archives of Biochemistry and Biophysics, 370(2), 183-189.
DOI Scopus129 WoS123 Europe PMC71
— Xu, K., Zhang, X. -M., Yu, G., Lu, M., Liu, C., Chen, H., . . . Fu, Y. -F. (n.d.). FT/FD-GRF5 repression loop directs growth to increase soybean yield.
— Nguyen, V., & Searle, I. R. (n.d.). An efficient root transformation system for recalcitrant Vicia sativa.
— Jia, C., Dong, D., Zhou, Q., Searle, I. R., & Liu, Z. (n.d.). Significant cell difference of pod ventral suture in shatter‐resistant and shatter‐susceptible common vetch accessions. Crop Science.
Year Citation 2019 Do, T., Qu, Z., & Searle, I. (2019). Purification and functional analysis of plant long noncoding RNAs (lncRNA). In J. Chekanova, & H. -L. Wang (Eds.), Plant long non-coding RNAs: methods and protocols (Vol. 1933, pp. 131-147). New York: Springer.
2018 Li, J., Wu, X., Do, T., Nguyen, V., Zhao, J., QinNg, P., . . . Searle, I. R. (2018). Quantitative and single nucleotide resolution profiling of RNA 5-methylcytosine.. In R. Gupta, & N. Wajapeyee (Eds.), Epitranscriptomics: Methods and Protocols.
Year Citation 2017 Yang, S. Y., Tate, M., Asenstorfer, R., Carragher, J., Paull, J., & Searle, I. (2017). Progress Towards Developing Low Toxin Common Vetch (Vicia sativa L.). In BIT’s 5th World Congress of Agriculture-2017. Shenyang, China. 2007 Searle, I., Mosher, R., Melnyk, C., & Baulcombe, D. (2007). Small RNAs hit the big time: Meetings. In New Phytologist Vol. 174 (pp. 479-482). England: WILEY.
Year Citation 2016 Liu, H., Able, A., Searle, I., & Able, J. (2016). Characterising water deficit stress-responsive microRNAs and their functional targets in different durum wheat genotypes. Poster session presented at the meeting of ComBio 2016. Brisbane, Australia.. 2015 Liu, H., Searle, I., Watson-Haigh, N., Baumann, U., Mather, D., Able, A., & Able, J. (2015). Identification of differentially expressed miRNAs and their targets in durum wheat during water deficit stress. Poster session presented at the meeting of 9th International Wheat Conference. Sydney, Australia.. 2015 David, R., Lim, H. M., & Searle, I. R. (2015). Identification of pla/ubp14, an Arabidopsis mutant that displays lengthened plastochron and larger organs. Poster session presented at the meeting of Annual Genetics Society of Australasia conference.
Year Citation 2016 Liu, H. (2016). Genome-wide characterisation of microRNAs and their target genes in different durum wheat genotypes under water limiting conditions. (PhD Thesis, University of Adelaide).
Year Citation 2015 Liu, H., Searle, I., Watson-Haigh., Baumann., Mather, D. E., Able, A. J., & Able, J. A. (2015). Genome-wide identification of differentially expressed microRNAs in leaves and the developing head of four durum genotypes during water deficit stress.
Competitive funding only listed below
- Yitpi foundation grant- Chief Investigators Searle and Nguyen (2020)
- SAGIT grant- Investigators Searle and Nagel (2020-2023)
- ARC Discovery Grant DP190101303- Investigators Searle and Studholme (2019-2021)
- Hermon Slade Foundation- Investigator Searle (2017-2020)
- ACSRF Australia-China Joint Research Centre of Grains for Health- Investigators, Searle, et al (2016-2019)
- ARC Future Fellowship FT130100525- Investigator Searle (2014-2018)
- ASTE Travel Grant- Investigator Searle (2015)
- ACSRF Australia-China Young Scientists Exchange Programme- Investigator Searle (2014)
- GRDC E-Innovation award- EzyCross- Investigators Searle & Salisbury (2013-2014)
- GRDC Travel Grant- Investigator Searle (2013)
- ANU Connect Ventures Direct Translation Fund- Investigators Lohe and Searle (2012)
- CSIRO SEIF top-up PhD scholarship- Investigators Searle and Helliwell (2011-2013)
- ARC Discovery Grant DP110103805- Investigators Searle and Helliwell (2011-2013)
- ARC QEII Fellowship DP0988846- Investigator Searle (2009-2014)
- Wellcome Trust Value-In-People Award- Investigator Searle (2008-2009)
- Epigenome travel scholarship- Investigator Searle (2007)
- Marie Curie International Incoming Fellowship- Investigator Searle (2006-2007)
- Interim UOC-UA Biotechnology program coordinator (from 1st Sept 2020-30th Dec 2021)
- BIOTECH 7040- Coordinator for Applications of Next Generation Sequencing
- GENETICS 2510- Genetics IIA
- GENETICS 3211- Gene Expression & Human Developmental Genetics III
- SCIENCE 3500- Opening Doors to the Middle Kingdom
Current Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2020 Principal Supervisor Application of Second and Third-Generation Sequencing to Vicia sativa Improvement Doctor of Philosophy Doctorate Full Time Mr Hangwei Xi 2019 Principal Supervisor Vetch as a New Protein Source for the Human Diet Doctor of Philosophy under a Jointly-awarded Degree Agreement with Doctorate Full Time Mr Samuel Arthur George Riley 2019 Principal Supervisor The role of RNA modifications on RNA Processing in Arabidopsis thaliana Doctor of Philosophy Doctorate Full Time Miss Pei Qin Ng 2018 Principal Supervisor The Role of RNA Modifications in Endosperm Development Doctor of Philosophy Doctorate Full Time Miss Huong Thi Thuy Ta 2017 Principal Supervisor Identification of an RNA m5C demethylose from plants Doctor of Philosophy Doctorate Full Time Miss Xingyu Wu 2017 Co-Supervisor Major Evolutionary Adaptive Events in Brassicaceous Plants and Their Insect Hosts Doctor of Philosophy Doctorate Full Time Mr Christopher Michael Ward 2017 Principal Supervisor Zero Toxin Grain Pulse Vetch Doctor of Philosophy Doctorate Full Time Miss Vy Hoang Thao Nguyen 2016 Principal Supervisor The Role of 5-Methly Cytosine during Plant Development Doctor of Philosophy Doctorate Full Time Miss Jing Zhao
Past Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2018 - 2021 Principal Supervisor The Genetic Basis of Stamen Orientation - An Outcrossing Mechanism in the Brassicaceae Master of Philosophy Master Full Time Mrs Jayashrini Sakunthala Madawala 2016 - 2019 Co-Supervisor Don't Cry for Me: Evolutionary and Functional Analysis of Two Rice Pollen Allergens, Ory s 1 and Ory s 12 Doctor of Philosophy Doctorate Full Time Ms Deborah Devis 2016 - 2020 Principal Supervisor Identification and functional analysis of RNA modifications in Arabidopsis thaliana and Mus musculus Doctor of Philosophy Doctorate Full Time Miss Jun Li 2014 - 2018 Principal Supervisor Identification and Functional Characterization of Long Noncoding RNAs Involved in Endosperm Development of Arabidopsis thaliana Doctor of Philosophy Doctorate Full Time Mr Quang Trung Do 2013 - 2016 Co-Supervisor Genome-wide Characterisation of microRNAs and their target genes in different durum wheat genotypes under water limiting conditions Doctor of Philosophy Doctorate Full Time Dr Haipei Liu 2013 - 2016 Principal Supervisor Conservation and Function of RNA 5-methylcytosine in Plants Doctor of Philosophy Doctorate Full Time Miss Alice Louise Burgess
Date Role Editorial Board Name Institution Country 2011 - ongoing Consulting Editor Frontiers in Genetics and Genomics — —
Date Office Name Institution Country 2018 - ongoing Australian Epigenetic Alliance- South Australian Representative Australian Epigenetic Alliance (AEpiA) Australia 2016 - 2017 Deputy Head of the Department of Genetics and Evolution School of Biological Sciences, The University of Adelaide Australia 2015 - ongoing GSA South Australian Representative on Executive Genetics Society of AustralAsia Australia
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