PhD projects: black tiger prawn genomics

Project 1 – Development of genomic resources and unravelling the genetic architecture of complex phenotypic traits in the black tiger prawn

(James Cook University & University of Sydney)

Dense SNP-based genomic maps are valuable in associating genetic loci (QTL, GWAS) with complex phenotypic traits and in understanding genome structures. They can also provide a framework for integrating various genomic data including a draft genome sequence assembly for the black tiger prawn (Penaeus monodon). 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 – Physiological responses to environmental stressors in the black tiger prawn

(James Cook University and CSIRO)

Physiological and gene expression responses of the black tiger prawn (Penaeus monodon) 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 prawn 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 analysing RNA.

Project 3 – Towards genomic selection in the black tiger prawn

(University of Sydney)

Future breeding programs for the black tiger prawn (Penaeus monodon) will require integration of genomic data to improve the efficiency of selection. The Holy Grail is to make selection decisions

largely on determining a genomic-based breeding value (gEBV) or using an approach termed genomic selection. Breeding programs integrating genomic selection to improve P. monodon genetics will require breeding designs to be optimised and the best algorithms to predict genetic performance to be determined. The project will involve modelling various genomic selection scenarios using simulated and real datasets, along with formulation of an economic breeding objective for the black tiger prawn.

The desired candidate will preferably have a good background in statistics and/or quantitative genetics, animal production and computational analyses.

Project 4 – Genetic diversity of commercial black tiger prawns and evidence for selection signatures

(University of Sydney & James Cook University)

This project will use genotype-by-sequencing approaches to determine differences in genetic diversity between populations of farmed black tiger prawns (Penaeus monodon) 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 prawns.

The desired candidate will preferably have a background in population genetics/genomics, computational analyses and basic molecular genetics methodologies.

Project 5 – Functional transcriptomics of viral infection in the black tiger prawn

(James Cook University and CSIRO)

This project will examine whether the manner in which a black tiger prawn (Penaeus monodon) is challenged with Gill-associated virus (GAV) affects what defence response pathways can be activated to protect the prawn 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 prawn defence 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 – Comparative, evolutionary and functional genomics of the black tiger prawn

(University of Sydney & James Cook University)

This project will be a component of the full genome assembly of an inbred black tiger prawn (Penaeus monodon) 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, Litopenaeus vannamei and potentially of other decapods/crustaceans.

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 – Genotype by environment under commercial scenarios on performance of black tiger prawn genotypes

(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 black tiger prawn to guide the design of both traditional and genome-informed breeding programs. The project will require phenotype and pedigree data to be generated for prawns 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 analysed against as many traits as can be measured.

The desired candidate will have an understanding of quantitative genetics and computational analyses.

Successful students will either be enrolled through James Cook University or the University of Sydney and will work embedded or alongside partners of the ARC Research Hub for Advanced Prawn Breeding depending on the project (ie CSIRO, AGRF). For more information on what the Hub will achieve and partners please visit https://research.jcu.edu.au/itrh-apb

For further details on projects and information on how to apply please contact Professor Dean Jerry, Director ARC Hub for Advanced Prawn Breeding, Townsville, Australia, email: dean.jerry@jcu.edu.au

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