AQUACULTURE GENETICS GROUP
COMPARATIVE GENOMICS CENTRE

Mail Address: School of Marine and Tropical Biology, James Cook University,
Townsville, 4811, Queensland, Australia
Telephone: 61-7-4781 5586 Fax:  61-7-4781 4585

CONTENTS:





RESEARCH OVERVIEW:

    Aquaculture is the fastest growing animal production industry, despite the fact that most species farmed have undergone very little genetic improvement. Increases in production within the industry have resulted from improvements in animal husbandry and nutrition, however, recently there has been an increased impetus towards the application of quantitative and molecular-based animal breeding methodologies to the improvement of aquaculture species.

    The research focus of the Aquaculture Genetics Group at James Cook University is to acquire the statistical information and develop molecular tools that will allow the design and conduct of highly efficient selection programs for aquaculture species, primarily those farmed in tropical waters. Research conducted by the group falls within four major research strands – quantitative genetics, population genetics and development of molecular tools, gene expression analyses and chromosome manipulation. Aquaculture species currently worked with include the pearl oysters Pinctada maxima, P. margaritifera, P. fucata, barramundi Lates calcarifer,  Pacific white shrimp Penaeus vannamei and redclaw Cherax quadricarinaus.



Understanding the genetics underlying pearl production
    The production of a quality cultured pearl is a manifestation of the biological products of two pearl oysters. Here a small piece (~5mm) of mantle tissue from a donor oyster is implanted along with a nuclei bead into the gonad of a host oyster. The tissue from the donor oyster then grows around the bead to produce a pearl sac and secretes the nacreous layer that is distinctive of a pearl. What is not currently known is which is more important in the production of a quality pearl. Is it the genetics of the host oyster, the genetics of the donor oyster, or is there interplay between the two? Also unknown is what role the environment plays in pearl production and how it interacts with genetic systems. The aim of this research is to understand the fundamental genetic basis of pearl production and, more specifically, determine heritability of pearl traits, the effect genotype by environment interactions may have on pearl production, and to develop molecular tools that will aid selective breeding. Modern quantitative and population genetic approaches are being utilized to address these questions.
    We also are in the process of developing a high-density genetic linkage map for the silver-lipped pearl oyster Pinctada maxima based on SNPs derived from Next-generation sequencing and will be using this map to identify quantitative trait loci (QTL) for pearl quality traits. Once all the genetic information is available we will commence the first selection program for P. maxima with our commercial partner Atlas South Sea Pearl.

Genomic selection of commercial traits in the Pacific white shrimp
    The Pacific white-tailed shrimp Penaeus vannamei is the most widely farmed shrimp species globally. At present there are several selection programs for this species, largely focused on easy to improve traits such as growth. Shrimp aquaculture, however, is plagued by the incidence of several diseases such as taura syndrome virus (TSV), white spot syndrome virus (WSSV) and infectious myconecrosis virus (IMNV) which are hard to select for due to errors associated with estimating of low trait heritability, or requiring the use of sib-selection approaches which only utilise 50% of available genetic variance in populations. The aim of this research program is to in conjunction with our collaborators ProBio Technology Ltd and Global Gen Shrimp develop a high density SNP array derived from sequencing of the shrimp transcriptome to identify marker genes linked to disease and growth traits. At present we have developed a 10,000 SNP array and are in the process of genotyping Global gen families. Given the high-density of the SNP marker panel we will also evlaute its potential use for genomic-selection approaches.
       

Barramundi genetics
    Barramundi (Lates calcarifer) are widely distributed throughout lagoons and estuaries in tropical Australia, Asia and eastern Africa.  They are widely regarded as both a premier sport fish and table fish of superior quality.  As such the species supports substantial commercial and recreational fisheries, as well as a considerable aquaculture industry.  Recently, there has been interest in instigation of selective breeding programs for this species to further enhance productivity and increase the profitability of barramundi farming.  Important traits that may be included as breeding objectives in a selection program include growth rate, disease resistance and thermal tolerance.  Like that for pearl oysters there is currently very little information on the genetic basis of traits and few molecular tools that can aid selective breeding. The aim of barramundi research undertaken within the group therefore is to gather baseline genetic data to aid future selection programs, as well as to develop molecular genetic tools like DNA parentage marker suites and candidate genes to improve breeding efficiencies. Three current focuses of our work include a) understanding how hatchery practices affect genetic diversity in this species, b) identifying the effects of thermal stress on growth performance and c) identifying candidate growth genes that can be used in marker-assisted selection.
    
Triploidy in pearl oysters
    Culture of organisms that are triploid (ie have three sets of chromosomes instead of two) is commonly practiced in aquaculture as a way to increase growth rates or limit precocious spawning. This research area aims to induce triploids in the important pearl oyster species (P. maxima, P. margaritifera, P. fucata) and to examine their applicability to pearl oyster culture. In particular, we want to assess whether triploid pearl oysters grow faster and if implantation of triploid mantle tissue results in a quality pearl.

Genetics behind environmental stress in a coral reef fish
    Over the last century and as a result of global warming the Great Barrier Reef has experienced an increase in sea surface temperature. In addition, the coastal reefs from the Great Barrier Reef lagoon are likely to be impacted by direct anthropogenic disturbances, as they receive outflow from fifteen river catchments. Toxic compounds such as pesticides can spread to fringing reefs and impact the health of these ecosystems and their inhabitants. In this research area we are looking at how coral reef fish respond and cope with environmental stresses, at the gene regulation level, biochemically, and on their overall phenotypic responses.


Development of tools to aid selective breeding of aquaculture species.
    One of the major impediments to undertaking efficient selection programs in aquaculture species is an inability to retain pedigree of individuals through traditional physical tagging methods. As a consequence, there are several advantages to using genetic markers (coupled with parentage analysis) to retain pedigree information in aquaculture breeding programs. Firstly, they allow the communal rearing of larvae from multiple families which minimizes the potential confounding effect of tank and early rearing environment on trait performance and reduces the amount of infrastructure requisite to individually raise families to a size where they can be physically tagged. Secondly, genetic markers also permit all progeny from a family to be evaluated, instead of only a random few. This is because physical tagging is labour and time consuming, while all individuals can a posteriori be assigned to their family of origin based on their gene profile. Finally, genetic markers also cannot be lost during the growth phase, a particular consideration for species which are constantly graded and cleaned of biofouling, or crustaceans which moult their exoskeleton as they grow. Therefore, the objective of this research strand is to develop DNA parentage marker systems for important aquaculture species that can be used to assign pedigree to animals reared in selection programs.


STAFF:

Group Head:
•    Associate Professor Dean Jerry

Research Staff
•    Dr Carolyn Smith-Keune
•    Dr Kyall Zenger

Graduate Students
•    Renate Kvingedal
•    James Newton
•    Erin McGinty
•    Emmanuelle Botte
•    Christian De Santis
•    Jose Domingos
•    Hoc Tan Dao
•    David Jones
•    Erica Todd



POSITIONS IN THE AQUACULTURE GENETICS GROUP:

Postgraduate
Students interested in undertaking a PhD or Masters project in the Aquaculture Genetics Group should contact Dean Jerry to discuss projects of mutual interest. Most higher degrees students would be expected to eligible for a scholarship through the Australian Postgraduate Award (APA) scheme, the James Cook University Postgraduate Research Scholarship or an equivalent national or international scholarship.

The Australian Postgraduate Award (APA) and James Cook University Postgraduate Research Scholarship (JCUPRS) are open to applicants with, or who expect to hold, a first class honours degree or equivalent by the end of the year and who wish to undertake full-time research Masters or PhD program. In 2010 the stipends for an APA were $22,500 pa (full time) or $12,176 (part-time). APA applicants must be Australian citizens or have been granted permanent resident status and lived in Australia continuously for 12 months prior to receiving the award; Information and application forms can be obtained from the Graduate Research School.  Closing Date: 31 October of each year.

Honours

Students who have completed their undergraduate training in a BSc, BBiomedSc, BMedlabSc or equivalent program and are interested in participating in either the Science, Biochemistry or Molecular Biology Honours Program are encouraged to contact are encouraged to contact Dean Jerry for a description of currently available projects. Honours studies require a full-time commitment for one year (two semesters) and can start in either February or August.Follow this link for details.

Undergraduate

There are two main opportunities for undergraduates to participate in the ongoing research of  Dean Jerry.

Students enrolled in BC3203 (Special Topics in Biochemistry and Molecular Biology - second semester) could ask that they undertake their research project in the Aquaculture Genetics Laboratory.

Students can apply for a Comparative Genomics Centre Vacation Scholar Award. The successful applicants receive instruction in the latest recombinant DNA and genetics techniques, receiving a stipend of $200 per week for a full-time commitment of between 6 and 10 weeks over the summer break. Applications for the CGC Vacation Studentships are announced in September each year and close in late October. Contact Dean Jerry for further details
 


RECENT PUBLICATIONS:

Hardy, C.M., Adams, M., Jerry, D.R., Court, L.N., Morgan, M.J. and Hartley, D.M. (in press). DNA barcoding to support conservation: species identification, genetic structure and biogeography of fishes in the Murray-Darling River Basin, Australia. Marine and Freshwater Research.

De Santis. C. & Jerry, D.R. (2011). Differential tissue-regulation of myostatin genes in the teleost fish Lates calcarifer in response to fasting. Evidence for functional differentiation. Molecular and Cellular Endocrinology 325, 158-165.

McGinty, E., Zenger,  K.R., Taylor, J.U., Evans, B.S., & Jerry, D.R. (2011). Diagnostic genetic markers unravel the interplay between host and donor oyster contribution in cultured pearl formation. Aquaculture 316, 20-24.

De Santis, C., Smith-Keune, C. and Jerry, D.R. (2010). Normalising RT-qPCR data: are we getting the right answers? An appraisal of normalization approaches and internal reference genes from a case study in the finfish Lates calcarifer. Marine Biotechnology 10, .

Newton, J.R., Smith-Keune, C., and Jerry, D.R. (2010). Thermal tolerance varies in tropical and sub-tropical populations of barramundi (Lates calcarifer) consistent with local adaptation. Aquaculture 308 (Suppl 1), S128-S132.

Robinson, N.A., Schipp, G., Bosmans, J., and Jerry, D.R. (2010). Modelling selective breeding in protandrous, batch reared Asian sea bass (Lates calcarifer, Bloch) using walkback selection. Aquaculture Research 41, 643-655.

Jones, D.B., Jerry, D.R., McCormick, M.I., and Bay, L.K. (2010) The population genetic structure of a common tropical damselfish on the Great Barrier Reef and eastern Papua New Guinea. Coral Reefs, 29 (2). pp. 455-467. ISSN 1432-0975

Guy, Jeffrey A., Jerry, Dean R., and Rowland, Stuart J. (2009) Heterosis in fingerlings from a diallel cross between two wild strains of silver perch (Bidyanus bidyanus). Aquaculture Research, 40 (11). pp. 1291-1300. ISSN 1365-2109

Smith-Keune, Carolyn, and Jerry, Dean R. (2009) High levels of intra-specific variation in the NG repeat region of the Pinctada maxima N66 organic matrix protein. Aquaculture Research, 40 (9). pp. 1054-1063. ISSN 1365-2109

Fauvelot, C., Smith-Keune, C., Jerry, D.R., Buston, P.M., and Planes, S. (2009) Isolation and characterization of 16 microsatellite loci in the humbug damselfish, Dascyllus aruanus (family Pomacentridae). Molecular Ecology Resources, 9 (2). pp. 651-653. ISSN 1755-0998

Lind, Curtis E., Evans, Brad S., Knauer, Jens, Taylor, Joseph J.U., and Jerry, Dean R. (2009) Decreased genetic diversity and a reduced effective population size in cultured silver-lipped pearl oysters (Pinctada maxima). Aquaculture, 286 (1-2). pp. 12-19. ISSN 1873-5622

Edmunds, Richard C., van Herwerden, Lynne, Smith-Keune, Carolyn, and Jerry, Dean R. (2009) Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus. International Journal of Biological Sciences, 5 (6). pp. 558-569. ISSN 1449-2288

Lind, Curtis E., Evans, Brad S., Taylor, Joseph J.U., and Jerry, Dean R. (2009) The consequences of differential family survival rates and equalizing maternal contributions on the effective population size (Ne) of cultured silver-lipped pearl oysters, Pinctada maxima. Aquaculture Research, . pp. 1-14. ISSN 1365-2109

Kvingedal, Renate, Evans, Bradley S., Taylor, Joseph J.U., Knauer, Jens, and Jerry, Dean R. (2008) Family by environment interactions in shell size of 43-day old silver-lip pearl oyster (Pinctada maxima), five families reared under different nursery conditions. Aquaculture, 279 (1-4). pp. 23-28. ISSN 1873-5622

Jerry, Dean R. (2008) Phylogeography of the freshwater catfish Tandanus tandanus (Plotosidae): a model species to understand evolution of the eastern Australian freshwater fish fauna. Marine and Freshwater Research, 59 (4). pp. 351-360. ISSN 1448-6059

McGinty, Erin L., Smith-Keune, Carolyn, and Jerry, Dean R. (2008) A high through-put protocol for quantifying nucleic acids in individual microcrustaceans using new generation RNA and DNA specific dyes. Journal of Shellfish Research, 27 (2). pp. 449-455. ISSN 1943-6319

Jones, David, Jerry, Dean, McCormick, Mark, and Bay, Line (2008) Development of nine microsatellite markers for Pomacentrus amboinensis. Molecular Ecology Resources, 8 (6). pp. 1332-1334. ISSN 1755-0998

Whalan, S., de Nys, R., Smith-Keune, C., Evans, B.S., Battershill, C., and Jerry, D.R. (2008) Low genetic variability within and among populations of the brooding sponge Rhopaloeides odorabile on the central Great Barrier Reef. Aquatic Biology, 3 (2). pp. 111-119. ISSN 1864-7790

de Santis, Christian, Evans, Brad S., Smith-Keune, Carolyn, and Jerry, Dean R. (2008) Molecular characterization, tissue expression and sequence variability of the barramundi (Lates calcarifer) myostatin gene. BMC Genomics, 9 . pp. 82-96. ISSN 1471-2164

Wada, Katsuhiko T., and Jerry, Dean R. (2008) Population genetics and stock improvement. In: The Pearl Oyster. Elsevier, Oxford, UK, pp. 437-471. ISBN 978-0-444-52976-3

Lind, Curtis E., Evans, Brad S., Taylor, Joseph J.U., and Jerry, Dean R. (2007) Population genetics of a marine bivalve, Pinctada maxima, throughout the Indo-Australian Archipelago shows differentiation and decreased diversity at range limits. Molecular Ecology, 16 (24). pp. 5193-5203. ISSN 1365-294X

De Santis, Christian, and Jerry, Dean R. (2007) Candidate growth genes in finfish - where should we be looking? Aquaculture, 272 (1-4). pp. 22-38. ISSN 1873-5622

Munkres, Katherine P., Bay, Line K., Jerry, Dean R., McCormick, Mark I., and van Herwerden, Lynne (2007) Development and characterization of microsatellite markers for parentage analyses of the coral reef damselfish (Pomacentrus amboinensis: Pomacentridae). Conservation Genetics, 8 (4). pp. 987-990. ISSN 1572-9737

Acosta-Salmón, Héctor, Jerry, Dean R., and Southgate, Paul C. (2007) Effects of cryoprotectant agents and freezing protocol on motility of black-lip pearl oyster (Pinctada margaritifera L.) spermatozoa. Cryobiology, 54 (1). pp. 13-18. ISSN 1090-2392


LINKS:


Autoimmunity Research Group, Medical Genomics Rseearch Group, James Cook University, Key words: Immunology, immune, immunogenetics, disease, risk, vaccine, Genetics, Genomics, Phenomics, Proteinomics, Gene, Autoimmune diabetes, Type 1 diabetes mellitus, childhood diabetes, lupus, systemic lupus erythematosus, haemolytic anaemia, hemolytic anemia, Coombs' test, antinuclear antibodies, renal failure, glomerulonephritis, gastritis, type A gastritis, pernicious anemia, immunology, popular science, biology.