NRSP-8 Aquaculture Research Progress Report for 2006

Aquaculture Coordinator: John Liu

Progress toward Objective 1: Enhance and integrate genetic and physical maps of agriculturally important animals for cross species comparisons and sequence annotation:

Catfish: Two framework genetic linkage maps were reported. One was constructed using channel catfish intraspecific resource families (Waldbieser et al., 2001), and the other was made with channel catfish x blue catfish interspecific families (Liu et al., 2003). The major objective for intraspecific mapping is to aid genetic improvements using various channel catfish lines, while the major objective for interspecific mapping is to aid genetic improvements through the use of interspecific hybrids and introgression. Several hundred more microsatellites have been added in the past year to the linkage maps, especially the gene-associated type I markers. A gene-based linkage map has been constructed.

The physical maps of the catfish genome have been constructed by fingerprinting CHORI 212 BAC library (5.6X genome coverage) and CCBL1 BAC library (7X genome coverage). A total of 3256 contigs were assembled with the CHORI 212 library, and 1782 contigs were assembled with the CCBL1 BAC library. Estimated map lengths were approximately 930 Mb. A large number of BAC end sequences have been generated and over 20,000 have been deposited to GenBank from Auburn University. A large number of BAC-associated microsatellites have been identified for the integration of linkage and physical maps.

Salmonids: Linkage mapping efforts are ongoing with several salmonids species. In particular, work with the cGRASP Project in Canada has mapped hundreds more microsatellites, especially those from the BAC ends to the linkage map of Atlantic salmon. Over 228,000 BAC clones have been fingerprinted from the Atlantic salmon BAC library, and 4338 contigs have been assembled. For rainbow trout, a NRI grant was just awarded to construct a BAC contig-based physical map of the rainbow trout genome. Efforts to obtain genome sequences for rainbow trout and Atlantic salmon continued. A working group from cGRASP, Consortium for Genome Research on All Salmonids Program, met in Leetown, WV on May 10 -12 to outline strategies for obtaining whole genome sequences. A subsequent workshop was held at Simon Fraser University, October 10-12, consisting of scientists and representatives from sequencing centers and funding agencies. A meeting report and revised version of a white paper has been generated by the Executive Committee. Initial sequencing has been initiated under the support of Canadian and Norwegian governments.

Tilapia: A BAC-based physical map, and the 2nd generation genetic map was published in the last year by Thomas Kocher’s group. His proposal to sequence the ends of 35,000 BAC clones was approved by Genoscope, with sequencing to begin in early 2007. The proposal to sequence the tilapia genome was approved by the NIH, with sequencing to begin in late 2007. NIH-NHGRI has committed to producing a draft assembly of the tilapia genome, together with 2x sequencing from each of three closely related haplochromine cichlid fish.

 

Oysters: Gaffney’s lab at the University of Delaware is completing a project on SNP marker development and mapping in the Pacific oyster. Primer sets have been designed and tested for multiple Type I markers, based on the existing EST database. A total of 53 loci have been amplified and sequenced in multiple individuals representing the geographic range of the species, as well as two parents from a mapping family provided by the Hedgecock lab. Although virtually every locus has been found to be polymorphic, often with multiple SNPs, the inbred mapping family is invariant for some of the loci. For the remaining loci, temperature gradient capillary electrophoresis (TGCE) is being used to score parents and progeny (N = 48-72) to enable these loci to be placed on the framework microsatellite map produced by the Hedgecock lab. As part of the EU-funded project Aquafirst, French researchers have developed approximately 50 SNPs; these will be mapped using an F2 family segregating for resistance to summer mortality, which has already been mapped for 100 microsatellite loci. A BAC-based physical map of the C. gigas genome will be constructed by BAC fingerprinting, in a USDA NRI project scheduled to begin in 2007.

For the eastern oyster, Dr. Ximing Guo’s lab at Rutgers developed 53 SSR and 44 SNP markers from putative host-defense gene and ESTs. These are now being scored in two mapping families for placement on the AFLP scaffold linkage map.

The Gaffney lab conducted PCR trials of primers developed for C. gigas and C. virginica were tested on other Crassostrea species, including members of the Atlantic clade (C. rhizophorae, C. gasar, C. corteziensis) and the Asian clade (C. ariakensis, C. sikamea, C. hongkongensis). Several targets were sequenced for all species, to provide preliminary data for comparative genomics applications.

Shrimps: A genetic linkage map of the Pacific white shrimp was constructed, and more markers were added to the existing genetic linkage map of the tiger shrimp.

Striped Bass: One of the largest efforts currently in the U.S. focused on genomics in striped bass is a research collaboration between researchers at North Carolina State University and the USDA National Center for Cool and Coldwater Aquaculture in Kearneysville, WV. This collaboration was funded by a grant from the University of North Carolina Office of the President Genomic Initiative to Dr. Craig Sullivan (NCSU) to develop polymorphic microsatellite markers for use in large-scale common garden breeding experiments and for future development of the first linkage map in this species. This research project ended in May 2005 and has led to the discovery and characterization of over 500 microsatellite markers in striped bass that have now been deposited in GenBank. Additional work by the same group focused on DNA pooling for estimation of allele frequencies. Based on this progress this same group received funding for development of the first genetic linkage map for striped bass from the Sea Grant National Marine Aquaculture Initiative in 2006. This research should result in development of a genetic linkage map for striped bass in 2008.

 

Progress toward Objective 2: Facilitate integration of genomic, transcriptional, proteomic and metabolomic approaches toward better understanding of biological mechanisms underlying economically important traits:

Catfish: The Joint Genome Institute is sequencing 300,000 EST clones from catfish, of which 200,000 will be sequenced from channel catfish and 100,000 will be sequenced from blue catfish.

Melanie Wilson’s group has completed the sequencing of 9 BACs covering part of the catfish immunoglobulin heavy chain locus and are continuing mapping of this important locus. A manuscript concerning the annotation has been published. Characterization and functional studies of catfish immune molecules, such as, T Cell Receptors and their accessary molecules CD4 and CD8, Novel Immune Type Receptors, Leukocyte Immune Type Receptors (LITR), Immunoglobulin D, FcRs and the B cell accessary molecules CD79a and 79b, are ongoing. Monoclonal and polyclonal antibodies specific for various LITRs, IgD, CD79b and IpFcR have been produced and are being characterized. Her group is also producing antibodies to other immune related genes. The University of Mississippi Medical Center is coordinating the channel catfish part of the US Veterinary Immune Reagent Network Grant for production of recombinant proteins and/or peptides for development of reagents for basic research and diagnostic purposes for various animals important in US agriculture.

Work in John Liu’s lab was focused on the development of genome resources including previously prepared 23 cDNA libraries from various tissues, and construction of four normalized cDNA libraries to support the JGI approved large-scale catfish EST project. Using existing EST as resources, comparative sets of chromosome-specific ESTs were identified by anchoring catfish ESTs to Tetraodon genome. Much effort was made to characterization of innate immune genes and analysis of their expression in the resistant blue catfish as compared to expression in the susceptible channel catfish after infection with the most serious bacterial disease enteric septicemia of catfish (ESC). A total of 26 CC chemokine genes, 6 CXC genes, 4 antimicrobial peptide genes, interleukin-1 beta gene, 23 selenoprotein genes, 6 toll-like receptors, and a few dozens of other genes were completely sequenced, mapped to BACs, and expression was analyzed. Conserved syntenies were analyzed comparatively with zebrafish or Tetraodon genomes. A 28K gene array was constructed with the Nimblegen platform, and used to analyze differentially expressed genes after infection of bacterial disease enteric septicemia of catfish.

Work in Geoff Waldbieser’s lab using microarrays for the analysis of catfish response to LPS injection has been published. His lab has also conducted investigations on growth hormone – IGF pathway and its interaction with the immune system, and prepared several cDNA libraries for the JGI EST project.

 

Salmonids: The number of ESTs for rainbow trout increased 9% to 262,330 and Atlantic salmon increased 131% to 431,754. This represents the majority of nucleotide data for the salmonids, which has 708,862 nucleotides and 5507 proteins in GenBank. Several microarrays are available for functional genome research. These data have provided an excellent starting point for candidate gene investigation including uncoupling proteins, myostatins, pro-opiomelanocortins, and tapasins. Significant progress continues to be made in identifying genes which affect development rate, oxygen consumption, and sex determination.

Tilapia: USDA-NRICGP has just approved a project to sequence 100,000 ESTs from a variety of tilapia cDNA libraries. These sequences will complement existing EST resources for related cichlid fish, allowing the production of 2nd generation microarrays for tilapia.

Oysters: The Oyster Genome Consortium entered into a user agreement with the US DOE Joint Genome Institute for sequencing of EST and BAC libraries for the Pacific oyster. JGI will do paired-end sequencing of 150,000 cDNAs. JGI will also sequence four BAC contigs containing genes identified by Cunningham et al. (2006), in order to assess levels of DNA polymorphism in coding and non-coding regions, which could ultimately influence whole genome shotgun sequencing strategy. A transcriptomic analysis of inbred and hybrid oysters (Hedgecock et al. 2007) revealed candidate genes for heterosis, several of which have been identified through BLAST searches. Work is in progress to find SNPs in these genes and to place them on the QTL map. For the Pacific oyster, Dr. Hedgecock’s lab reported QTL-mapping results on the number, location, and mode of action of genes affecting yield in an F2 family derived from a naturalized C. gigas population in Dabob Bay (WA). Three dominant QTL for yield on three different chromosomes were detected. They also have mapped a recessive QTL for an abnormal "hook-hinge" condition segregating in this same family as well as an additive QTL for shell pigmentation. In France, a study of the relationship between genetic variation in amylase genes and growth in C. gigas has been published. Current work on other genes (project "Polygigas") is in progress, supported by the Bureau des Ressources Genetiques. Using a F2 family segregating for resistance to summer mortality, researchers under the EU project Aquafirst will seek to identify QTL for this trait in 2007.

In the eastern oyster, Dr. Guo’s lab identified and mapped 12 putative disease-resistance QTLs. For the flat oyster, French researchers are in the process of mapping QTL of resistance to bonamiosis, a major disease for this species. Gaffney’s lab is mapping SNPs using a F2 family segregating for resistance to summer mortality.

Shrimps: Six high quality tissue specific cDNA libraries have been constructed and analyzed for depth and redundancy, with 1000 EST being collected from each library to date. Redundancy depletion and shipment to JGI is 83% complete (100,000 clones), awaiting JGI to perform full double pass sequencing. Preliminary characterization of the libraries and analysis of existing ESTs was published. Full annotation and metagenomic analysis to follow. - The first generation microarray has been printed and initial validation and QA/QC have been completed. These microarrays contain in excess of 3000 unigenes and are currently in use; the first experimental research work is in press. Studies on the effects of long dsRNA and RNAi in relation to viral challenge and WSSV in the Pacific Whiteleg Shrimp, Litopenaeus vannamei are ongoing. Continuing research in the area of antimicrobial peptides and their importance in shrimp immunity has yielded data on the structure of the Penaeidin gene family, its control elements, and specificity for microbial targets.

Striped Bass: Significant progress was made in 2006 involving integration of genomic approaches toward better understanding of biological mechanisms underlying economically important traits in striped bass. Much of this work is described in three dissertations submitted to North Carolina State University (Couch, C.R., 2006; Garber, A.F., 2006) and Texas A&M University (Wang, X., 2006). Each of these dissertations studies used microsatellite markers to assess economically important traits such as growth, disease resistance, and carcass-quality in striped bass. These new studies will be important going forward as the genetic linkage map is produced for striped bass and will eventually aid in the identification of QTL for economically important traits.

Progress Toward Objective 3: Facilitate and implement bioinformatic tools to extract, analyze, store and disseminate information. (See Attachment 1 for more details on objectives.):

Catfish: John Liu’s lab continues their efforts on development of comparative genome tools such as chromosome-anchored ESTs of catfish. Large scale informatic mining of microsatellites and SNPs are underway; The CGRU in 2006 will continue development and enhancement of microarray tools, and further use of arrays to identify candidate genes for disease resistance.

Salmonids: The Atlantic salmon and rainbow trout gene indices have relocated to the Dana Farber Cancer Institute and have been updated to versions 3.0 and 6.0, respectively. http://compbio.dfci.harvard.edu/tgi/tgipage.html.

Tilapia: Dr. Kocher’s group has implemented the Gbrowse software to facilitate viewing of tilapia sequences on the Tetraodon genome assembly (http://hcgs.unh.edu/gbrowse/).

Oysters: Within the EU project Aquafirst, QTL data will be hosted by the Roslin Institute on ArkDB. EST data will be held on the INRA platform "Sigenae" in Toulouse.

Shrimps: The marine genomics group at the Hollings Marine Laboratory and MUSC continues to maintain www.marinegenomics.org for the archiving of EST and microarray data, and as a resource for on-line tools that can be used in the analysis of genomic and transcriptomic data, which are being used to archive and analyze shrimp metagenomic and microarray data. In addition, contracting with Clemson University Genome Institute is underway to enhance EST analysis capabilities.

Publications:

Catfish publications:

Arias, C. R., Abernathy, and Liu, Z. J. 2006. Combined use of 16S ribosomal DNA and automated ribosomal intergenic spacer analysis (ARISA) to study the bacterial community in catfish ponds. Letters in Applied Microbiology 43:287-92.

Bao B, Peatman E., Xu P, Li P, Zeng H, He C, and Liu Z.J. 2006. The catfish liver-expressed antimicrobial peptide 2 (LEAP-2) gene is expressed in a wide range of tissues and developmentally regulated. Molecular Immunology 43, 367-377.

Bao B., Peatman, E., Xu P., Baoprasertkul B., Wang G., Liu Z.J. 2006. Characterization of 23 CC chemokine genes and analysis of their expression in channel catfish (Ictalurus punctatus). Developmental and Comparative Immunology 30, 783-796.

Baoprasertkul P., Peatman, E., Somridhivej, B., Liu, Z.J. 2006. Toll-like receptor 3 and TICAM genes in catfish: species-specific expression profiles following infection with Edwardsiella ictaluri. Immunogenetics 58(10):817-830.

Baoprasertkul, B., Peatman, E., Abernathy, J., Liu, Z.J. 2007. Structural characterization and expression analysis of Toll-like receptor 2 gene from catfish. Fish and Shellfish Immunology 22, 418-426.

Bengtén E., S. Quiniou, J. Hikima, G. Waldbieser, G.W. Warr, N.W. Miller and M. Wilson. 2006. Structure of the catfish IGH locus: analysis of the region including the single functional IGHM gene. Immunogenetics 58:831-844.

Bengtén, E., L.W. Clem, N.W. Miller, G.W. Warr and M. Wilson. 2006. Channel catfish immunoglobulins: repertoire and expression. Dev. Comp. Immunol. 30: 77-92.

Dunham, R., Liu, Z.J. 2006. Transgenic fish-where we are and where do we go? Israel Journal of Aquaculture-Bamidgeh 58(4), 297-319.

Edholm E.-S., J.L. Stafford, S.M. Quiniou, G. Waldbieser, N.W. Miller, E. Bengtén and M. Wilson. 2007 Channel catfish, Ictalurus punctatus, CD4-like molecules. Dev. Comp. Immunol. 31:172-187.

Hikima, J., M.L. Lennard, M.R. Wilson, N.W. Miller and G.W. Warr. 2005. Regulation of immunoglobulin heavy chain locus expression at the phylogenetic level of a bony fish: transcription factor interaction with two variant octamer motifs. Gene 377: 119-129.

Hikima, J., M.L. Lennard, M.R. Wilson, N.W. Miller, L.W. Clem and G.W. Warr. 2006. Conservation and divergence of the E3' enhancer in the IGH locus of teleost fish. Immunogenetics 58: 226-234.

Hou, L., Bi, X., Zou, X., He, C., Yang, L. Qu, R., Liu Z.J. 2006. Molecular systematics of bisexual Artemia populations. Aquaculture Research 37, 671-680.

Lennard M.L., J. Hikima, D.A. Ross, C. Kruiswijk, M.R. Wilson, N.W. Miller, L.W. Clem and G.W Warr. 2006. Characterization of an Oct-1 orthologue in the channel catfish, Ictalurus punctatus: a negative regulator of transcription? (Submitted).

Lennard, M.L., M.R. Wilson, N.W. Miller. L.W. Clem, G.W. Warr, J. Hikima. 2006. Oct2 transcription factors in fish-a comparative genomic analysis. Fish & Shellfish Immunology 20: 144-151.

Li RW, Waldbieser GC. Genomic organisation and expression of the natural killer cell enhancing factor (NKEF) gene in channel catfish, Ictalurus punctatus (Rafinesque). Fish Shellfish Immunol. 2006 Jan;20(1):72-82.

Li RW, Waldbieser GC. 2006. Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus. BMC Genomics. 7:134.

Liu, Z.J. 2006. Transcriptome characterization through the generation and analysis of expressed sequence tags: Factors to consider for a successful EST project. Israel Journal of Aquaculture-Bamidgeh 58(4), 328-341.

Liu, Z.J. 2006. Catfish genome mapping toward genetic enhancement of broodstocks. In "The Genome: A Series on Genome Mapping, Molecular Breeding & Genomics of Economic Species" (C. Kole ed.) Vol. 6, Oxford & IBH and Science Pub. Inc.

Liu, Z.J., Peatman, E. 2006. Chemokines in fish: a rapidly expanding repertoire. pp. 121-144. In Focus on Immunology Research, (Editor, Barbara A. Veskler), Nova Science Publishers, Inc., New York.

Long, S. I. Milev-Milovanovic, M. Wilson, E. Bengtén, L.W. Clem, N.W. Miller and V.G. Chinchar. 2005. Identification and expression analysis of cDNAs encoding channel catfish interferons. Fish and Shellfish Immunology 21: 42-59.

Milev-Milovanovic, S. Long, M. Wilson, E. Bengtén, N.W. Miller and V.G. Chinchar. 2006. Identification and expression analysis of interferon gamma genes in channel catfish. Immunogenetics 58: 70-80.

Peatman E.,, Bao B., Xu P., Baoprasertkul P., Liu Z.J. 2006. Catfish CC chemokines: genomic clustering, duplications, and expression after bacterial infection with Edwardsiella ictaluri. Molecular Genetics and Genomics 275, 297-309.

Peatman, E., and Liu, Z.J. 2006. CC chemokines in zebrafish: evidence for extensive intrachromosomal gene duplications. Genomics 88, 381-385.

Simmons, M., Mickett K., Kucuktas H., Li P., Dunham R., Liu, Z.J. 2006. Comparison of domestic and wild catfish populations provide no evidence for genetic impact. Aquaculture 252,133-146.

Small BC, Murdock CA, Waldbieser GC, Peterson BC. Reduction in channel catfish hepatic growth hormone receptor expression in response to food deprivation and exogenous cortisol. Domest Anim Endocrinol. 2006 Nov;31(4):340-56. Epub 2006 Jan 6. PMID: 16423501 [PubMed - indexed for MEDLINE]

Stafford J.L., E. Bengtén, L.Du Pasquier, N.W. Miller and M. Wilson. 2006. Alloantigen-stimulated channel catfish (Ictalurus punctatus) lymphocytes express multiple leukocyte immune-type receptors (LITRs) containing a putative MHC class I binding site. Immunogenetics Epub.

Stafford J.L., E. Bengtén, L.Du Pasquier, R.D. McIntosh, S.M. Quiniou, L.W. Clem, N.W. Miller and M. Wilson. 2005. A Novel Family of diversified and immunoregulatory receptors in teleosts is homologous to Mammalian Fc Receptors and molecules encoded within the Leukocyte Receptor Complex. Immunogenetics 58: 758-773.

Stafford, J.L., M. Wilson, D. Nayak, S. Quiniou, L.W. Clem, N.W. Miller and E. Bengtén. 2006. Identification of an Fc-receptor homolog in channel catfish, Ictalurus punctatus. J. Immunol. 177: 2505-2517.

Wang Q, Bao B, Wang Y, Peatman E, and Liu Z.J. 2006. Characterization of a NK-lysin antimicrobial peptide gene from channel catfish. Fish and Shellfish Immunology 20:419-426.

Wang Q., Wang Y., Xu P., Liu Z.J. 2006. NK-lysin of channel catfish: gene triplication, sequence variation, and expression analysis. Molecular Immunology 43, 1676-1686.

Wang Y., Wang Q., Baoprasertkul P., Peatman E., Liu Z.J. 2006. Genomic organization, gene duplication, and expression analysis of interleukin-1beta in channel catfish (Ictalurus punctatus). Molecular Immunology 43: 1653-1664.

Wernersson, S., J.M. Reimer, M. Poorafshar, U. Karlson, N.Wermenstam, E. Bengtén, M. Wilson, L. Pilstrom and L. Hellman. 2006. Granzyme-like sequences in bony fish shed light on the emergence of hematopoietic serine proteases during vertebrate evolution. Dev. Comp. Immunol. 30: 901-918.

Willett KL, Ganesan S, Patel M, Metzger C, Quiniou S, Waldbieser G, Scheffler B. In vivo and in vitro CYP1B mRNA expression in channel catfish. Mar Environ Res. 2006 Jul;62 Suppl:S332-6. Epub 2006 Apr 18. PMID: 16697458 [PubMed - in process]

Xu, P., Wang, S., Liu, L., Peatman, E., Somridhivej, B., Thimmapuram, J., Gong, G., Liu, Z.J. 2006. Channel catfish BAC end sequences for marker development and assessment of syntenic conservation with other fish species. Animal Genetics 37, 321-326.

Yang F, Waldbieser GC, Lobb CJ. The nucleotide targets of somatic mutation and the role of selection in immunoglobulin heavy chains of a teleost fish. J Immunol. 2006 Feb 1;176(3):1655-67. PMID: 16424195 [PubMed - indexed for MEDLINE]

Zhang, Y.,Chen, S., Liu, Y., Sha, Z., and Liu, Z.J. 2006. Major histocompatibility complex class II B allele polymorphism and its association with resistance/susceptibility to Vibrio Anguillarum in Japanese flounder Paralichthys olivaceus. Marine Biotechnology 8: 600-610.

Salmonids publications:

Artieri C. G., Mitchell L. A., Ng S. H., Parisotto S. E., Danzmann R. G., Hoyheim B., Phillips R. B., Morasch M., Koop B. F., and Davidson W. S. (2006). Identification of the sex-determining locus of Atlantic salmon (Salmo salar) on chromosome 2. Cytogenet Genome Res 112: 152-9.

Brown K. H., Lee R. W., and Thorgaard G. H. (2006). Use of androgenesis for estimating maternal and mitochondrial genome effects on development and oxygen consumption in rainbow trout, Oncorhynchus mykiss. Comp Biochem Physiol B Biochem Mol Biol 143: 415-21.

Coulibaly I., Gahr S. A., Palti Y., Yao J., and Rexroad C. E., 3rd (2006). Genomic structure and expression of uncoupling protein 2 genes in rainbow trout (Oncorhynchus mykiss). BMC Genomics 7: 203.

Garikipati D. K., Gahr S. A., and Rodgers B. D. (2006). Identification, characterization, and quantitative expression analysis of rainbow trout myostatin-1a and myostatin-1b genes. J Endocrinol 190: 879-88.

Landis E. D., Palti Y., Dekoning J., Drew R., Phillips R. B., and Hansen J. D. (2006). Identification and regulatory analysis of rainbow trout tapasin and tapasin-related genes. Immunogenetics 58: 56-69.

Leder E. H., and Silverstein J. T. (2006). The pro-opiomelanocortin genes in rainbow trout (Oncorhynchus mykiss): duplications, splice variants, and differential expression. J Endocrinol 188: 355-63.

Phillips R. B., Nichols K. M., DeKoning J. J., Morasch M. R., Keatley K. A., Rexroad C., 3rd, Gahr S. A., Danzmann R. G., Drew R. E., and Thorgaard G. H. (2006). Assignment of rainbow trout linkage groups to specific chromosomes. Genetics 174: 1661-70.

Tilapia publications:

Alves-Costa FA, Wasko AP, Oliveira C, Foresti F, Martins C. Genomic organization and evolution of the 5S ribosomal DNA in Tilapiini fishes. Genetica. 2006 May;127(1-3):243-52.

Bellinger FP, Fox BK, Chan WY, Davis LK, Andres MA, Hirano T, Grau EG, Cooke IM. Ionotropic glutamate receptor activation increases intracellular calcium in prolactin-releasing cells of the adenohypophysis. Am J Physiol Endocrinol Metab. 2006 Dec;291(6):E1188-96.

Berishvili G, D'Cotta H, Baroiller JF, Segner H, Reinecke M. Differential expression of IGF-I mRNA and peptide in the male and female gonad during early development of a bony fish, the tilapia Oreochromis niloticus. Gen Comp Endocrinol. 2006 May 1;146(3):204-10.

Fiess JC, Kunkel-Patterson A, Mathias L, Riley LG, Yancey PH, Hirano T, Grau EG. Effects of environmental salinity and temperature on osmoregulatory ability, organic osmolytes, and plasma hormone profiles in the Mozambique tilapia (Oreochromis mossambicus). Comp Biochem Physiol A Mol Integr Physiol. 2006 Oct 21; [Epub ahead of print] PMID: 17134926

Fiol DF, Chan SY, Kultz D. Regulation of osmotic stress transcription factor 1 (Ostf1) in tilapia (Oreochromis mossambicus) gill epithelium during salinity stress. J Exp Biol. 2006 Aug;209(Pt 16):3257-65.

Fox BK, Riley LG, Hirano T, Grau EG. Effects of fasting on growth hormone, growth hormone receptor, and insulin-like growth factor-I axis in seawater-acclimated tilapia, Oreochromis mossambicus. Gen Comp Endocrinol. 2006 Sep 15;148(3):340-7.

Levavi-Sivan B, Biran J, Fireman E. Sex steroids are involved in the regulation of gonadotropin-releasing hormone and dopamine D2 receptors in female tilapia pituitary. Biol Reprod. 2006 Oct;75(4):642-50.

Praveen K, Leary JH 3rd, Evans DL, Jaso-Friedmann L. Molecular characterization and expression of a granzyme of an ectothermic vertebrate with chymase-like activity expressed in the cytotoxic cells of Nile tilapia (Oreochromis niloticus). Immunogenetics. 2006 Feb;58(1):41-55.

Seale AP, Fiess JC, Hirano T, Cooke IM, Grau EG. Disparate release of prolactin and growth hormone from the tilapia pituitary in response to osmotic stimulation. Gen Comp Endocrinol. 2006 Feb;145(3):222-31.

Shirak A, Seroussi E, Cnaani A, Howe AE, Domokhovsky R, Zilberman N, Kocher TD, Hulata G, Ron M. Amh and Dmrta2 genes map to tilapia (Oreochromis spp.) linkage group 23 within quantitative trait locus regions for sex determination. Genetics. 2006 Nov;174(3):157

Shirak A, Bendersky A, Hulata G, Ron M, Avtalion RR. Altered self-erythrocyte recognition and destruction in an inbred line of tilapia (Oreochromis aureus). J Immunol. 2006 Jan 1;176(1):390-4.

Shoemaker JM, Riley LG, Hirano T, Grau EG, Rubin DA. Differential expression of tuberoinfundibular peptide 38 and glucose-6-phosphatase in tilapia. Gen Comp Endocrinol. 2006 Apr;146(2):186-94.

Spady TC, Parry JW, Robinson PR, Hunt DM, Bowmaker JK, Carleton KL. Evolution of the cichlid visual palette through ontogenetic subfunctionalization of the opsin gene arrays. Mol Biol Evol. 2006 Aug;23(8):1538-47.

Takahashi H, Sakamoto T, Hyodo S, Shepherd BS, Kaneko T, Grau EG. Expression of glucocorticoid receptor in the intestine of a euryhaline teleost, the Mozambique tilapia (Oreochromis mossambicus): effect of seawater exposure and cortisol treatment. Life Sci. 2006 Apr 11;78(20):2329-35.

Wang LH, Tsai CL. Influence of temperature and gonadal steroids on the ontogenetic expression of brain serotonin 1A and 1D receptors during the critical period of sexual differentiation in tilapia, Oreochromis mossambicus. Comp Biochem Physiol B Biochem Mol Biol. 2006 Jan;143(1):116-25.

Oysters publications:

Cunningham C, Hikima J, Jenny MJ, Chapman RW, Fang G-C, Saski C, Lundqvist ML, Wing RA, Cupit PM, Gross PS, Warr GW, Tomkins JP. (2006) New Resources for Marine Genomics:BAC libraries for the Eastern and Pacific oysters (Crassostrea virginica and C. gigas) Marine Biotechnology. In Press

Curole, J. P. and D. Hedgecock.  2007. Chapter 29. Bivalve Genomics. In: Aquaculture Genome Technologies, Zhanjiang Liu, editor.  Blackwell, Ames, IA.

Gaffney, P., H. Jung, W.-J. Kim, R. Varney, and C. Milbury. 2006. Development and application of Type I markers for linkage mapping and population genetics in Crassostrea species. Journal Of Shellfish Research 25:727.

Hedgecock, D., J.-Z.Lin, S. DeCola,C. D. Haudenschild, E. Meyer, D. T. Manahan, and B. Bowen. 2007. Transcriptomic Analysis of Growth Heterosis in Larval Pacific Oysters (Crassostrea gigas).  Proc. Natl. Acad. Sci. USA (in press)

Hedgecock, D., P. M. Gaffney, P. Goulletquer, X. Guo, K. Reece, and G. W. Warr.  2005.  The case for sequencing the Pacific oyster genome. Journal of Shellfish Research 24:429-441.

Jenny MJ, Warr GW, Ringwood AH, Baltzegar DA, Chapman RW. (2006) Regulation of metallothionein genes in the American oyster (Crassostrea virginica):ontogeny and differential expression in response to different stressors. Gene, 379:156-65.

Jenny MJ, Warr GW, Ringwood AH, Baltzegar DA, Chapman RW. (2006) Regulation of Metallothionein Genes in the American Oyster (Crassostrea virginica): Ontogeny and Differential Expression in Response to Different Stressors. Gene, In Press.

Jung, H., W.-J. Kim, and P. Gaffney. 2006. Development of single nucleotide polymorphisms (SNPs) in Crassostrea ariakensis and related Crassostrea species. Journal Of Shellfish Research 24:742. (abstract)

Kim, W.-J., H. Jung, and P. Gaffney. 2006. Development of single nucleotide polymorphisms (SNPs) in the Pacific oyster Crassostrea gigas. Journal Of Shellfish Research 24:744. (abstract)

Lee, J.H. and X. Guo. 2006. Mining EST database for single-nucleotide polymorphisms in the eastern oyster (Crassostrea virginica). J. Shellfish Research 25(2):748-749. (abstract)

Shilts, M.H., M. S. Pascual and D Ó Foighil. Systematic, taxonomic and biogeographic relationships of Argentine flat oysters Molecular Phylogenetics and Evolution (in press).

Varney, R. L., and P. Gaffney. 2006. Population structure in the eastern oyster Crassostrea virginica assessed by single nucleotide polymorphisms. Journal Of Shellfish Research 24:785. (abstract)

Wang, Y. and X. Guo. 2006. Development and characterization of EST-SSR markers in the eastern oyster Crassostrea virginica. J. Shellfish Research 25(2):790. (abstract)

Yamtich, J., M.-L. Voigt, G. Li, and D. Hedgecock. 2005.  Eight microsatellite loci for the Pacific oyster Crassostrea gigas.  Animal Genetics 36:524-526.

Yu, Z. and X. Guo. 2006. Identification and mapping of disease-resistance QTL in the eastern oyster, Crassostrea virginica Gmelin. Aquaculture, 254:160-170. (abstract)

Shrimps publications:

Cuthbertson, B.J., E.E. Büllesbach, K. & P.S. Gross (2006). Discovery of synthetic penaeidin activity against antibiotic resistant fungi. Chem. Biol. Drug Design. 68:120-127.

O’Leary, N., M. Thompson Peck, H. Trent, D. McKillen, P.S. Gross (2006). Analysis of multiple tissue-specific cDNA libraries from the Pacific whiteleg shrimp, Litopenaeus vannamei. . Integ. Comp. Biol. 46:931-939.

O’Leary, N.A. and P.S. Gross (2006). Genomic structure and transcriptional regulation of the penaeidin gene family from Litopenaeus vannamei. Gene 371:75–83.

Robalino, J., C. Payne, P. Parnell , E. Shepard, A.C. Grimes, A. Metz, S. Prior, J. Witteveldt, J.M. Vlak, P.S. Gross, G.W. Warr, C.L. Browdy (2006) Inactivation of White Spot Syndrome Virus (WSSV) by normal rabbit serum: Implications for the role of the envelope protein VP28 in WSSV infection of shrimp. Virus Res. 118(1-2):55-61.

Robalino, J., J.S. Almeida, D. McKillen, J. Colglazier, H.F. Trent III, Y.A. Chen, M.E.T. Peck, C.L. Browdy, R.W. Chapman, G.W. Warr, P.S. Gross (in press). Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: EST analysis, tissue-specific signatures of gene expression, and the response to a lethal viral infection. Physiol. Genomics

Robalino, J., T. Bartlett, R.W. Chapman, P.S. Gross, C.L. Browdy, & G.W. Warr (in review). Gene silencing mediated by double-stranded RNA is impaired in shrimp infected with White Spot Syndrome Virus or with Taura Syndrome Virus.

Robalino, J., T.C. Bartlett, R.W. Chapman, P.S. Gross, C.L. Browdy, and G.W. Warr (in press). Double stranded RNA and antiviral immunity in invertebrates: Inducible host mechanisms and evolution of viral counter-responses in marine shrimp. Dev. Comp. Immunol.

Striped bass publications:

Couch, C.R. 2006. Microsatellite DNA marker-assisted selective breeding of striped bass, Morone saxatilis. Ph.D. Dissertation. Department of Zoology, North Carolina State University, Raleigh. 314 pp.

Couch, C.R., Garber, A.F., Rexroad III, C.E., Abrams, J.M., Stannard, J.A., Westerman, M.A., and C.V. Sullivan. 2006. Isolation and characterization of 149 novel microsatellite DNA markers for striped bass, Morone saxatilis, and cross-species amplification in white bass, M. chrysops, and their hybrid. Molecular Ecology Notes 6:667–669 (GenBank accession numbers 678169-678309; 678652-678663).

Garber, A.F. 2006. Assessing genetic contributions to performance of communally reared families of wild and domesticated reciprocal hybrid striped bass. Ph.D. Dissertation. Department of Zoology, North Carolina State University, Raleigh. 231 pp. 231.

Garber, A.F., and C.V. Sullivan. 2006. Selective breeding for the hybrid striped bass (Morone chrysops, Rafinesque X M. saxatilis, Walbaum) industry: Status and perspectives. Aquaculture Research 37:319-338.

Picha, M.E., Silverstein, J.T., Borski, R.J. 2006. Discordant regulation of hepatic IGF-I mRNA and circulating IGF-I during compensatory growth in a teleost, the hybrid striped bass (Morone chrysops x Morone saxatilis). Gen Comp Endocrinol. 2006 Jun;147(2):196-205. Epub 2006 Feb 28.

Rexroad III, C.E., Vallejo, R., Coulibaly, I., Westerman, M.E., and C.V. Sullivan. 2006. Identification and characterization of microsatellites for striped bass from repeat-enriched libraries. Conservation Genetics 7 (6): 971-982.

Skalski, G.T., Couch, C.R., Garber, A.F., Weir, B.S., and C.V. Sullivan. 2006. Evaluation of DNA pooling for the estimation of microsatellite allele frequencies: a case study using striped bass (Morone saxatilis). Genetics 173 (2): 863-875.

Wang, X., 2006. Quantitative genetics of growth, carcass-quality traits, and disease resistance in hybrid striped bass (Morone chrysops x Morone saxatilis). Ph.D. Dissertation.

Wang, X., Ross, K.E., Saillant, E., Gatlin III, D.M., Gold, J.R. 2006. Quantitative genetics and heritability of growth-related traits in hybrid striped bass (Morone chrysops x Morone saxatilis). Aquaculture 261: 535-545.

Wang, X., Ross, K.E., Saillant, E., Gatlin III, D.M., Gold, J.R. (submitted). Genetic effects on carcass-quality traits in hybrid striped bass (Morone chrysops x Morone saxatilis).