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Project 1 (James Cook University and University of Sydney): Development of genomic resources and unraveling the genetic architecture of complex phenotypic traits in the giant tiger shrimp.
In order to construct a comprehensive genome mapping resource as part of this project, a genetic linkage (LA) map and a locus ordering map based on pairwise linkage disequilbria (LODE) will be developed. These maps will then be used to create a high-density map by integrating all mapping data together and imputing all loci to their most likely position. This high-density map will then be applied to examine the architecture of commercial production traits using GWAS and QTL analyses to associate genome structures with variable phenotypic traits.
The desired candidate will preferably have a background in molecular and quantitative genetics, along with basic skills in computational analyses.
Project 2 (James Cook University and CSIRO): Physiological responses to environmental stressors in the giant tiger shrimp.
Physiological and gene expression responses of the giant tiger shrimp to environmental stressors such as temperature, salinity and hypoxia will be examined, as well as how combinations of stressors affect these responses as well as shrimp survival. In addition, candidate gene and/or RNAseq analyses will be undertaken to identify whether common response pathways are activated by differing environmental stressors.
The desired candidate will have a strong interest in animal physiology or a background in molecular genetics, in particular working with and analyzing RNA.
Project 3 (University of Sydney): Towards genomic selection in the giant tiger shrimp.
This project will involve modeling various genomic selection scenarios using simulated and real datasets, along with formulation of an economic breeding objective for the giant tiger shrimp.
The desired candidate will preferably have a good background in statistics and/or quantitative genetics, animal production and computational analyses.
Project 4 (University of Sydney and James Cook University): Genetic diversity of commercial giant tiger shrimp and evidence for selection signatures.
This project will use genotype-by-sequencing approaches to determine differences in genetic diversity between populations of farmed giant tiger shrimp originating from diverse geographical locations and determine how selection over several generations leaves selection signatures. Essential components of the project will be the identification of genome-wide SNP loci and SNP-based genotyping of large numbers of founder and breeding program shrimp.
The desired candidate will preferably have a background in population genetics/genomics, computational analyses and basic molecular genetics methodologies.
Project 5 (James Cook University and CSIRO): Functional transcriptomics of viral infection in the giant tiger shrimp.
This project will examine whether the manner in which a giant tiger shrimp is challenged with gill-associated virus (GAV) affects what defense response pathways can be activated to protect the shrimp against infection/disease. Essential components of the project will be GAV challenge trials in P. monodon and the generation and interrogation of RNAseq data to identify/predict genes and gene pathways activated in response to GAV challenge via the various infection routes examined. Silencing of gene expression using RNA interference (RNAi) will also be employed to further explore the functioning of genes predicted to have pivotal roles in the shrimp defense response.
The desired candidate will preferably have a background in molecular genetics along with skills in next-generation sequencing approaches and computational analyses.
Project 6 (University of Sydney and James Cook University): Comparative, evolutionary and functional genomics of the giant tiger shrimp. This project will be a component of the full genome assembly of an inbred giant tiger shrimp based on a combination of short-read sequences and standard mate-pair end Illumina together with the use of long-read sequencing data based on PacBio, HiC, Nanopore platforms for improved hybrid assembly (scaffold/chromosome level). After the genome is annotated thoroughly, the project will aim to find syntenic blocks and reconstruct the evolutionary history of decapods/crustaceans by comparing the P. monodon genome to the genomes of Daphnia, Artemia, P. vannamei and potentially other decapods.
The desired candidate will preferably have a good background in computational biology or bioinformatics (scripting skills in R and Python/Perl) and experience with handling large datasets in a HPC environment.
Project 7 (University of Sydney and James Cook University): This project aims to understand the influence of genotype by environment (GxE) interactions on realizing the genetic potential of the giant tiger shrimp to guide the design of both traditional and genome-informed breeding programs. The project will require phenotype and pedigree data to be generated for shrimp reared in commercial ponds to determine GxE influences on production traits and how these might be selected for in future breeding programs. To accomplish this, SNP-based pedigree data generated for individuals and/or pools of individuals from ponds will be analyzed against as many traits as can be measured.
The desired candidate will have an understanding of quantitative genetics and computational analyses.
The Academic Institutions: Successful students will either be enrolled through James Cook University andUniversity of Sydney and will work embedded or alongside partners of the ARC Research Hub for Advanced Prawn Breeding depending on the project.
Information on How to Apply: Professor Dean Jerry, Hub Director, James Cook University, ARC Research Hub for Advanced Prawn Breeding, Sir George Fisher Building 32, Townsville, Queensland 4811 (phone +61-07-4781-5586, email dean.jerry@jcu.edu.au, webpage https://research.jcu.edu.au/itrh-apb).
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