Dr Loan Nguyen

Research Fellow/Senior Research off

Centre for Animal Science
Queensland Alliance for Agriculture and Food Innovation
t.nguyen3@uq.edu.au
+61 7 334 62179

Overview

Dr. Nguyen is an expert in applying long-read Oxford Nanopore Sequencing Technologies (ONT) in agriculture, particularly livestock and other sectors. Her groundbreaking contributions include being the pioneer in sequencing the genomes of Brahman and Wagyu cattle, developing an innovative epigenetic clock for age prediction in cattle, and successfully implementing ONT portable sequencers for Blockchain traceability systems in Australia.

As a leader in the field, Dr. Nguyen spearheads the use of ONT long-read technology to scaffold genome assemblies in livestock, plants, protists, and insects. Her multidisciplinary expertise in molecular biology, advanced genomics, and animal sciences also empowers her to explore causative markers for commercial SNP arrays and identify significant DNA variants from low-coverage sequencing data sets.

Dr. Nguyen's exceptional achievements and expertise have been acknowledged through the prestigious ARC Industry Fellowship, recognising her as a promising early career researcher. Her work has significantly contributed to advancing genomic research in agriculture and has opened new avenues for utilising ONT sequencing technologies across diverse domains.

Qualifications

  • Doctor of Philosophy, The University of Queensland

Publications

  • Lamb, H. J., Nguyen, L. T., Copley, J. P., Engle, B. N., Hayes, B. J. and Ross, E. M. (2023). Imputation strategies for genomic prediction using nanopore sequencing. BMC Biology, 21 (1) 286, 286. doi: 10.1186/s12915-023-01782-0

  • Yadav, Seema, Ross, Elizabeth M., Wei, Xianming, Liu, Shouye, Nguyen, Loan To, Powell, Owen, Hickey, Lee T., Deomano, Emily, Atkin, Felicity, Voss‐Fels, Kai P. and Hayes, Ben J. (2023). Use of continuous genotypes for genomic prediction in sugarcane. The Plant Genome e20417, e20417. doi: 10.1002/tpg2.20417

  • Madani, Khalil Saber H., Nguyen, Loan, Phan, Anh Dao Thi, Netzel, Michael E. and Sultanbawa, Yasmina (2023). Protocol Modification for DNA Extraction from Human Faecal Samples. Queensland Annual Chemistry Symposium (QACS), Brisbane, QLD, Australia, 24 November 2023.

View all Publications

Supervision

View all Supervision

Available Projects

  • Cattle are a major source of methane, a potent greenhouse gas. Recently, it has been discovered that feeding some seaweeds to cattle, particularly red seaweed (Asparagopsis taxiformis) greatly reduces methane emissions. In this project, the successful candidate will sequence the red seaweed genome, and discover the gene pathways that led to the production of anti-methanogenic compounds. This knowledge could lead to new innovations to reduce methane emissions and so contribute to a large scale reduction in global warming. The student will learn skills in genome sequencing with state of the art (Nanopore) technology as well as cutting edge bioinformatics techniques.

  • Tools to predict birthdates of cattle are desperately required by industry to ensure compliance with breed registration requirements and to increase the rate of genetic gain for traits such as growth rate and fertility. This study will use new methods of gene targeting and sequencing to investigate the predictive ability of the methylation status of key genes related to age in mammals. Several studies found age-related-conserved sites among species. From these a list of 43 age related genes in cattle has been derived. In this study these genes will be targeted for sequencing and methylation calling in cattle of varying ages. A predictive statistical approach will then the used to associated the methylation rates of those genes with animal age, which can then be used to calculate birthdate.

    This project will apply long-read Oxford Nanopore Sequencing CAS9 targeted enrichment. The project aims to use this approach to target age-related-conversed genes among humans, dogs, and cattle. Finally, validation in large populations will be performed with the most significant age-related sites using quantitative methylation-specific PCR. The ultimate aim of this work is to develop an on farm diagnostic tool that will allows producers to record accurate birthdates and improve the profitability of the beef industry through genetic gain for key traits.

    This project will develop skills in bioinformatics and molecular biology. Students will learn how to design experiments, perform sequencing, and manage very large sequence data sets.

  • Precise gene annotations are essential to understanding the complexity of a species transcriptome and to connect genomic sequence to gene function and ultimately phenotype. RNA sequencing has been widely applied to build a reference transcriptome using short-read sequencing, followed by the assembly or mapping reads to accessible reference genomes. However, short-read sequencing is facing the challenge of lengthy transcripts, repetitive regions, and transposable elements. Long read-sequencing technology, represented by Pacbio Sequencing and Oxford Nanopore sequencing, has overwhelmed this challenge by generating full-length transcripts. Another advantage of Oxford Nanopore sequencing is the potential to direct sequence RNA molecules to remove PCR bias and identify the base modifications.

    In this study, students will perform direct cDNA sequencing and direct RNA sequencing from the liver samples from two cattle genomes using Pacbio isoform sequencing and Nanopore sequencing. The generated sequencing datasets will be compared between technologies and published sequencing data from the same tissues (RNAseq and CAGEseq). The ultimate aim of this project is to advance our understanding of emerging technologies and deeping our understanding of the cattle transcriptome.

    This project will developed molecular techniques (DNA extraction, library preparation and sequencing) and bioinformatics skills. Students will learn how to work with RNA samples and manage extensive sequencing data sets.

View all Available Projects

Publications

Journal Article

Conference Publication

  • Madani, Khalil Saber H., Nguyen, Loan, Phan, Anh Dao Thi, Netzel, Michael E. and Sultanbawa, Yasmina (2023). Protocol Modification for DNA Extraction from Human Faecal Samples. Queensland Annual Chemistry Symposium (QACS), Brisbane, QLD, Australia, 24 November 2023.

  • Ross, E.M., Nguyen, L.T., Engle, B.N., Chamberlain, A.J., Kho, E. and Hayes, B.J. (2022). Bos indicus genome percentage effects gene expression profile and differentially expressed genes in Brahman cattle whole blood. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, The Netherlands, 3-8 July 2022. Wageningen, The Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_628

  • Mantilla Valdivieso, E. , Nguyen, L., Ross, E., Raza, A., James, P., Hayes, B., Jonsson, N. and Tabor, A. (2022). Identification of differentially expressed transcription factors in Brangus skin infested with Rhipicephalus australis. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_557

  • Lamb, H.J., Nguyen, L.T., Randhawa, I.A.S., Hayes, B.J. and Ross, E.M. (2022). The long and short of Nanopore genomic prediction: the effect of read length on prediction accuracy. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_279

  • Lamb, H. J. , Nguyen, L. T., Engle, B. N., Hayes, B. J. and Ross, E. M. (2021). Accuracy of genomic prediction in Brahman cattle using simulated genotypes from low-coverage nanopore sequencing. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

  • Ross, E. M., Lamb, H. J., Engle, B. N. , Nguyen, L. T. and Hayes, B. J. (2021). Assessing the potential of parentage testing using portable long read sequencing technologies. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

  • Forutan, M., Vander Jagt, C.J., Ross, E., Chamberlain, A. J., Mason, B., Nguyen, L., Moore, S., Garner, J. B., Xiang, R. and Hayes, B. J. (2021). Genome wide analysis of bovine enhancers and promoters across developmental stages in liver. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

  • Forutan, Mehrnush, Ross, Elizabeth, Nguyen, Loan and Hayes, Ben (2021). Genome-wide analysis of transcription start sites across Bos indicus tissues. 38th International Conference on Animal Genetics, Online, 26 - 30 July 2021.

  • Nguyen, Loan T., Forutan, Mehrnush, Hayes, Ben J. and Ross, Elizabeth M. (2021). A Bos indicus epigenetic clock predicts age from tail hair. 38th International Society of Animal Genetics (ISAG), Virtual, 26 - 30 July 2021.

  • Alexandre, Pâmela A., Naval-Sánchez, Marina, Menzies, Moira, Nguyen, Loan T., Porto-Neto, Laercio, Fortes, Marina R.S. and Reverter, Antonio (2021). Chromatin accessibility and regulatory vocabulary in indicine cattle. 38th International Society of Animal Genetics (ISAG), Virtual, 26-30 July 2021. Champaign, IL United States: ISAG.

  • Lamb, Harrison, Nguyen, Loan T., Hayes, Ben J., Randhawa, Imtiaz A. S. and Ross, Elizabeth M. (2021). Genomic prediction using low-coverage Nanopore sequencing. 38th International Society of Animal Genetics, Virtual, 26 - 30 July 2021.

  • Nguyen, Loan T., Reverter, Antonio, Cánovas, Angela, Porto-Neto, L.R., Venus, Bronwyn, Islas-Trejo, Alma, Lehnert, Sigrid A., Medrano, Juan F., Thomas, Milton G., Moore, Stephen S. and Fortes, Marina R.S. (2019). Pre- and post-puberty co-expression gene networks from RNA-sequencing of Brahman heifers. Proceedings of the Association for the Advancement of Animal Breeding and Genetics, Armidale, NSW, Australia, 27 October - 1 November 2019.

  • Fonseca, P. A. D. S., Id-Lahoucine, S., Casellas, J., Miglior, F., Reverter, A., Fortes, M. R., Nguyen, L. T., Porto-Neto, L. R., Sargolzaei, M., Brito, L. F., Miller, S. P., Schenkel, F. S., Lohuis, M., Medrano, J. F. and Canovas, A. (2018). Functional Characterization of Genes Mapped in Transmission Ratio Distortion Regions of the Bovine Genome Affecting Reproduction. CARY: OXFORD UNIV PRESS INC.

  • Nguyen, Loan To, Fortes, Marina R.S. and Reverter, Antonio (2017). A pipeline for the analysis of multi-omics data. The Association for the Advancement of Animal Breeding and Genetics, Townsville, QLD, Australia, 2-5 July 2017.

  • Nguyen, L. T., Reverter-Gomez, A., Canovas, A., Venus, B., Islas-Trejo, A., Lehnert, S. A., Medrano, J. F., Moore, S. S. and Fortes, M. R. (2016). Liver transcriptome from pre versus post-pubertal Brahman heifers. Animal Genomes (FAANG) ASAS-ISAG Joint Symposium, Salt Lake City, UT United States, 23 July 2016. Cary, NC United States: Oxford University Press. doi: 10.1093/ansci/94.supplement4.20

  • Nguyen, L. T., Camargo, G. M. F. D, Lyons, R. E., Lehnert, S. A. and Fortes, M. R. S. (2015). Effects of TEX11 and AR polymorphisms on reproduction and growth traits in Australian beef cattle. Proceedings of the Association for the Advancement of Animal Breeding and Genetics, Lorne, VIC, Australia, 28-30 September 2015. Bundoora, VIC, Australia: Association for the Advancement of Animal Breeding and Genetics.

  • Fortes, M. R. S., Almughlliq, F. B., Nguyen, L. T., Porto Neto, L. R. and Lehnert, S. A. (2015). Non-synonimous polymorphism in helb is associated with male and female reproductive traits in cattle. Association for the Advancement of Animal Breeding and Genetics, Lorne, VIC, Australia, 28-30 September 2015. Bundoora, VIC, Australia: Association for the Advancement of Animal Breeding and Genetics.

Other Outputs

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

Possible Research Projects

Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.

  • Cattle are a major source of methane, a potent greenhouse gas. Recently, it has been discovered that feeding some seaweeds to cattle, particularly red seaweed (Asparagopsis taxiformis) greatly reduces methane emissions. In this project, the successful candidate will sequence the red seaweed genome, and discover the gene pathways that led to the production of anti-methanogenic compounds. This knowledge could lead to new innovations to reduce methane emissions and so contribute to a large scale reduction in global warming. The student will learn skills in genome sequencing with state of the art (Nanopore) technology as well as cutting edge bioinformatics techniques.

  • Tools to predict birthdates of cattle are desperately required by industry to ensure compliance with breed registration requirements and to increase the rate of genetic gain for traits such as growth rate and fertility. This study will use new methods of gene targeting and sequencing to investigate the predictive ability of the methylation status of key genes related to age in mammals. Several studies found age-related-conserved sites among species. From these a list of 43 age related genes in cattle has been derived. In this study these genes will be targeted for sequencing and methylation calling in cattle of varying ages. A predictive statistical approach will then the used to associated the methylation rates of those genes with animal age, which can then be used to calculate birthdate.

    This project will apply long-read Oxford Nanopore Sequencing CAS9 targeted enrichment. The project aims to use this approach to target age-related-conversed genes among humans, dogs, and cattle. Finally, validation in large populations will be performed with the most significant age-related sites using quantitative methylation-specific PCR. The ultimate aim of this work is to develop an on farm diagnostic tool that will allows producers to record accurate birthdates and improve the profitability of the beef industry through genetic gain for key traits.

    This project will develop skills in bioinformatics and molecular biology. Students will learn how to design experiments, perform sequencing, and manage very large sequence data sets.

  • Precise gene annotations are essential to understanding the complexity of a species transcriptome and to connect genomic sequence to gene function and ultimately phenotype. RNA sequencing has been widely applied to build a reference transcriptome using short-read sequencing, followed by the assembly or mapping reads to accessible reference genomes. However, short-read sequencing is facing the challenge of lengthy transcripts, repetitive regions, and transposable elements. Long read-sequencing technology, represented by Pacbio Sequencing and Oxford Nanopore sequencing, has overwhelmed this challenge by generating full-length transcripts. Another advantage of Oxford Nanopore sequencing is the potential to direct sequence RNA molecules to remove PCR bias and identify the base modifications.

    In this study, students will perform direct cDNA sequencing and direct RNA sequencing from the liver samples from two cattle genomes using Pacbio isoform sequencing and Nanopore sequencing. The generated sequencing datasets will be compared between technologies and published sequencing data from the same tissues (RNAseq and CAGEseq). The ultimate aim of this project is to advance our understanding of emerging technologies and deeping our understanding of the cattle transcriptome.

    This project will developed molecular techniques (DNA extraction, library preparation and sequencing) and bioinformatics skills. Students will learn how to work with RNA samples and manage extensive sequencing data sets.

  • Cattle diet history information can be obtained by studying non-invasive samples, like dried faecal samples. Additionally, the analysis of faecal samples can also provide the information about the digestive efficiency of an animal. The advent of improved sequencing methodologies has simplified the characterization of complex faecal DNA and allows for the characterization of diet profiles by matching the faecal sequence data with available sequence databases of potential food sources. In this study, student will employ different extraction protocols to isolate DNA from faecal samples using a variety of molecular techniques in the lab.

  • In humans, the methylation state of CpG sites changes with age and can therefore be utilized as an accurate biomarker for aging. In cattle, biological age prediction based on methylation status could provide key information for genetic improvement programs. Additionally, comparing chronological age with biological age (based on methylation status) can provide important information about the stress an animal has been under during its lifetime. However, relatively little is known about DNA methylation patterns in cattle. Students will use cutting edge data sources including reduce representation bisulphite sequencing data, whole genome bisulphite sequencing, long read sequencing and human methylation data to identify differentially methylated regions between old and young animals and validate those regions with modern molecular technologies.

  • DNA methylation is an epigenetic mechanism driving the gene expression in specific tissues at a particular stage. However, the mechanism of how DNA-methylation regulates gene expression in cattle is still unknown. Here, the student will use two types of datasets, whole genome sequencing from Oxford Nanopore sequencing versus RNA sequencing, to explore the relationship between methylation and gene expression. This will be conducted in two tissues, lung and liver.