Research Project: Genetic Improvement of North American Atlantic Salmon and the Eastern Oyster for Aquaculture Production

Location: National Cold Water Marine Aquaculture Center

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Intermittent detections of ISAV-HPR0 in a salmon recirculating aquaculture system, and implications for sampling - (Peer Reviewed Journal)
Pietrak, M.R., Warg, J., Gustafson, L., Peterson, B.C. 2024. Intermittent detections of ISAV-HPR0 in a salmon recirculating aquaculture system, and implications for sampling. Fishes. 9(8):325-337. https://doi.org/10.3390/fishes9080325.

Salmon hatcheries can demographically boost wild populations at the cost of diversity: quantitative genetic modelling of Alaska pink salmon - (Peer Reviewed Journal)
May, S.A., Shedd, K.R., Gruenthal, K.M., Hard, J.J., Templin, W.D., Waters, C.D., Adkison, M.D., Ward, E.J., Habicht, C., Wilson, L.I., Wertheimer, A.C., Westley, P.A. 2024. Salmon hatcheries can demographically boost wild populations at the cost of diversity: quantitative genetic modelling of Alaska pink salmon. Royal Society Open Science. 11(7). https://doi.org/10.1098/rsos.240455.

Microhaplotypes generate higher breeding value accuracy compared to SNPs for imputation-based breeding strategies - (Peer Reviewed Journal)
Delomas, T.A., Hollenbeck, C.M., Matt, J.L., Thompson, N.F. 2024. Microhaplotypes generate higher breeding value accuracy compared to SNPs for imputation-based breeding strategies. Aquaculture. 586:740779. https://doi.org/10.1016/j.aquaculture.2024.740779.

Rapid differentiation of infectious salmon anemia virus avirulent (HPR0) from virulent (HPR) variants using multiplex RT-qPCR - (Peer Reviewed Journal)
Rounsville, T., Polinski, M.P., Marini, A., Turner, S., Vendramin, N., Cuenca, A., Pietrak, M.R., Peterson, B.C., Bouchard, D. 2024. Rapid differentiation of infectious salmon anemia virus avirulent (HPR0) from virulent (HPR) variants using multiplex RT-qPCR. Journal of Veterinary Diagnostic Investigation. 36(3):329-337. https://doi.org/10.1177/10406387231223290.

Sex-specific gene expression in eastern oyster gonad and mantle tissues - (Peer Reviewed Journal)
Proestou, D.A., Delomas, T.A., Sullivan, M.E., Markey Lundgren, K.R. 2024. Sex-specific gene expression in eastern oyster gonad and mantle tissues. Invertebrate Biology. 143(1):e12418. https://doi.org/10.1111/ivb.12418.

Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data - (Peer Reviewed Journal)
Delomas, T.A., Willis, S.C. 2023. Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data. Bioinformatics. https://doi.org/10.1186/s12859-023-05554-z.

Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline - (Peer Reviewed Journal)
Hargrove, J.S., Delomas, T.A., Powell, J.H., Hess, J.E., Narum, S.R., Campbell, M.R. 2023. Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline. Evolutionary Applications. 17(2):e13610. https://doi.org/10.1111%2Feva.13610.

Gene expression signatures for physiological resilience of sea urchin larva to food deprivation - (Peer Reviewed Journal)
Li, N., Griffith, A.W., Manahan, D. 2023. Gene expression signatures for physiological resilience of sea urchin larva to food deprivation. Molecular Ecology. https://doi.org/10.1111/mec.17120.

Fine-scale environmentally associated spatial structure of Lumpfish (Cyclopterus lumpus) across the Northwest Atlantic - (Peer Reviewed Journal)
Langille, B.L., Kess, T., Brachmann, M., Nugent, C.M., Messmer, A., Duffy, S.J., Holborn, M.K., Van Wyngaarden, M., Knutsen, T., Kent, M., Boyce, D., Gregory, R.S., Gauthier, J., Fairchild, E.A., Pietrak, M.R., Eddy, S., De Leaniz, C., Whittaker, B., Bentzen, P., Bradbury, I.R. 2023. Fine-scale environmentally associated spatial structure of Lumpfish (Cyclopterus lumpus) across the Northwest Atlantic. Evolutionary Applications. https://doi.org/10.1111/eva.13590.

Integration of physiological and gene expression analyses to reveal biomarkers for protein dynamic mechanisms regulating higher growth and survival among larval oyster families (Crassostrea gigas) - (Peer Reviewed Journal)
Li, N., Pan, T., Griffith, A.W., Dellatore, M., Manahan, D. 2023. Integration of physiological and gene expression analyses to reveal biomarkers for protein dynamic mechanisms regulating higher growth and survival among larval oyster families (Crassostrea gigas). Aquaculture. https://doi.org/10.1016/j.aquaculture.2023.739918.

Use of Multiplex PCR and Genomic MinION Sequencing to improve our understanding of Genetic Diversity and Relatedness of PRV-1 in Wild and Farmed Salmon in the Northeast Pacific - (Abstract Only)

Heart inflammation is affected by the host stain of Atlantic salmon during piscine orthoreovirs infection - (Abstract Only)
Polinski, M.P., Garver, K. 2023. Heart inflammation is affected by the host stain of Atlantic salmon during piscine orthoreovirs infection. Western Fish Disease Workshop. https://doi.org/10.1186/s12917-022-03409-y.

Rapid Differentiation of Infectious Salmon Anemia Virus avirulent from virulent variants using Multiplex RT-qPCR - (Abstract Only)

Using skin mucus for the identification of ovulation biomarkers in North American Atlantic salmon (Salmo salar) - (Peer Reviewed Journal)
Legacki, E.L., Peterson, B.C., Boggs, A. 2023. Using skin mucus for the identification of ovulation biomarkers in North American Atlantic salmon (Salmo salar). Aquaculture. https://doi.org/10.1016/j.aquaculture.2023.739717.

Surveillance of Piscine Orthoreovirus genotype-1 (PRV-1) in wild Pacific Salmon of British Columbia, Canada: 2011-2020 - (Peer Reviewed Journal)
Turcotte, L.D., Johnson, S.C., Bradshaw, J.C. 2023. Surveillance of Piscine Orthoreovirus genotype-1 (PRV-1) in wild Pacific Salmon of British Columbia, Canada: 2011-2020. Journal of Fish Diseases. https://doi.org/10.3390/fishes8050252.

A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference - (Peer Reviewed Journal)
Puritz, J., Guo, X., Hare, M., He, Y., Hillier, L., Jin, S., Liu, M., Lotterhos, K., Minx, P., Modak, T., Proestou, D.A., Rice, E., Tomlison, C., Warren, W., Witkop, E., Zhao, H., Gomez-Chiarri, M. 2023. A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13801.

British Columbia freshwater salmon hatcheries demonstrate minimal contribution to piscine orthoreovirus (PRV) regional occurrence with no evidence for non-endemic - (Peer Reviewed Journal)
Polinski, M.P., Haddad, C.A., Siah, A., Fuller, C., Higgins, M. 2023. British Columbia freshwater salmon hatcheries demonstrate minimal contribution to piscine orthoreovirus (PRV) regional occurrence with no evidence for non-endemic. Aquaculture Research. https://doi.org/10.1139/facets-2022-0218.

A New Multiplex RT-qPCR For The Rapid Differentiation Of ISAV-HPR0 From ISAV HPR-delete - (Abstract Only)

Infectious Diseases of Coldwater Fish in Fresh Water - (Book / Chapter)
Cain, K.D., Polinski, M.P. 2023. Infectious Diseases of Coldwater Fish in Fresh Water. In: Woo, P.T.K., Subasinghe, R.P., editors. Climate Change on Diseases and Disorders of Finfish in Cage Culture. 3rd edition. Oxfordshire, London: CAB International. p. 76-124.

Multiplex PCR and Minion sequencing for direct whole genome assembly of aquatic viruses from tissue and environmental samples: a case study involving PRV-1 - (Abstract Only)

Understanding Crassostrea virginica tolerance of Perkinsus marinus through global gene expression analysis - (Peer Reviewed Journal)
Proestou, D.A., Sullivan, M.E., Markey Lundgren, K.R., Ben-Horin, T., Witkop, E.M., Hart, K.M. 2023. Understanding Crassostrea virginica tolerance of Perkinsus marinus through global gene expression analysis. Frontiers in Genetics. https://doi.org/10.3389/fgene.2023.1054558.

Development and evaluation of high-density SNP arrays for the eastern oyster Crassostrea virginica - (Peer Reviewed Journal)
Guo, X., Puritz, J., Zhenwei, W., Proestou, D.A., Allen, S., Small, J., Verbyla, K., Zhao, H., Haggard, J., Chriss, N., Zeng, D., Markey Lundgren, K.R., Allam, B., Bushek, D., Gomez-Chiarri, M., Hare, M., Hollenbeck, C., Lapeyre, J., Liu, M., Lotterhos, K., Plough, L., Rawson, P., Rikard, S., Sallient, E., Varney, R., Wikfors, G., Wilbur, A. 2023. Development and evaluation of high-density SNP arrays for the eastern oyster Crassostrea virginica. Marine Biotechnology. https://doi.org/10.1007/s10126-022-10191-3.

Introducing the USDA/NEFSC Northeast Oyster Breeding Center (NOBC) - (Abstract Only)

Design and partial build of the Milford Laboratory CUDLS hatchery to support the Northeast Oyster Breeding Center - (Abstract Only)

Evaluating cost-effective genotyping strategies for genomic selection in oysters - (Peer Reviewed Journal)
Delomas, T.A., Hollenbeck, C.M., Matt, J.L., Thompson, N. 2023. Evaluating cost-effective genotyping strategies for genomic selection in oysters. Aquaculture. 562:738844. https://doi.org/10.1016/j.aquaculture.2022.738844.

A glimpse into the bio-physical environment of the sea louse (Lepeophtheirus salmonis (Kroyer 1837)) digestive tract - (Peer Reviewed Journal)

Heart inflammation and piscine orthoreovirus genotype-1 in Pacific Canada Atlantic salmon net-pen farms: 2016-2019 - (Peer Reviewed Journal)
Polinski, M.P., Gross, L., Marty, G.D., Garver, K.A. 2022. Heart inflammation and piscine orthoreovirus genotype-1 in Pacific Canada Atlantic salmon net-pen farms: 2016-2019. BMC Veterinary Research. https://doi.org/10.1186/s12917-022-03409-y.

Longitudinal patterns in progesterone metabolites in pregnant and non-pregnant Steller sea lions - (Peer Reviewed Journal)

Piscine orthoreovirus (PRV) detection, distribution and transmission in the Northeastern Pacific - (Abstract Only)
Polinski, M.P., Johnson, S.C., Garver, K.A. 2022. Piscine orthoreovirus (PRV) detection, distribution and transmission in the Northeastern Pacific. American Fisheries Society Annual Meeting. https://doi.org/10.3390/fishes8050252.

Perkinsus marinus suppresses in vitro eastern oyster apoptosis via IAP-dependent and caspase-independent pathways involving TNFR, NF-kB, and oxidative pathway crosstalk. - (Peer Reviewed Journal)
Witkop, E., Wikfors, G.H., Proestou, D.A., Markey Lundgren, K.R., Sullivan, M.E., Gomez-Chiarri 2022. Perkinsus marinus suppresses in vitro eastern oyster apoptosis via IAP-dependent and caspase-independent pathways involving TNFR, NF-kB, and oxidative pathway crosstalk. Developmental and Comparative Immunology. https://doi.org/10.1016/j.dci.2022.104339.

The expanded Inhibitor of Apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge - (Peer Reviewed Journal)
Witkop, E.M., Proestou, D.A., Gomez-Chiarri, M. 2022. The expanded Inhibitor of Apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge. BMC Genomics. https://doi.org/10.1186/s12864-021-08233-6.

Pan-Piscine Orthoreovirus (PRV) Detection Using Reverse Transcription Quantitative PCR - (Peer Reviewed Journal)
Zhao, J., Vendramin, N., Cuenca, A., Polinski, M.P., Hawley, L., Garver, K. 2021. Pan-Piscine Orthoreovirus (PRV) detection using reverse transcription quantitative PCR. Pathogens. https://doi.org/10.3390/pathogens10121548.

DEVELOPMENT AND EVALUATION OF HIGH-DENSITY SNP ARRAYS FOR THE EASTERN OYSTER CRASSOSTREA VIRGINICA - (Abstract Only)

Comparing the performance of selectively-bred and wild eastern oyster stocks in Rhode Island - (Abstract Only)

THE ROLE OF MITOCHONDRIAL AND LYSOSOMAL PERMEABILIZATION IN EASTERN OYSTER APOPTOTIC RESPONSE TO PERKINSUS MARINUS - (Abstract Only)

Evaluation of novel non-GMO soybean cultivars for nutrient availability, reducing metabolic waste and increased energy efficiency in Atlantic salmon Salmo salar - (Abstract Only)