NRSP-8 Salmonids Aquaculture Research Progress Report for 2012

Objective 1:
Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest.

CATFISH Channel catfish genome sequencing: To date 60X genome equivalent of Illumina sequences and mate paired reads of 3Kb, 8Kb, and 36 Kb with sequences equivalent to 3.1X, 0.5X, and 0.15X (clonal coverage of 47X, 21X and 27X), respectively have been generated. PacBio sequences equivalent to 9.5X genome coverage with an average length of 3.5 Kb have been generated. The channel catfish genome is under assembly.

Blue catfish genome sequencing: Doubled haploid blue catfish were produced and used as template for sequencing using Moleculo’s Long Reads product to generate extremely long and accurate reads. A preliminary assembly with only the long reads using 99% sequence overlap identity produced 46,098 contigs with an N50 length of 12.9 kb and N80 length of 8.5 kb. A further 42,141 long reads remained singlets with an N80 length of 4.6kb and N50 length of 7.0kb.

Transcriptome and annotation resources: RNA-Seq of the doubled haploid catfish generated a transcriptome assembly including 25,144 unique protein encoding genes, with over 14,000 full-length transcripts. This resources has been used for expression profiling of mucosal surfaces for catfish challenged with the pathogen Flavobacterium columnare.

Microarray development and use: An Agilent 8x60K microarray is publicly available and has been utilized for profiling channel and blue catfish skin responses to Aeromonas hydrophila infection.

OYSTER Oyster Genome Sequence: International efforts to develop BAC physical maps, large volumes of SNPs and integrated cytogenetic maps culminated in the acquisition of an oyster genome sequence.

SALMONIDS Rainbow Trout Reference Genome sequence: A pooling and tagging scheme was used for sequencing of the ~15,000 clones of the BAC fingerprinting physical map minimal tiling path (MTP). Sequencing is complete and the assembly is underway. The current version of the assembly is estimated to cover 70% of the rainbow trout genome.

Rainbow Trout SNP discovery from RADs: We employed restriction-site associated DNA (RAD) technology to generate a large SNPs data set from deep sequencing of a panel of 11 homozygous lines. The dataset is composed of 145,168 high-quality putative SNPs that were genotyped in at least 9 of the 11 lines, of which 71,446 (49%) had minor allele frequencies (MAF) of at least 18%.

SHRIMP

Genome sequencing of Pacific White Shrimp, Litopenaeus vannamei: Due to the high levels of heterozygosity and the complexity of the shrimp genome, it is very difficult to assemble the short reads generated by next-generation sequencing technologies. Efforts have been turned to finding shrimp inbred lines with relatively high homozygosity or sequencing BAC libraries.

Development of a high-density SNP genotyping platform: A deep sequencing of restriction-site associated DNA marker (RAD-Seq) method was used to find genetic markers involved in disease resistance in Pacific White Shrimp.

RNA-seq: A large scale RNA-seq project was initiated to characterize disease resistance mechanisms in shrimp.

STRIPED BASS Striped Bass transcriptome: A database (> 11,000 entries) for gene transcripts expressed by the striped bass ovary at all maturational stages was developed and published to provide a foundation for gene expression research on reproduction and breeding of the striped bass and its relatives.

Striped Bass Genetic Map: The first genetic map of the genome of the striped bass was developed and published. This medium-density linkage map is based on 298 microsatellite markers and is enabling detection of QTL affecting production traits.

Objective 2: Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes.

CATFISH Selection for improved growth and filet yield in Year 1 of the Delta Select strain F2 Generation was completed. Channel, blue, and hybrid catfish were raised in intensive raceway environments and phenotyped for selective breeding.

SALMONIDS Multi-year pedigreed rainbow trout populations phenotyped for plasma cortisol in response to stress, resistance to bacterial cold water disease (BCWD), spleen size, or growth on fish meal free/plant based diets have been developed and propagated for release to industry and identification of biological mechanisms underlying these traits.

SHRIMP Most of the shrimp populations developed for research are from breeding companies, and mainly support disease resistance studies. Resource populations exist for public and collaborative research.

STRIPED BASS

Broodstock populations have been established in support of genetic improvement programs for Morone species. An experimental method for accelerating puberty and maturation of Morone species based on administration of the neuropeptide kisspeptin was demonstrated, opening the door to development of practical methods for application to these late-maturing species and pinpointing the proximal signal for maturation of Morone species.

Objective 3: Develop, integrate and implement bioinformatics resources to support the discovery of genetic mechanisms that underlie traits of interest.

CATFISH The catfish RNASeq, ESTs, and related SNP information has been disseminated through the Catfish Genome Database, cBARBEL, http://www.catfishgenome.org/cbarbel/ , that has generated tens of thousands of hits from over 30 countries.

SALMONIDS

QTL Database: A rainbow trout QTL database is now available through the Animal Genome website of the NRSP-8 bioinformatics group (http://www.animalgenome.org/cgibin/QTLdb/index) and is being continually updated.

SHRIMP A website for the shrimp genomics community will be established, and various kinds of genomics resources for shrimp research will be assembled in the database.

CATFISH Li C, Wang R, Su B, Luo Y, Terhune J, Beck B, Peatman E. Evasion of Mucosal Defenses During Aeromonas hydrophila Infection of Channel Catfish (Ictalurus punctatus) Skin. Dev Comp Immunol (in press; http://dx.doi.org/10.1016/j.dci.2012.11.009)

Beck BH, Farmer BD, Straus D, Li C, Peatman E (2012) Putative roles for a rhamnose binding lectin in Flavobacterium columnare pathogenesis in channel catfish Ictalurus punctatus. Fish Shellfish Immunology 33:1008-1015

Arias CR, Cai W, Peatman E, Bullard SA (2012) Channel Catfish x Blue Catfish Hybrid Exhibits Higher Resistance to Columnaris Disease as Compared to Its Parental Species. Diseases of Aquatic Organisms 100(1):77-81.

Li C, Zhang Y, Wang R, Lu J, Nandi S, Mohanty S, Terhune S, Liu Z, and Peatman E (2012) RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunology 32(5):816-27

Sun* F, Peatman* E, Li C, Liu S, Jiang Y, Zhou Z, Kucuktas H, Liu Z (2012) Host Signatures of Attachment, NF-κB Suppression and IFN Stimulation in the Channel Catfish (Ictalurus punctatus) Gill Transcriptome Following Flavobacterium Columnare Challenge. Dev Comp Immunol 38(1):169-80

Ninwichian, Peatman E, Perrera D, Liu S, Dunham R, Liu Z (2012) Identification of a sex-linked marker in channel catfish. Animal Genetics 43(4):476

Rajendran KV, Zhang J, Liu S, Peatman E, Kucuktas H, Wang X, Liu H, Wood T, Terhune J, Liu Z (2012) Pathogen recognition receptors in channel catfish: II. Identification, phylogeny and expression of retinoic acid-inducible gene I (RIG-I)-like receptors. Dev Comp Immunol 37(34):381-9

Zhang H, Peatman E, Liu H, Feng T, Chen L, Liu Z (2012) Molecular characterization of three L-type lectin genes from channel catfish, Ictalurus punctatus and their responses to Edwardsiella ictaluri challenge. Fish Shellfish Immunology 32(4):598-608.

Rajendran KV, Zhang J, Liu S, Kucuktas H, Wang X, Liu H, Sha Z, Terhune J, Peatman E, Liu Z (2012) Pathogen recognition receptors in channel catfish: I. Identification, phylogeny and expression of NOD-like receptors. Dev Comp Immunol 37(1):77-86

Zhou Z, Liu H, Liu S, Sun F, Peatman E, Kucuktas H, Kaltenboeck L, Feng T, Zhang H, Niu D, Lu J, Waldbieser G, Liu Z (2012) Alternative complement pathway of channel catfish (Ictalurus punctatus): Molecular characterization, mapping and expression analysis of factors Bf/C2 and Df. Fish Shellfish Immunol 32:186-95.

Zhang H, Peatman E, Liu H, Niu D, Feng T, Kucuktas H, Waldbieser G, Chen L, Liu Z (2012) Characterization of a mannose-binding lectin from channel catfish (Ictalurus punctatus). Research in Veterinary Medicine 92(3):408-13

Lu J, Peatman E, Tang H, Lewis J, and Liu Z (2012) Genome expansion in zebrafish is mediated by recent tandem duplications. BMC Genomics 13:246

Lu J, Peatman E, Tang H, Lewis J, Liu ZJ. 2012. Profiling of gene duplication patterns of teleost genomes: Evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications. BMC Genomics 13:246.

Ninwichian* P, Peatman* E, Liu H, Kucuktas H, Somridhivej B, Liu S, Li P, Jiang Y, Sha Z, Kaltenboeck M, Abernathy JA, Wang W, Chen F, Lee Y, Wong L, Wang S, Lu J, Liu Z (2012) Second Generation Genetic Linkage Map of Catfish and Its Integration with the BAC-based Physical Map. G3: Genes, Genomes, Genetics 2(10):1233-41.

Liu S, Zhang S, Zhou Z, Waldbieser G, Sun F, Lu J, Zhang J, Jiang Y, Zhang H, Wang X, Rajendran KV, Khoo L, Kucuktas H, Peatman E, Liu Z (2012) Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote. BMC Genomics 13 (1), 595

Liu, S, Zhang Y, Sun F, Jiang Y, Wang R, Li C, Zhang J, Liu ZJ. 2012. Approaches for Functional Genomics in aquaculture. pp. 1-40. In: Functional Genomics in Aquaculture, Wiley and Blackwell Publishing, Ames, IA.

Zhang J, Jiang Y, Wang R, Li C, Zhang Y, Sun F, Liu, S, Liu ZJ. 2012. Chapter 2, Genomic resources for aquaculture functional genomics. pp. 41-77. In: Functional Genomics in Aquaculture, Wiley and Blackwell Publishing, Ames, IA.

Browdy, C.L., Hulata, G., Liu, Z., Allan, G.L., Sommerville, C., Passos de Andrade, T., Pereira, R., Yarish, C., Shpigel, M., Chopin, T., Robinson, S., Avnimelech, Y. & Lovatelli, A. 2012. Novel and emerging technologies: can they contribute to improving aquaculture sustainability? In R.P. Subasinghe, J.R. Arthur, D.M. Bartley, S.S. De Silva, M. Halwart, N. Hishamunda, C.V. Mohan & P. Sorgeloos, eds. Farming the Waters for People and Food. Proceedings of the Global Conference on Aquaculture 2010, Phuket, Thailand. 22–25 September 2010. pp. 149-191. FAO, Rome and NACA, Bangkok.

OYSTER Zhang, G., Fang, X., Guo, X., Li, L., Luo, R., Xu, F., Yang, P., Zhang, L., Wang, X., Qi, H., Xiong, Z., Que, H., Xie, Y., Holland, P.W.H., Paps, J., Zhu, Y., Wu, F., Chen, Y., Wang, J., Peng, C., Meng, J., Yang, L., Liu, J., Wen, B., Zhang, N., Huang, Z., Zhu, Q., Feng, Y., Mount, A., Hedgecock, D., Xu, Z., Liu, Y., Domazet-Loso, T., Du, Y., Sun, X., Zhang, S., Liu, B., Cheng, P., Jiang, X., Li, J., Fan, D., Wang, W., Fu, W., Wang, T., Wang, B., Zhang, J., Peng, Z., Li, Y., Li, N., Wang, J., Chen, M., He, Y., Tan, F., Song, X., Zheng, Q., Huang, R., Yang, H., Du, X., Chen, L., Yang, M., Gaffney, P.M., Wang, S., Luo, L., She, Z., Ming, Y., Huang, W., Zhang, S., Huang, B., Zhang, Y., Qu, T., Ni, P., Miao, G., Wang, J., Wang, Q., Steinberg, C.E.W., Wang, H., Li, N., Qian, L., Zhang, G., Li, Y., Yang, H., Liu, X., Wang, J., Yin, Y. & Wang, J. (2012). The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490: 49-54.

SALMONIDS Burki, R., Krasnov, A., Bettge, K., Rexroad, C.E., 3rd, Afanasyev, S., Antikainen, M., Burkhardt-Holm, P., Wahli, T. & Segner, H. (2012). Pathogenic infection confounds induction of the estrogenic biomarker vitellogenin in rainbow trout. Environ Toxicol Chem, 31: 2318-2323.

Aussanasuwannakul A, Weber GM, Salem M, Yao J, Slider S, Manor ML, Kenney PB. 2012. Effect of sexual maturation on thermal stability, viscoelastic properties, and texture of female rainbow trout, Oncorhynchus mykiss, fillets. J Food Sci 77: S77-83.

Bernardi, G., Wiley, E.O., Mansour, H., Miller, M.R., Orti, G., Haussler, D., O'brien, S.J., Ryder, O.A. & Venkatesh, B. (2012). The fishes of Genome 10K. Marine Genomics, 7: 3-6.

Braden, L.M., Barker, D.E., Koop, B.F. & Jones, S.R.M. (2012). Comparative defense-associated responses in salmon skin elicited by the ectoparasite Lepeophtheirus salmonis. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 7: 100-109.

Bridle, A.R., Koop, B.F. & Nowak, B.F. (2012). Identification of Surrogates of Protection against Yersiniosis in Immersion Vaccinated Atlantic Salmon. PLoS ONE, 7: e40841.

Everett, M., Miller, M. & Seeb, J. (2012). Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genomics, 13: 521.

Faber-Hammond, J., Phillips, R.B. & Park, L.K. (2012). The Sockeye Salmon Neo-Y Chromosome Is a Fusion between Linkage Groups Orthologous to the Coho Y Chromosome and the Long Arm of Rainbow Trout Chromosome 2. Cytogenetic and Genome Research, 136: 69-74.

Campbell, M.R., C.C. Kozfkay, T. Copeland, W.C. Schrader, M.W. Ackerman, and S.R. Narum. 2012. Estimating abundance and life history characteristics of threatened wild Snake River steelhead stocks by using genetic stock identification. Transactions of the American Fisheries Society 141:1310-1327.

Campbell, N. R., Amish, S. J., Pritchard, V. L., McKelvey, K. S., Young, M. K., Schwartz, M. K., Garza, J. C., Luikart, G. and Narum, S. R. 2012. Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa. Molecular Ecology Resources, 12: 942–949.

Gomez-Uchida, D., Seeb, James e., Habicht, C. & Seeb, Lisa w. (2012). Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka). Canadian Journal of Fisheries and Aquatic Sciences, 69: 916-929.

Hecht, B.C., Campbell, N.R., Holecek, D.E. & Narum, S.R. (2012a). Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout. Molecular Ecology: n/a-n/a.

Hecht, B.C., Thrower, F.P., Hale, M.C., Miller, M.R. & Nichols, K.M. (2012b). Genetic Architecture of Migration-Related Traits in Rainbow and Steelhead Trout, Oncorhynchus mykiss. G3: Genes|Genomes|Genetics, 2: 1113-1127.

Hess, M.A., Rabe, C.D., Vogel, J.L., Stephenson, J.J., Nelson, D.D. & Narum, S.R. (2012). Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon. Molecular Ecology, 21: 5236-5250.

Johnstone, K.A., Lubieniecki, K.P., Koop, B.F. & Davidson, W.S. (2012). Identification of olfactory receptor genes in Atlantic salmon Salmo salar. Journal of Fish Biology, 81: 559-575.

Lai, Y.Y.Y., Lubieniecki, K.P., Koop, B.F. & Davidson, W.S. (2012). Characterization of the Atlantic salmon (Salmo salar) brain-type fatty acid binding protein (fabp7) genes reveals the fates of teleost fabp7 genes following whole genome duplications. Gene, 504: 253-261.

Limborg, M.T., Blankenship, S.M., Young, S.F., Utter, F.M., Seeb, L.W., Hansen, M.H.H. & Seeb, J.E. (2012). Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss. Ecology and Evolution, 2: 1-18.

Liu, S., Rexroad, C., Iii, Couch, C., Cordes, J., Reece, K. & Sullivan, C. (2012). A Microsatellite Linkage Map of Striped Bass (Morone saxatilis) Reveals Conserved Synteny with the Three-Spined Stickleback (Gasterosteus aculeatus). Marine Biotechnology, 14: 237-244.

Ma, H., Hostuttler, M., Wei, H., Rexroad, C.E., Iii & Yao, J. (2012). Characterization of the Rainbow Trout Egg MicroRNA Transcriptome. PLoS ONE, 7: e39649.

Manor ML, Weber GM Salem M, Yao J, Aussanasuwannakul, Kenney PB. 2012. Effect of sexual maturation and triploidy on chemical composition and fatty acid content of energy stores in female rainbow trout, Oncorhynchus mykiss. Aquaculture 364–365: 312–321.

Matala, A.P., W. Young, J.L. Vogel, and S.R. Narum. 2012. Influences of hatchery supplementation, spawner distribution, and habitat on genetic structure of Chinook salmon in the South Fork Salmon River, Idaho. North American Journal of Fisheries Management 32:346-359.

Miller, M.R., Brunelli, J.P., Wheeler, P.A., Liu, S., Rexroad, C.E., Palti, Y., Doe, C.Q. & Thorgaard, G.H. (2012). A conserved haplotype controls parallel adaptation in geographically distant salmonid populations. Molecular Ecology, 21: 237-249.

Overturf, K., Vallejo, R., Palti, Y., Barrows, F. & Parsons, J. (2012). Microarray analysis of differential utilization of plant-based diets by rainbow trout. Aquaculture International, 20: 213 - 232.

Palti, Y., Genet, C., Gao, G., Hu, Y., You, F., Boussaha, M., Rexroad, C. & Luo, M.-C. (2012). A Second Generation Integrated Map of the Rainbow Trout (Oncorhynchus mykiss) Genome: Analysis of Conserved Synteny with Model Fish Genomes. Marine Biotechnology, 14: 343-357.

Rexroad, C., Vallejo, R., Liu, S., Palti, Y. & Weber, G. (2012). QTL affecting stress response to crowding in a rainbow trout broodstock population. BMC Genetics, 13: 97.

Salem, M., Vallejo, R.L., Leeds, T.D., Palti, Y., Liu, S., Sabbagh, A., Rexroad, C.E., Iii & Yao,

J. (2012). RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout. PLoS ONE, 7: e36264.

Storer, C.G., Pascal, C.E., Roberts, S.B., Templin, W.D., Seeb, L.W. & Seeb, J.E. (2012). Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism. PLoS ONE, 7: e49018.

Sutherland, B.J.G., Jantzen, S.G., Yasuike, M., Sanderson, D.S., Koop, B.F. & Jones, S.R.M. (2012). Transcriptomics of coping strategies in free-swimming Lepeophtheirus salmonis (Copepoda) larvae responding to abiotic stress. Molecular Ecology, 21: 6000-6014.

Yasuike, M., Leong, J., Jantzen, S., Schalburg, K., Nilsen, F., Jones, S.M. & Koop, B. (2012). Genomic Resources for Sea Lice: Analysis of ESTs and Mitochondrial Genomes. Marine Biotechnology, 14: 155-166.

SHRIMP Aranguren LF, Salazar M, Tang K, Caraballo X, Lightner D. 2013. Characterization of a new strain of Taura syndrome virus (TSV) from Colombian shrimp farms and the implication in the selection of TSV resistant lines. J Invertebr Pathol. 112:68-73.

Aranguren LF, Tang KF, Lightner DV. 2012. Protection from yellow head virus (YHV) infection in Penaeus vannamei pre-infected with Taura syndrome virus (TSV). Dis Aquat Organ. 98:185-92.

Bartholomay LC, Loy DS, Dustin Loy J, Harris DL. 2012. Nucleic-acid based antivirals: augmenting RNA interference to 'vaccinate'Litopenaeus vannamei. J Invertebr Pathol. 110:261-6.

Gui L, Wang B, Li FH, Sun YM, Luo Z, Xiang JH. 2012. Blocking the large extracellular loop (LEL) domain of FcTetraspanin-3 could inhibit the infection of white spot syndrome virus (WSSV) in Chinese shrimp, Fenneropenaeus chinensis. Fish Shellfish Immunol. 32:1008-15.

Li F, Xiang J. 2013. Recent advances in researches on the innate immunity of shrimp in China. Dev Comp Immunol. 39:11-26.

Li F, Xiang J. 2012. Signaling pathways regulating innate immune responses in shrimp. Fish Shellfish Immunol. doi: 10.1016/j.fsi.2012.08.023.

Li S, Li F, Wen R, Xiang J. 2012. Identification and characterization of the sex-determiner transformer-2 homologue in Chinese shrimp, Fenneropenaeus chinensis. Sex Dev. 6:267-78.

Li S, Li F, Sun Z, Xiang J. 2012. Two spliced variants of insulin-like androgenic gland hormone gene in the Chinese shrimp, Fenneropenaeus chinensis. Gen Comp Endocrinol. 177(2):246-55.

Lightner DV, Redman RM, Pantoja CR, Tang KF, Noble BL, Schofield P, Mohney LL, Nunan LM, Navarro SA. 2012. Historic emergence, impact and current status of shrimp pathogens in the Americas. J Invertebr Pathol. 110:174-83.

Loy JD, Mogler MA, Loy DS, Janke B, Kamrud K, Scura ED, Harris DL, Bartholomay LC. 2012. dsRNA provides sequence-dependent protection against infectious myonecrosis virus in Litopenaeus vannamei. J Gen Virol. 93:880-8.

Moss SM, Moss DR, Arce SM, Lightner DV, Lotz JM. 2012. The role of selective breeding and biosecurity in the prevention of disease in penaeid shrimp aquaculture. J Invertebr Pathol. 110:247-50.

Nunan LM, Pantoja CR, Gomez-Jimenez S, Lightner DV. 2012. 'Candidatus Hepatobacter penaei', an intracellular pathogenic bacterium enteric in the hepatopancreas of the marine shrimp Penaeus vannamei (Crustacea:Decopoda). Appl Environ Microbiol. PubMed PMID: 23241970.

Qian Z, Liu X, Wang L, Wang X, Li Y, Xiang J, Wang P. 2012. Gene expression profiles of four heat shock proteins in response to different acute stresses in shrimp, Litopenaeus vannamei. Comp Biochem Physiol C Toxicol Pharmacol. 156):211-20.

Stentiford GD, Neil DM, Peeler EJ, Shields JD, Small HJ, Flegel TW, Vlak JM, Jones B, Morado F, Moss S, Lotz J, Bartholomay L, Behringer DC, Hauton C, Lightner DV. 2012. Disease will limit future food supply from the global crustacean fishery and aquaculture sectors. J Invertebr Pathol. 110:141-57.

Tang KF, Navarro SA, Pantoja CR, Aranguren FL, Lightner DV. 2012. New genotypes of white spot syndrome virus (WSSV) and Taura syndrome virus (TSV) from the Kingdom of Saudi Arabia. Dis Aquat Organ. 99:179-85

Wang D, Li F, Chi Y, Xiang J. 2012. Potential relationship among three antioxidant enzymes in eliminating hydrogen peroxide in penaeid shrimp. Cell Stress Chaperones. 17:423-33.

Wang D, Li F, Li S, Chi Y, Wen R, Feng N, Xiang J. 2012. An IκB homologue (FcCactus) in Chinese shrimp Fenneropenaeus chinensis. Dev Comp Immunol. doi: 10.1016/j.dci.2012.12.005.

Wang L, Li F, Wang B, Xiang J. 2012. Structure and partial protein profiles of the peritrophic membrane (PM) from the gut of the shrimp Litopenaeus vannamei. Fish Shellfish Immunol. 33:1285-91.

Wen R, Li F, Sun Z, Li S, Xiang J. 2012. Shrimp MyD88 responsive to bacteria and white spot syndrome virus. Fish Shellfish Immunol. doi: 10.1016/j.fsi.2012.11.034.

Wen R, Li F, Xie Y, Li S, Xiang J. 2012. A homolog of the cell apoptosis susceptibility gene involved in ovary development of Chinese shrimp Fenneropenaeus chinensis. Biol Reprod. 86:1-7.

Zhang J, Wang J, Li F, Sun Y, Yang C, Xiang J. 2012. A trehalose-6-phosphate synthase gene from Chinese shrimp, Fenneropenaeus chinensis. Mol Biol Rep. 39:10219-25.

Zhao C, Zhang X, Li F, Huan P, Xiang J. 2013. Functional analysis of the promoter of the heat shock cognate 70 gene of the Pacific white shrimp, Litopenaeus vannamei. Fish Shellfish Immunol. 34:397-401.

STRIPED BASS Beck, B.H., Fuller, S.A., Peatman, E., McEntire, M.E., Darwish, A., and Freeman, D.W. 2012. Chronic exogenous kisspeptin administration accelerates gonadal development in basses of the genus Morone. Comp. Biochem. Physiol. A. 162:265-273.

Liu, S., Rexroad III, C.E., Couch, C.R., Cordes, J., Reece, K., and C.V. Sullivan. 2012. A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the threespined stickleback (Gasterosteus aculeatus). Mar Biotechnology 14(2):237-244. doi: 10.1007/s10126-011-9407-2.

Reading,B.J., Chapman, R.W., Schaff, J.E., Scholl, E.H., Opperman, C.H., and Sullivan, C.V. 2012. An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish. BMC Research Notes 5:111 doi:10.1186/1756-0500-5-111.

Workshop Report

Theme

Linking Genomic Variation to Phenotype

Attendees

Number = 83

Countries = 8 (US, Mexico, France, Spain, China, Japan, Canada, Finland)

Invited Presentations (4)

NGS-Enabled Research Tools for Crops and Livestock Patrick S. Schnable, Iowa State University

TALEN-mediated gene editing in terrestrial and aquatic species. Daniel F. Carlson, Recombinetics, Inc.

Use of Single Nucleotide Polymorphisms (SNP) to Fine-Map Quantitative Trait Loci (QTL) in Swine Gary A. Rohrer, USDA, ARS, USMARC; Amanda K. Lindholm-Perry, USDA-ARS, U.S. Meat Animal Research Center; Steven D. Shackelford, USDA, ARS, USMARC; D.A. King, USDA-ARS, U.S. Meat Animal Research Center; T.L. Wheeler, USDA-ARS, U.S. Meat Animal Research Center; Dan Nonneman, USDA, ARS, USMARC

Ruminations On Lessons To Be Hatched From Genomics Research In Cattle and Goats Tad Sonstegard and Curtis P. Van Tassell, USDA-ARS-BFGL

Contributed Presentations (20)

Association Mapping Of Disease Resistance Traits In Rainbow Trout Using RAD Sequencing Nathan Campbell, Columbia River Inter-Tribal Fish Commission; Ken Overturf, USDAARS; Scott LaPatra, Clear Springs Foods; Richard Towner, Gentec Consulting; Shawn Narum, Columbia River Inter-Tribal Fish Commission

Epigentic Landscapes In A Marine Mollusc: What DNA Methylation Patterns Tell Us About Gene Regulation In The Pacific Oyster (Crassostrea gigas) Mackenzie Gavery, University of Washington; Steven Roberts, University of Washington

RNA-Seq Analysis Of Stress Response In Rainbow Trout Sixin Liu, USDA - ARS - NCCCWA; Guangtu Gao, USDA/ARS/NCCCWA; Yniv Palti, USDA-ARS-NCCCWA; Gregory Weber, National Center for Cool and Cold Water Aquaculture; Caird E. Rexroad III, USDA-ARS-NAA-NCCCWA

Characterization Of Specific miRNAs Involved In Maternal-Zygotic Transition In Rainbow Trout Embryos (Oncorhynchus mykiss) Hao Ma, West Virginia University; Mark Hostuttler, National Center for Cool and Cold Water Aquaculture; Hairong Wei, Michigan Technological University; Caird E. Rexroad

III, USDA-ARS-NAA-NCCCWA; Jianbo Yao, West Virgina University

Whole Genome SNP Discovery and Analysis Of Catfish Genetic Diversity Luyang Sun, Auburn University; Shikai Liu, Auburn University; Yu Zhang, Auburn University; Jiaren Zhang, Auburn University; Jianbin Feng, Auburn University; Geoff Waldbieser, USDA-ARS; John Liu, Auburn University; Huseyin Kucuktas, Auburn University; Ludmilla Kaltenboeck, Auburn University

Pathgenomics of the Oyster and Transcriptomic Infection Responses Reveals a Highly Evolved Innate Immune System Linlin Zhang, Institute of Oceanology, Chinese Academy of Sciences; Ximing Guo, Rutgers University; Li Li, Institute of Oceanology, Chinese Academy of Sciences; Guofan Zhang, Institute of Oceanology, Chinese Academy of Sciences

Development Of The Catfish 250K SNP Array Shikai Liu, Auburn University; Luyang Sun, Auburn University; Fanyue Sun, Auburn University; Yanliang Jiang, Auburn University; Yu Zhang, Auburn University; Jiaren Zhang, Auburn University; Jianbin Feng, Auburn University; Ludmilla Kaltenboeck, Auburn University; Huseyin Kucuktas, Auburn University; John Liu, Auburn University

Genome and Sex Determination Mechanism In Half-Smooth Tongue Sole (Cynoglossus semilaevis) Songlin Chen, Yellow Sea Fisheries Research Institute, CAFS; Guojie Zhang, Shenzhen Laboratory of Transomics Biotechnologies, BGI; Changwei Shao, Yellow Sea Fisheries Research Institute, CAFS; Jun Wang, BGI-Shenzen; Manfred Schartl, University of Wuerzburg; Qisheng Tang, Yellow Sea Fisheries Research Institute, CAFS; Wentao Song, Yellow Sea Fisheries Resarch Institute,

Production Of Long (1.5kb – 15.0kb), Accurate, DNA Sequencing Reads Using An Illumina HiSeq2000 To Support De Novo Assembly Of The Blue Catfish Genome Geoff Waldbieser, USDA-ARS; Michael Kertesz, Moleculo, Inc.; Dmitry Pushkarev, Moleculo, Inc.; Tim Blauwkamp, Moleculo, Inc.; John Liu, Auburn University

Chromosomal Rearrangements In The Genus Of Salmo Song Lin, Simon Fraser University; Jieying Li, Simon Fraser University; William S. Davidson, Simon Fraser University

RNA-Seq Approaches to the Study of Early Interactions Between Catfish and Flavobacterium columnare Eric Peatman, Auburn University

Three Sex Loci and An sdY In Tasmanian Atlantic Salmon William D. Eisbrenner, Simon Fraser University; Natasha Botwright, CSIRO; Mathew Cook, CSIRO; Evelyn A. Davidson, Simon Fraser University; Sonja Dominik, CSIRO; John Henshall, CSIRO; Stacy L Jones, Simon Fraser University; Peter D. Kube, CSIRO; Krzysztof P. Lubieniecki, Simon Fraser University; Nick G. Elliott, CSIRO; Sophia Peng, Simon Fraser University; William S. Davidson, Simon Fraser University

Cyberinfrastructure Initiatives for Biology and Opportunities to Involve Aquaculture Jeffrey T. Silverstein, USDA-Agricultural Research Service

The Organization Of The Atlantic Salmon (Salmo salar) sdY Gene and Its Potential Genomic Environments Emily I. Palibroda, Simon Fraser University; Krzysztof P. Lubieniecki, Simon Fraser University; Yvonne Y. Y. Lai, Simon Fraser University; William D. Eisbrenner, Simon Fraser University; William S. Davidson, Simon Fraser University

Genome-wide Genic SNPs Development and Association Analysis with Abiotic Stress in the Pacific Oyster Crassostrea gigas Li Li, Institute of Oceanology, Chinese Academy of Sciences; Haigang Qi, Institute of Oceanology, Chinese Academy of Sciences; Jiafeng Wang, Institute of Oceanology, Chinese Academy of Sciences; Zhicai She, Institute of Oceanology, Chinese Academy of Sciences; Fei Xu, Institute of Oceanology, Chinese Academy of Sciences; Linlin Zhang, Institute of Oceanology, Chinese Academy of Sciences; Jinpeng Wang, Institute of Oceanology, Chinese Academy of Sciences; Guofan Zhang, Institute of Oceanology, Chinese Academy of Sciences

Genome-Wide SNP Association Analysis of Body Weight in Atlantic Salmon (Salmo salar) Alejandro P. Gutierrez, Simon Fraser University; Krzysztof P. Lubieniecki, Simon Fraser University; Evelyn A. Davidson, Simon Fraser University; Steve Fukui, Mainstream Canada; Ruth E. Withler, Pacific Biological Station; Bruce Swift, TRI-GEN Fish Improvement Ltd.; Sigbjørn Lien, CIGENE, Norwegian University of Life Sciences; Matthew P. Kent, CIGENE, Norwegian University of Life Sciences; William S. Davidson, Simon Fraser University

Transcriptome and Expression Profiling Of Response To Acute Hypoxia In The Gill Of Adult Catfish Jianbin Feng, Auburn University; Shikai Liu, Auburn University; Yu Zhang, Auburn University; Jiaren Zhang, Auburn University; Ludmilla Kaltenboeck, Auburn University; Huseyin Kucuktas, Auburn University; John Liu, Auburn University

The Transcriptome Of The Eastern Oyster Crassostrae virginica In Response To Bacterial Challenge Marta Gomez-Chiarri, University of Rhode Island; Ian McDowell, University of Rhode Island; Chamilani Nikapitiya, University of Rhode Island; Saebom Sohn, University of Rhode Island

Diploid and Triploid Hybrids Derived from Female Megalobrama amblycephala Yih × Male Xenocypris davidi Bleeker Jie Hu, DFO West Vancouver Lab Gene Expression in Early Development of Rainbow Trout with Divergent Life Histories Garrett McKinney, Purdue University; Frank Thrower, NOAA; Krista Nichols, NOAA

Poster Session Participants (30)

Business Meeting Minutes

Call to order (Liu)

Bioinformatics Update (Reecy) - Stated system open to help all systems. The AnGenMap subscription list is seeing growth. NRSP-8 community file sharing is available, this can be private and public. Animal Genome Tracks can be stored on the site. AnimalQTLdb also highlighted, 100 new papers last year. Future Developments: Helping the community deal will re-sequencing projects. Now available for fish community- correlation database (CorrDB). NRSP-8 Bioinformatics can host services. New effort to get information for aquaculture species gene ontology. Last year spending time with iPlant to develop pipelines for genome resequencing. iRODS overcomes large data transfer issues. iPlant collaborative is open to working with aquaculture community on pipelines.

Recognized and commended Peatman for organizing this year's workshop. Announced that persons should contact Roberts (sr320@uw.edu) with suggestions for next year's workshop speakers and themes.

Recognition of Travel Award Winners (10)

William Eisbrenner Song Lin Mackenzie Gavery Emily Palibroda Alejandro Gutierrez Luyang Sun Jianbin Feng Shikai Liu Garrett J McKinney Jie Hu

Nomination and election for chair-elect Nomination: Roger Vallejo Voted unamiously as new chair-elect

Request for community to contribute content to newsletter.

Meeting adjourned 4:55