NAGRP Aquaculture Genome Projects

Research Statements

Abigail Elizur

We are looking at the contribution of microarray technology to industry development in aquaculture. We have constructed a crab, fish brain and pearl oyster array and are looking for genes differentially expressed in response to various biological stimuli.

Alan Mileham

Our interest is in the development of the molecular tools that will enhance the effectiveness of Sygen's (SyAqua) shrimp breeding program. DNA-based animal identification and gene discovery can contribute significantly to the development of genotypes more suitable for the BioZEST system. Efficient and cost-effective shrimp identification procedures that avoid tagging, allow co-rearing of shrimp from multiple genetic backgrounds, and estimation of different familial/population contribution have been developed and are in the testing/optimization stage. Another area of interess is identification of candidate genes and markers that control genetic variation in economically important traits. Markers will enable the development of Marker Assisted Selection (MAS) as an important component of our breeding program. This is of particular interest for traits such as survival and meat quality that are difficult to improve by traditional quantitative breeding methods. Candidate genes can be based on the physiology of traits, the detection of chromosomal regions associated with Quantitative Trait Loci (QTL), and gene expression data (through micro-arrays or other gene expression platforms ). There is also a significant effort directed towards genetic protection systems and different options are evaluated and tested.

Amir Sagi

Comparative and applied endocrinology. Sexual plasticity. Regulation of sex-differentiation, reproduction and growth in decapod crustaceans. The vitellogenin gene.

Andrew Fidler

The Cawthron aquaculture group is undertaking selective breeding of Perna canaliculus (green-lipped mussel). In addition a Perna canaliculus gonadal EST database is being constructed and analysed to provide more information on the neuroendocrine control of gametogenesis in this species.

Arnaud HUVET

Aim: Understanding the physiological processes and their regulation by exogenous and endogenous factors in marine bivalves with functional exploration of molecular mechanisms implicated in key steps of main physiological functions of interest for aquaculture; and next investigate relationships between polymorphism of genes of interest and these functions. For reproduction, the origin and the mechanisms of annual renewal of germ cells, still unknown in marine bivalves, are under characterization in C. gigas using the oyster vasa-like gene (Oyvlg) we characterized and used as a specific marker of germline cells in oyster. (Fabioux et al, 2004a,b Biophys Biochem Res Com).

For adaptation, we developed a multidisciplinary project with the aim of understanding the causes of summer mortality of C. gigas. Two approaches are under study: enzymatic and molecular analysis of glucid metabolism and especially of glycogen reserves in relation to reproduction and health of animals; analysis of physiological bases of summer survival resistance through resistant and susceptible oyster families produced by a divergent selection on summer survival. That was firstly engaged with subtractive libraries realized between resistant and susceptible oyster families (Huvet et al, 2004 Gene) and need now the development of genomic tools such as micro-arrays with the ESTs we share on C. gigas with several French and non-French laboratories. For growth and nutrition, based on relationships observed between growth variability, assimilation rate and digestive enzymes, we developed a molecular approach on the two amylase genes we characterized in oyster. The aim was to establish relationships between amylase polymorphism, enzymatic and molecular expression of amylase genes and assimilation and growth rates of oyster to evaluate the ability of improving growth in oyster strains using amylase genes as genetic marker (Moal et al, 2000 J Comp Physiol B; Sellos et al, 2003 Mar Biotechnol; Huvet et al, 2003 Aquaculture).

Bachère Evelyne

Characterization and ontogenesis of the immune response of oyster and shrimp to infections and stress with particular attention to antimicrobial effectors. Objectives of health management.

Bernie May

We have been engaged in QTL mapping in rainbow trout and tilapia and breeding studies in white sturgeon. We are now working on developing broodstock for Lion's paw scallops and in restoration programs for endangered Sacramento perch and Shasta crayfish.

Christopher J. Bayne

Evolution of immune systems through studies on rainbow trout and molluscs.

Functional genomics. The acute phase response, in particular gene transcription in the teleost liver in response to inflammatory stimuli. In parallel, we study cell-based immunity in a mollusc and its role in achieving resistance to a parasite that the mollusc can transmit to humans, Schistosoma mansoni. We have produced an oligo DNA array that contains 1500 features with relevance to immunity, cancer, toxicology and endocrinology of trout.

Craig Sullivan

Another central focus of our aquaculture research is selective breeding of an improved cultivar for the hybrid striped bass industry, a major component of finfish aquaculture in the United States. We established broodstocks of the parent species (striped bass and white bass), developed reliable techniques for their hatchery propagation, and domesticated both species over several generations. Our current efforts are directed at discovering the degree to which important production traits, such as growth rate or body conformation, have a genetic basis or have been altered by the process of domestication. Because genetic contributions to fish "performance" differ between life history stages, these studies involve all phases of aquaculture production. They include rearing of larvae in nursery ponds for ~30 days until they are recovered as juveniles, growout of the fish in tanks or ponds for 9-12 months until they are recovered as subadults, and growth of these advanced fingerlings to market-size. Aquaculture ponds are notoriously variable environments and effects of environmental variation between ponds have the potential to mask genetic contributions to fish performance. Accordingly, we are conducting "common garden" performance evaluations in which progeny from different parental crosses are reared communally in the same pond(s). We utilize microsatellite DNA markers to identify offspring produced by each parental pair involved in a series of crosses designed to provide information on the genetic basis of specific traits. Currently, Charlene Couch (Ph.D. student) is working toward selective breeding of striped bass and Amber Garber (Ph.D. student) with hybrid striped bass. We also are working to develop hundreds of new markers as the first step toward mapping the Morone genome and discovering markers linked to genes regulating fish performance (quantitative trait loci) that can be used to predict performance in selective breeding programs. This project is a collaborative effort between our laboratory (Sullivan), Kent SeaTech Corporation (Dr. Mark Westerman), the USDA National Center for Cool and Cold Water Aquaculture (Dr. Caird Rexroad III).

Daniel Ciobanu

Our interest is in the development of the molecular tools that will enhance the effectiveness of Sygen's (SyAqua) shrimp breeding program. DNA-based animal identification and gene discovery can contribute significantly to the development of genotypes more suitable for the BioZEST system. Efficient and cost-effective shrimp identification procedures that avoid tagging, allow co-rearing of shrimp from multiple genetic backgrounds, and estimation of different familial/population contribution have been developed and are in the testing/optimization stage. Another area of interess is identification of candidate genes and markers that control genetic variation in economically important traits. Markers will enable the development of Marker Assisted Selection (MAS) as an important component of our breeding program. This is of particular interest for traits such as survival and meat quality that are difficult to improve by traditional quantitative breeding methods. Candidate genes can be based on the physiology of traits, the detection of chromosomal regions associated with Quantitative Trait Loci (QTL), and gene expression data (through micro-arrays or other gene expression platforms ). There is also a significant effort directed towards genetic protection systems and different options are evaluated and tested.

Dennis Hedgecock

My research focuses on the population, quantitative, evolutionary and conservation genetics of marine fish and shellfish, including Pacific oysters and white seabass. We use genetic mapping and functional genomics to study the genetic basis of hybrid vigor in Pacific oysters, a commercially important species. We have developed crossbreeding techniques for farmed Pacific oysters and produced high-yielding hybrid oyster varieties. Ultimately, we hope to shed light on the basis for hybrid vigor in corn and other crops and on the maintenance of genetic diversity in natural populations.

Filip Volckaert

The main objective of BASSMAP is to prepare a medium density linkage map of sea bass (Dicentrarchus labrax L.) that includes both type 1 and type 2 markers in a single project so that it is immediately available as a practical tool by the end of the project for the aquaculture industry. Type1 genetic markers will include at least 100 Expressed Sequence Tags (ESTs) located within corresponding functional genes. Type 2 markers will include about 200 Amplified Fragment Length Polymorphisms (AFLPs) and 300 DNA microsatellite markers. The linkage map will be used as a tool for a pilot study to map several economically important Quantitative Traits Loci (QTLs) of this species and to characterize some candidate genes that are possibly responsible for these QTLs.

Geoffrey Waldbieser

We integrate quantitative and molecular genetics, physiology, immunology, microbiology and virology in an applied breeding program for catfish genetic improvement. My research is in the production of molecular tools, such as genetic maps, markers, and assays, to assist our correlation of performance with allelic inheritance and help us identify genetically superior broodstock. Geneticallly improved fish are released to the catfish industry

Gideon Hulata

To enumerate the genes controlling sex determination in commercial strains of tilapia, with the ultimate aim of breeding inbred lines which can be crossed to produce all-male progenies for commercial production. To this end, our immediate goals are to:

1) Identify genetic markers linked to sex-determining genes in various experimental and commercial stocks of O. niloticus and O. aureus, as well as red tilapias;

2) Develop additional markers tightly linked to these sex determiners, and develop practical, non-destructive genetic tests for identifying genotypic sex in young tilapia;

3) Map additional sex-modifier loci through a combination of approaches, including gynogenesis, crossing of hormonally sex-reversed broodstock, and environmental manipulation, with the aim of eliminating particular alleles from selected inbred lines.

By identifying the sex determining regions, and quantifying their relative strength, our results will simplify the selection of broodstock animals and improve the efficiency of all three methods currently used to produce all-male fingerlings for commercial production.

Hans Magnus Gjøen

Utilisation of high-resolution phenotypic records (e.g. microarray data) in optimisation of breeding programs for fish.

Jan F. Cordes

Molecular species Identification of Asian Pacific oysters; population genetics of Crassostrea ariakensis

Jean François SAMAIN

Aim: Understanding the physiological processes and their regulation by exogenous and endogenous factors in marine bivalves with functional exploration of molecular mechanisms implicated in key steps of main physiological functions of interest for aquaculture; and next investigate relationships between polymorphism of genes of interest and these functions. For reproduction, the origin and the mechanisms of annual renewal of germ cells, still unknown in marine bivalves, are under characterization in C. gigas using the oyster vasa-like gene (Oyvlg) we characterized and used as a specific marker of germline cells in oyster. (Fabioux et al, 2004a,b Biophys Biochem Res Com).

For adaptation, we developed a multidisciplinary project with the aim of understanding the causes of summer mortality of C. gigas. Two approaches are under study: enzymatic and molecular analysis of glucid metabolism and especially of glycogen reserves in relation to reproduction and health of animals; analysis of physiological bases of summer survival resistance through resistant and susceptible oyster families produced by a divergent selection on summer survival. That was firstly engaged with subtractive libraries realized between resistant and susceptible oyster families (Huvet et al, 2004 Gene) and need now the development of genomic tools such as micro-arrays with the ESTs we share on C. gigas with several French and non-French laboratories. For growth and nutrition, based on relationships observed between growth variability, assimilation rate and digestive enzymes, we developed a molecular approach on the two amylase genes we characterized in oyster. The aim was to establish relationships between amylase polymorphism, enzymatic and molecular expression of amylase genes and assimilation and growth rates of oyster to evaluate the ability of improving growth in oyster strains using amylase genes as genetic marker (Moal et al, 2000 J Comp Physiol B; Sellos et al, 2003 Mar Biotechnol; Huvet et al, 2003 Aquaculture).

Jeanne MOAL

Aim: Understanding the physiological processes and their regulation by exogenous and endogenous factors in marine bivalves with functional exploration of molecular mechanisms implicated in key steps of main physiological functions of interest for aquaculture; and next investigate relationships between polymorphism of genes of interest and these functions. For reproduction, the origin and the mechanisms of annual renewal of germ cells, still unknown in marine bivalves, are under characterization in C. gigas using the oyster vasa-like gene (Oyvlg) we characterized and used as a specific marker of germline cells in oyster. (Fabioux et al, 2004a,b Biophys Biochem Res Com).

For adaptation, we developed a multidisciplinary project with the aim of understanding the causes of summer mortality of C. gigas. Two approaches are under study: enzymatic and molecular analysis of glucid metabolism and especially of glycogen reserves in relation to reproduction and health of animals; analysis of physiological bases of summer survival resistance through resistant and susceptible oyster families produced by a divergent selection on summer survival. That was firstly engaged with subtractive libraries realized between resistant and susceptible oyster families (Huvet et al, 2004 Gene) and need now the development of genomic tools such as micro-arrays with the ESTs we share on C. gigas with several French and non-French laboratories. For growth and nutrition, based on relationships observed between growth variability, assimilation rate and digestive enzymes, we developed a molecular approach on the two amylase genes we characterized in oyster. The aim was to establish relationships between amylase polymorphism, enzymatic and molecular expression of amylase genes and assimilation and growth rates of oyster to evaluate the ability of improving growth in oyster strains using amylase genes as genetic marker (Moal et al, 2000 J Comp Physiol B; Sellos et al, 2003 Mar Biotechnol; Huvet et al, 2003 Aquaculture).

Jeffrey Silverstein

Animal breeding, quantitative genetics and physiology Identification and definition of traits for selective improvement, germplasm improvement through selective breeding Interests in QTL definition and marker/gene assisted selection

K. C. Majumdar

Growth enhancement through trangenesis, Genetic interrelationships through molecular markers including, mt DNA, STR, RAPD, etc

Kate Wilson

Genomics-related research on Penaeus monodon at AIMS has three areas of focus: a. Linkage mapping in P. monodon to create a framework genetic map b. Study of genes involved in response to specific environmental stresses and in genes involved in immunity c. The molecular genetics of reproduction

Keitaro Kato

Studies on the molecular mechanism of occurrence of vertebral deformities. Development of transgenic technologies in marine finfish. Application of proteome and transcriptome analysis in the molecular biological studies in marine finfish.

Marta Gomez-Chiarri

Infectious diseases have a serious impact on shellfish and finfish, constraining the expansion of aquaculture and endangering wild fisheries. My research interests include the use of multidisciplinary approaches to the prevention and management of infectious diseases in cultured and wild shellfish and finfish. These approaches include studying the patterns of disease prevalence and distribution using traditional and molecular diagnostic tools, evaluating the effect of environmental parameters on disease distribution and transmission, and using genomics and proteomics to investigate host-parasite interactions. The final goal is to increase our knowledge on mechanisms of disease resistance, and use this information to develop novel strategies to prevent diseases.

Masashi Sekino

Current interest is of genetic linkage mapping for oyster and abalone.

Max F. Rothschild

Shrimp Genomics

Melanie Wilson

Evolution of the immune system Phylogeny of antigen receptors, structure and function Immunoglobulin T cell receptor gene regulation in ectothermic vertebrates Recognition molecules on teleost NK-like cells

Nagaraj Chatakondi

Nagaraj Chatakondi 1. Mass selection to improve the commercial traits of channel catfish for three generations. The growth rate in some strains has a 25 -30 %, improved 12% in feed conversion and 17% increase in survival. About 0.8 million kgs of broodfish were sold to commercial producers in the last 5 years. Gold Kist fish has outperformed any other strain of fish that has been released to the industry.

2. Produced 20 million channel x blue hybrid catfish fry. Hybrid catfish are superiror catfish for pond environment that has outstanding commerical traits documented in research and commercial ponds. Has been the lead instituition in addressing all the facets of hybrid catfish production : hormone dose, broodfish preparation, gonadal maturity, egg quality and best production practices.

3. Initiated Marker assisted selection for channel catfish in colloboration with John Liu (AU); Developed an optimum feeding regime for broodfstock using microsatellite markers in colloboration with Geoff Waldbiesier (USDA CGRU) and developed optimum chemical treatments for developing embryos in colloboration with Brian Small (USDA, Stoneville, MS).

4. One generation of mass selection in channel catfish for smaller head has resulted an increase of 1.1% in processing yield compared to non-selects. 12 gram (significant increase) meat per fish.

5. Selection of channel catfish broodstock for non-carriers of channel catfish virus is presently developed and tested to produce CCV free broodstock in colloboration with MSU Veterinary College of Medicine, Starkville, MS.

Nick Elliott

CSIRO works with industry, research partners and funding agencies to realise the potential of Australian aquaculture. Advanced technologies are being applied to produce long-life products from healthy, genetically-superior animals raised on high-efficiency feeds in low-impact production systems. Our genetics projects are aimed at introducing and supporting selective breeding program with the use of novel, advanced and standard, quantitative and molecular genetic technologies.

Patrick J. Babin

Physiological genomics related to nutrition and reproduction of fish species. Comparative genomics.

Paul S. Gross

CURRENT RESEARCH ACTIVITIES

1. Role of antimicrobial peptides in shrimp and oysters.

2. A genomics approach to the study of the immune system of penaeoid shrimp with an emphasis on identification and characterization of expressed immune genes.

3. Response to immune challenge and comparison of the immune systems of two sister species of Litopenaeid shrimp the Pacific white shrimp, Litopenaeus vannamei and the Atlantic white shrimp, L. setiferus.

Perry B. Hackett

The Hackett lab research is focused on developing tools for transgenesis and studying gene expression in vertebrates. . The lab's main area of interest is using transposons as vectors for making transgenic animals and human gene therapy as well as tagging and mapping genes in vertebrate chromosomes. The transposon system, called Sleeping Beauty because it was resurrected from an evolutionary sleep of more than 10 million years. The Sleeping Beauty system appears to be the most efficacious method for inserting genes into human chromosomes without using viruses. The lab uses zebrafish as a model vertebrate organism to study genome structure and regulation of gene expression.

Pierre Boudry

Our genetic team in the lab is interested in developing researchs in:
- populations genetics with molecular markers (microsatellites, mtDNA,...) and phylogeography
- genetic maps (with microsatellites, AFLps, SNPs,...) and QTLs mapping (for traits related to environnemental or pathogen stress),
- selective breeding (genetics parameters and breeding programs),
- polyploidy (tetraploids and triploids) and aneuploidy.

Roy Danzmann

Roy Danzmann The lab is involved in developing and mapping anonymous DNA markers and type I gene markers onto the genetic maps of three model tetraploid salmonid species. These species were chosen to represent the three major genera within the subfamily Salmoninae of the teleost family Salmonidae. The genetic maps are then used to identify chromosomal regions having a genetic influence on important life history traits in these fish. Traits of interest include stress tolerance (i.e. thermal and salinity tolerance), spawn timing, maturation timing, disease resistance, and growth.

Standish K. Allen, Jr.

ABC engages in selective breeding of bivalves, especially oysters and hard clams. Of special interest is disease resistance. We also develop and release technology for the production of triploids and tetraploid bivalves.

Stig W. Omholt

Centre for Integrative Genetics (CIGENE) is hosted by the Agricultural University of Norway (NLH) as a national core facility in the Norwegian Functional Genomics Programme (FUGE) responsible for detection, genotyping and interpretation of SNPs. In addition to providing a high-throughput SNP-typing service of human, animal, fish, plant and microbial materials, CIGENE has a national responsibility for developing and dissipating key competence concerning identification and methodological integration of experimental and theoretical approaches for making a causal connection between genomic and phenotypic data on complex traits. CIGENE is by Norwegian authorities expected to make active use of its competence base within marine functional genomics, and the centre is very much focused on developing international collaboration. Current activities include SNP detection and validation in salmon, construction of advanced simulation software for studying genome dynamics, determination of linkage disequilibrium and haplotype blocks, calculation of statistical power of various designs to detect QTLs, fine-mapping of QTLs, dynamic modelling of physiological systems in salmon, and proteomics studies (including advanced multivariate analysis) as part of our concerted effort to understand the underlying determinants of salmon meat colour (which we have targeted as one of our proof of principal traits).

Sylvie Lapègue

Our genetic team in the lab is interested in developing researchs in:

- populations genetics with molecular markers (microsatellites, mtDNA,...) and phylogeography
- genetic maps (with microsatellites, AFLps, SNPs,...) and QTLs mapping (for traits related to environnemental or pathogen stress),
- selective breeding (genetics parameters and breeding programs),
- polyploidy (tetraploids and triploids) and aneuploidy.

Vi Gregory Chinchar

My lab is interested in antiviral immunity in channel catfish with emphasis on NK cells, CTLs, antimicrobial peptides, and anti-viral cytokines. In addition, we have a project examining infectious causes of amphibian decline, and are currently developing antisense strategies to knock down viral gene expression as a means of determining the role of those genes in virus replication and pathogenesis

Wazir S. Lakra

1. Population genetics of tiger shrimp Penaeus monodon and the giant freshwater prawn Macrobrachium rosenbergii

The fish genetics and biotechnology laboratory at CIFE is one of the most advanced labs in HRD in fish molecular biology and biotechnology. We are actively involved in the genetic characterization and upgradation of shrimps and prawns, molecular biology and biotechnology of selected fish and shell fish used in Indian aquaculture. This program is aimed to the identification of strains using chromosome, allozyme and DNA markers.

As a new initiative, an international project on genetic improvement in P. monodon has recently been launched by us in collaboration with CIBA Chennai and the AKVAFORSK, Norway.

2. Salt tolerant genes from tiger shrimp.

We are conducting research to identify and characterize genes responsible for salinity tolerance in the tiger shrimp P. monodon. This may be useful for shrimp aquaculture.

3. Cell culture systems:

Our laboratory is actively involved in he development of cell lines from fish species used in aquaculture. We have succeeded in developing primary cultures and cell lines from Labeo rohita, Catla catla, Lates calcarifer and Tor putitora for the first time.

William R. Wolters

Genetic improvement of Atlantic salmon

Willie Davidson

(1) Genomics Research on Atlantic Salmon Project. This involves physical mapping, integration of the physical and linkage map, comparisons of duplicated segments of the genome, and searching for the sex-determining gene. (2) Arctic charr broodstock development. This involves a breeding program in collaboration with Icy Waters International in Whitehorse in the Yukon, genetic mapping, QTL analysis, and sex-determination.

Yann Guiguen

AGENAE (Analysis of Livestock Species Genomes, http://www.inra.fr/agenae/) is an important project led by the French National Institute for Agricultural Research (INRA) that focuses on genomics of several livestock species (cattle, pig, chicken and rainbow trout). Objectives of this program are the identification and characterization of the expressed part of genomes, the mapping of entire genomes, and the study of genetic diversity in animal populations. As a first step for the characterization of the expressed part of the genome of rainbow trout, we initiated a high-throughput EST sequencing program. This sequence information is currently used as a basis for expression profiling experiments using micro-arrays with a well characterized cDNA clone collection (10 000 well characterized and annotated genes).

Zhanjiang (John) Liu

The focus of our laboratory is to understand the genomic structure, organization, and expression of catfish. Specifically, we are using genetic approaches to map various markers to the catfish linkage map. We are interested in improving performance and production traits using QTL mapping and marker-assisted selection. Several traits have been studied including growth rate, disease resistance, feed conversion efficiency, processing yield, and low oxygen tolerance. We are also working on the development of genome resources such as expressed sequence tags and BAC-based physical maps. To date, over 40,000 catfish ESTs have been sequenced from our laboratory. We have initiated the physical mapping project of catfish. Through the application of microarray technology, we are identifying the candidate genes involved in important traits such as disease resistance. We have used an interspecific hybrid system of channel catfish x blue catfish, which provided a terrific opportunity for QTL analysis, especially for the analysis of resistance against the major bacterial diseases. Our laboratory has devoted major efforts to understanding the transcriptome of catfish and systematic cloning, characterization, and expression analysis of genes involved in various pathways. Many genes important for biotechnology have been identified, cloned, and characterized.