Dr Xueyan Shen ~ Senior Lecturer Aquaculture

Dr. Xueyan Shen obtained her M.Sc in Aquaculture and Ph.D. in Biochemistry and Molecular Biology from the Ocean University of China in 2004 and 2007, respectively. After that, she started her Postdoctoral work on maintenance of genomic resources for the National BioResource Project Medak in NIBB (Okazaki, Japan). From 2010, she worked in the Temasek Life Sciences Laboratory (TLL), Singapore, where as a Research Fellow, she led several research teams towards increasing Singapore’s food fish supply through application of aquaculture genomics R&D. She has now joined James Cook University in Singapore where she will continue to apply her state-of-the-art teaching and genetic research approaches to help Singapore as well as other Asia counties achieve their aquaculture related food security strategy.

Research Focus

Dr. Shen’s research focus is on the development of “robust” aquaculture strains to boost seafood production. She has conducted genomics-assisted selection on two economically important fish, namely Asian seabass/barramundi and Mozambique tilapia, and also the ornamental fish Asian arowana. Specific areas of her research interest include: 1) Developing genomic resources and genetic tools like whole genome sequencing, high-density SNP arrays, etc., to support selective breeding; 2) Exploring genetic basis of important traits (growth, disease resistance) using RNA sequencing, QTL mapping, GWAS and genomic selection; 3) Conducting functional feed trials and specific pathogen tests to evaluating feed additives' impact on fish immunity; 4) Investigating nutrition, gene expression, gut microbiome and immunity in various fish species using omics approaches. As a Senior Lecturer at JCU Singapore, Dr. Shen is keen to continue to collaborate with partners from commercial industry, government universities/institutes to create ‘State of the art’genomic platforms to further improve the productivity and quality of food fish species.

Impact of Research

Her research into the genetic improvement of Asian seabass and tilapia have allowed for a ‘quantum leap’ in generation of more superior broodstock leading to more efficient and greater productivity of foodfish products. In addition, tools she has developed will be easily applicable and adaptable to the aquaculture systems of other tropical marine fish species, advancing their production systems from the current most traditional methods into modern, science-assisted aquaculture.

Teaching

• AQ3004: Aquaculture: Stock Improvement (Level 3; SIN)

Interests

Research

• • Aquaculture new genomic tools development and application • Aquaculture genetics • Aquaculture disease • Selective breeding

Research Disciplines

• Fisheries sciences (3005)
• Genetics (3105)
• Bioinformatics and computational biology (3102)

Socio-Economic Objectives

• Fisheries - aquaculture (1002)
• Expanding knowledge (2801)

Awards

• 2022 to 2026 - Supercharging barramundi production through adv. sel. breeding for improved disease resistance, growth, and and fillet traits. Awarded to Shen X; Domingos JA; Jerry DR; Erenst V; Tan YQ; Schrittwieser M; Vij S & Tan M. SFA SFS R&D (SGD 5,260,292)
• 2021 to 2024 - Developing genetic resources for red snapper, an important marine food fish for Singapore. Awarded to Vij S, Domingos JA; Jerry DR; Loo G; Shen X; Bing L; Voigtmann M; Tan M & Ban Tat L. SFA SFS R&D (SGD 1,622,915)
• 2021 to 2024 - Optimizing Feeds for Singaporean Red Snapper Aquaculture. Awarded to Hua K; Shen X; Chatterjee C; Ngoh SY & Voigtmann M. SFA SFS R&D (SGD 1,365,604)
• 2023 - R&D services in Exploring microbiome dynamics and potential pathogenic risks in aquatic exhibits at Singapore River Wonders. Awarded to Shen X & Gibson-Kueh S. Direct industry funding from Mandai Wildlife Group, Singapore (SGD 26,959)
• 2021 to 2022 - R&D services in the testing of monoglyceride feed additives for fish. Awarded to Gibson-Kueh S; Domingos JA & Shen X. Direct industry funding from Adisseo (SGD 170,228)
• 2019 to 2022 - Cobia Genome Consortium. Awarded to Domingos, JA, Shen X & Yanez, JM (University of Chile). Direct industry funding from Open Blue Cobia in Panama (USD 60,000)

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles

• Chew X, Gibson-Kueh S, Jerry D and Shen X (2023) Comparison of intestinal bacterial communities in asymptomatic and diseased Asian seabass (Lates calcarifer) with chronic enteritis and mixed bacterial infections. Aquaculture, 572.
• Shen X, Niu Y, Uichanco J, Phua N, Bhandare P, Thevasagayam N, Prakki S and Orbán L (2023) Mapping of a major QTL for increased robustness and detection of genome assembly errors in Asian seabass (Lates calcarifer). BMC Genomics, 24.
• Shen X, Yáñez J, Gomes G, Poon Z, Foster D, Alarcon J and Domingos J (2023) Comparative gonad transcriptome analysis in cobia (Rachycentron canadum). Frontiers in Genetics, 14.
• Poon Z, Shen X, Angelo J, Terence C, Chua S and Domingos J (2022) Comparative transcriptome analysis reveals factors involved in the influence of dietary astaxanthin on body colouration of Malabar Snapper (Lutjanus malabaricus). Aquaculture, 562.
• Domingos J, Shen X, Terence C, Senapin S, Dong H, Tan M, Gibson-Kueh S and Jerry D (2021) Scale Drop Disease Virus (SDDV) and Lates calcarifer Herpes Virus (LCHV) coinfection downregulate immune-relevant pathways and cause splenic and kidney necrosis in barramundi under commercial farming conditions. Frontiers in Genetics, 12.
• Gibson-Kueh S, Terence C, Chew X, Uichanco J and Shen X (2021) PCR, in-situ hybridization, and phylogenetic analysis suggest that ‘big belly’ disease in barramundi, Lates calcarifer (Bloch), is caused by a novel Vibrio species. Journal of Fish Diseases, 44 (12). pp. 1985-1992
• Orbán L, Shen X, Phua N and Varga L (2021) Toward genome-based selection in Asian seabass: what can we learn from other food fishes and farm animals? Frontiers in Genetics, 12.
• Li J, Bian C, Hu Y, Mu X, Shen X, Ravi V, Kuznetsova I, Sun Y, Xinxin Y, Qui Y, Zhang X, Yu H, Huang Y, Xu P, Gu R, Xu J, Orban L, Venkatesh B and Shi Q (2016) A chromosomelevel genome assembly of the Asian arowana, Scleropages formosus. Scientific Data, 3.
• Shen X, Ngoh S, Thevasagayam N, Prakki S, Bhandare P, Tan A, Tan G, Singh S, Phua N, Vij S and Orbán L (2016) BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome. Scientific Reports, 6.
• Vij S, Kuhl H, Kuznetsova I, Komissarov A, Yurchenko A, Van Heusden P, Singh S, Thevasagayam N, Prakki S, Purushothaman K, Saju J, Jiang J, Mbandi S, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh S, Liew W, Shen X, Hon L, Drake J, Boitano M, Hall R, Chin C, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck F, Vurture G, Gopalapillai G, Kumar Katneni V, Noble T, Scaria V, Sivasubbu S, Jerry D, O'Brien S, Schatz M, Dalmay T, Turner S, Lok S, Christoffels A and Orbán L (2016) Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding. PLoS Genetics, 12 (4). pp. 1-35

Advisory Accreditation: I can be on your Advisory Panel as a Primary or Secondary Advisor.

These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.

Current

• The Epidemiology of 'Scale Drop Disease' in Farmed Lates Calcarifer in Singapore (PhD , Secondary Advisor)
• Using Environmental DNA (eDNA) as an early Detection and Monitoring Tool for Fish Ectoparisites Affecting Aquaculture in Southeast Asia (PhD , External Advisor)
• Nutritional Requirement Study and Optimised Feed Development for Red Snapper (PhD , Primary Advisor)
• Genomic selection of barramundi (Lates calcarifer) for improved scale drop disease virus (SDDV) resistance, growth, and fillet traits (PhD , Secondary Advisor)

The map shows research collaborations by institution from the past 7 years.
Note: Map points are indicative of the countries or states that institutions are associated with.