PhD Project: Advancing structural variation exploitation in aquaculture genomics (started Oct 2021)
Supervised by: Prof. Dan Macqueen, Dr. James Prendergast and Dr Manu Kumar Gundappa
My PhD is funded by the Roslin Institute, University of Edinburgh. The project focuses on advancing the discovery and exploitation of SVs (structural variation) which constitute an important type of genetic variation that remains understudied in aquaculture species. A series of cutting-edge approaches, which have been successfully applied in fishes and livestock, with publicly available and unpublished whole genome sequencing datasets will be used for SV detection to catalogue novel SVs, improve SV detection accuracy, develop imputation methods to type SVs at low cost, and test the impact of SVs on gene expression phenotypes. My work will investigate SVs in several different aquaculture species.
Biography and previous work
Before my PhD, I studied aquaculture at Ocean University of China to get my bachelor and master’s degrees. My master’s research focussed on oysters, using whole genome re-sequencing data to detect SVs across the genome and to identify the key genes related to fast growth traits under the supervision of Prof. Shikai Liu at College of Fisheries, Ocean University of China. I am a bioinformatician and mainly write code and debug programmes!
Jiao Z, Tian Y, Hu B, Li Q. Liu S. Genome structural variation landscape and its selection signatures in the fast-growing strains of the Pacific oyster, Crassostrea gigas. Mar Biotechnol (NY), 2021 23: 736-748.
Tian J, Jiao Z, Fu H, Qi L, Li Q, Liu N and Liu S. Genome-wide identification and expression profiling revealed tissue-specific inducible expression of cytochrome P450s conferring cadmium tolerance in the Pacific oyster, Crassostrea gigas. Aquaculture Reports. 2021, 19:100582.
Fu H, Jiao Z, Li Y, Tian J, Ren L, Zhang F, Li Q and Liu S. Transient Receptor Potential (TRP) Channels in the Pacific Oyster (Crassostrea gigas): Genome-Wide Identification and Expression Profiling after Heat Stress between C. gigas and C. angulata. International Journal of Molecular Sciences, 2021, 22:3222.
Zhang F, Hu B, Fu H, Jiao Z, Li Q and Liu S. Comparative transcriptome analysis reveals molecular basis underlying fast growth of the selectively bred Pacific oyster, Crassostrea gigas. Frontiers in Genetics. 2019, 10:610.