Aquaculture

Publications

The aquaculture team's research, recorded in writing.

The Roslin Institute makes consistent contributions to the scientific community's body of knowledge on aquaculture topics. The below lists contain articles hosted on external sites to which the Roslin Institute has contributed. These articles cover a variety of topics but are centered on aquaculture research and innovation.

 

2022

 

The impact of genetic relationship between training and validation populations on genomic prediction accuracy in Atlantic salmon

Clemence Fraslin, JM Yáñez, Diego Robledo, Ross D Houston

Aquaculture Reports 23, 101033

 

Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon

Ophélie Gervais, Athina Papadopoulou, Remi Gratacap, Borghild Hillestad, Alan Tinch, Samuel AM Martin, Ross D Houston, Diego Robledo

bioRxiv 10.1101

 

Plasma Proteome Responses in Salmonid Fish Following Immunization

Monica Hongroe Solbakken, Kim Dawn Thompson, Bo Peng, Daniel J Macqueen, Helen Dooley, FK Bakke, MM Monte, DA Stead, DR Causey, A Douglas

Evolution and Comparative Immunology of Immune Systems in Marine Organisms

 

A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

Roberto De la Herran, Miguel Hermida, Juan Andres Rubiolo, Jessica Gomez-Garrido, Fernando Cruz, Rafael Navajas, Andres Blanco, Paula R Villamayor, Dorinda Torres, Pablo Sanchez-Quinteiro, Daniel Ramirez, Maria E Rodriguez, Alberto Arias-Perez, Ismael Cross, Neil J Duncan, Teresa Martinez-Pena, Ana Riaza, Adrian Millan, Marta J Gut, Carmen Bouza, Diego Robledo, Laureana Rebordinos, Tyler Alioto, Carmelo Ruiz-Rejon, Paulino Martinez

bioRxiv 10.1101

 

Genome-wide association and genomic prediction of resistance to Flavobacterium columnare in a farmed rainbow trout population

C Fraslin, H Koskinen, A Nousianen, RD Houston, A Kause

bioRxiv 10.1101

 

Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution

Manu Kumar Gundappa, Thu-Hien To, Lars Grønvold, Samuel AM Martin, Sigbjørn Lien, Juergen Geist, David Hazlerigg, Simen R Sandve, Daniel J Macqueen

Molecular Biology and Evolution 39 (1)

 

Understanding host response to infectious salmon anaemia virus in an Atlantic salmon cell line using single-cell RNA sequencing

Ophélie Gervais, Remi Gratacap, Athina Papadopoulou, Ross D Houston, Musa A Hassan, Diego Robledo

bioRxiv 10.1101

 

Methods for mapping genomic variants associated with production traits in aquaculture species

C Fraslin, RD Houston, D Robledo

Cellular and Molecular Approaches in Fish Biology, 193-220

 

2021

 

Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages

Daniel J Macqueen, Oliver Eve, Manu Kumar Gundappa, Rose Ruiz Daniels, Michael D Gallagher, Svein Alexandersen, Marius Karlsen

Viruses 13 (12), 2549

 

Evolution of ray-finned fish genomes: Status and directions with a primer on microRNA characterization

Richard S. Taylor, Rose Ruiz Daniels, Diego Perojil Morata, Manu Kumar Gundappa, Daniel J. Macqueen

Cellular and Molecular Approaches in Fish Biology 309-336

 

Methods for mapping genomic variants associated with production traits in aquaculture species

Clémence Fraslin, Ross D Houston, Diego Robledo

Cellular and Molecular Approaches in Fish Biology 193

 

Assessment of Marine Gill Disease in Farmed Atlantic Salmon (Salmo salar) in Chile Using a Novel Total Gross Gill Scoring System: A Case Study

Sophie Fridman, Smaragda Tsairidou, Nilantha Jayasuriya, Halina Sobolewska, Alastair Hamilton, Carlos Lobos, Ross D Houston, Hamish Rodger, James Bron, Tharangani Herath

Microorganisms 9 (12), 2605

 

Validation and mapping of flat oyster genetic markers associated with the Bonamia ostreae status following a population genomics approach

I Martinez, A Chiclan, A Blanco Garcia, M Gundappa, T Bean, Daniel J Macqueen, Ross D Houston, A Villalba, M Vera, P Kamermans, Paulino Martinez

NORA 4 Reconnecting across Europe 1

 

Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes

María Saura, Armando Caballero, Enrique Santiago, Almudena Fernández, Elisabeth Morales-González, Jesús Fernández, Santiago Cabaleiro, Adrián Millán, Paulino Martínez, Christos Palaiokostas, Martin Kocour, Muhammad L Aslam, Ross D Houston, Martin Prchal, Luca Bargelloni, Kostas Tzokas, Pierrick Haffray, Jean-Sebastien Bruant, Beatriz Villanueva

Genetics Selection Evolution 53 (1), 1-8

 

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

Gareth B Gillard, Lars Grønvold, Line L Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F Koop, Eric B Rondeau, Manu Kumar Gundappa, John Mendoza, Daniel J Macqueen, Rori V Rohlfs, Simen R Sandve, Torgeir R Hvidsten

Genome Biology 22 (1), 1-18

 

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing

Carolina P Moraleda, Diego Robledo, Alejandro P Gutiérrez, Jorge Del-Pozo, José M Yáñez, Ross D Houston

BMC Genomics 22 (1), 156

 

Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies

Kelly S Bateman, Rose Kerr, Grant D Stentiford, Tim P Bean, Chantelle Hooper, Benigna Van Eynde, Daan Delbare, Jamie Bojko, Olivier Christiaens, Clauvis NT Taning, Guy Smagghe, Monique M Van Oers, Ronny van Aerle

Viruses 13 (9)

 

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

Ophelie Gervais, Agustin Barria, Athina Papadopoulou, RL Gratacap, Borghild Hillestad, Alan E Tinch, Sam AM Martin, Diego Robledo, Ross D Houston

BMC Genomics 22 (1), 345

 

Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution

Tim Regan, Lewis Stevens, Carolina Peñaloza, Ross D Houston, Diego Robledo, Tim P Bean

Genome Biology and Evolution 13 (8)

 

The nedd-8 activating enzyme gene underlies genetic resistance to infectious pancreatic necrosis virus in Atlantic salmon

Jon Pavelin, Yehwa Jin, Remi L Gratacap, John B Taggart, Alastair Hamilton, David W Verner-Jeffreys, Richard K Paley, Carl-johan Rubin, Stephen C Bishop, James E Bron, Diego Robledo, Ross D Houston

Genomics 113 (6), 3842-3850

 

A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus)

Agustin Barría, Trọng Quốc Trịnh, Mahirah Mahmuddin, Carolina Peñaloza, Athina Papadopoulou, Ophelie Gervais, V Mohan Chadag, John AH Benzie, Ross D Houston

Heredity 1-9

 

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing

Carolina P Moraleda, Diego Robledo, Alejandro P Gutiérrez, Jorge Del-Pozo, José M Yáñez, Ross D Houston 

BMC Genomics 22 (1), 156

 

Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution

Manu Kumar Gundappa, Thu-Hien To, Lars Grønvold, Samuel AM Martin, Sigbjørn Lien, Juergen Geist, David Hazlerigg, Simen R Sandve, Daniel J Macqueen

bioRxiv 447185

 

Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries

Pierre Boudry, François Allal, Muhammad L Aslam, Luca Bargelloni, Tim P Bean, Sophie Brard-Fudulea, Marine SO Brieuc, Federico CF Calboli, John Gilbey, Pierrick Haffray, Jean-Baptiste Lamy, Romain Morvezen, Catherine Purcell, Paulo A Prodöhl, Marc Vandeputte, Geoffrey C Waldbieser, Anna K Sonesson, Ross D Houston

Aquaculture Reports (20) 100700

 

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

Gareth B Gillard, Lars Grønvold, Line L Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F Koop, Eric B Rondeau, Manu Kumar Gundappa, John Mendoza, Daniel J Macqueen, Rori V Rohlfs, Simen R Sandve, Torgeir R Hvidsten

Genome Biology 22 (1), 1-18

 

Optimizing hatchery practices for genetic improvement of marine bivalves

Jennifer C Nascimento‐Schulze, Tim P Bean, Ross D Houston, Eduarda M Santos, Matthew B Sanders, Ceri Lewis, Robert P Ellis

Reviews in Aquaculture

 

Nanopore whole genome sequencing and partionioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7)

Andrew J Tighe, Michael D Gallagher, Jens Carlsson, Iveta Matejusova, Fiona Swords, Daniel J Macqueen, Neil M Ruane

Diseases of Aquatic Organisms, 142, 203-211

 

Potential of genomic technologies to improve disease resistance in molluscan aquaculture

RWA Potts, AP Gutierrez, CS Penaloza, T Regan, TP Bean, RD Houston

Philosophical Transactions of the Royal Society B 376 (1825), 20200168

 

What do the terms resistance, tolerance, and resilience mean in the case of Ostrea edulis infected by the haplosporidian parasite Bonamia ostreae

Zoë Holbrook, Tim P Bean, Sharon A Lynch, Chris Hauton

Journal of Invertebrate Pathology 107579

 

Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)

Carolina Penaloza, Tereza Manousaki, R Franch, A Tsakogiannis, Anna Kristina Sonesson, ML Aslam, Francois Allal, L Bargelloni, RD Houston, CS Tsigenopoulos

Genomics (113) 4, 2096-2107

 

Surrogate broodstock to enhance biotechnology research and applications in aquaculture

YH Jin, D Robledo, J Hickey, M McGrew, R Houston 

Biotechnology Advances, 107756

 

A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiated ZZ/ZW sex determination of turbot (Scophthalmus maximus)

Paulino Martínez, Diego Robledo, Xoana Taboada, Andrés Blanco, Michel Moser, Francesco Maroso, Miguel Hermida, Antonio Gómez-Tato, Blanca Álvarez-Blázquez, Santiago Cabaleiro, Francesc Piferrer, Carmen Bouza, Sigbjorn Lien, Ana M Viñas

Genomics Journal

 

The role of energy reserves in common carp performance inferred from phenotypic and genetic parameters

Jinfeng Zhao, Martin Prchal, Antti Kause, Marc Vandeputte, David Gela, Hana Kocour Kroupová, Veronika Piačková, Pavel Šauer, Christoph Steinbach, Jean-Michel Allamellou, Christos Palaiokostas, Ross D Houston, Martin Kocour

Aquaculture, 736-799

 

Quantitative trait loci and transcriptome signatures associated with avian heritable resistance to Camplobacter

Androniki Psifidi, Andreas Kranis, Lisa M Rothwell, Abi Bremner, Kay Russell, Diego Robledo, Stephen J Bush, Mark Fife, Paul M Hocking, Georgios Banos, David A Hume, Jim Kaufman, Richard A Bailey, Santiago Avendano, Kellie A Watson, Pete Kaiser, Mark P Stevens

Scientific reports 11

 

Genetic improvement technologies to support the sustainable growth of UK aquaculture

Tim Regan, Tim P Bean, Tim Ellis, Andrew Davie, Stefano Carboni, Herve Migaud, Ross D Houston

Reviews in Aquaculture

 

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

Carolina Peñaloza, Alejandro P Gutierrez, Lél Eöry, Shan Wang, Ximing Guo, Alan L Archibald, Tim P Bean, Ross D Houston

GigaScience 10 (3)

 

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

Ophelie Gervais, Agustin Barria, Athina Papadopoulou, RL Gratacap, Borghild Hillestad, Alan E Tinch, Sam AM Martin, Diego Robledo, Ross D Houston

BMC Genomics 22 (1), 345

 

Aquaculture breeding

G Simm, G Pollott, R Mrode, R Houston, K Marshall

Genetic improvement of farmed animals, 414-434

 

Predicting breeding values

G Simm, G Pollott, R Mrode, R Houston, K Marshall

Genetic improvement of farmed animals, 193-233

 

Analysing genetic variation in farm animals

G Simm, G Pollott, R Mrode, R Houston, K Marshall

Genetic improvement of farmed animals, 178-192

 

Strategies for genetic improvement

G Simm, G Pollott, R Mrode, R Houston, K Marshall

Genetic improvement of farmed animals, 59-96

 

Genes, genetic codes and genetic variation

G Simm, G Pollott, R Mrode, R Houston, K Marshall

Genetic improvement of farmed animals, 11-58

 

Loss of active neurogenesis in the adult shark retina

Ismael Hernández-Núñez, Diego Robledo, Hélène Mayeur, Sylvie Mazan, Laura Elena Sanchez, Fátima Adrio, Antón Barreiro-Iglesias, Eva Candal

Frontiers in cell and developmental biology 9, 115

 

Genomic diversity of the Ostreid Herpesvirus Type 1 across time and location and among host species

Benjamin Morga, Maude Jacquot, Camille Pelletier, Germain Chevignon, Lionel Dégremont, Antoine Biétry, Jean-François Pepin, Serge Heurtebise, Jean-Michel Escoubas, Tim P Bean, Umberto Rosani, Chang-Ming Bai, Tristan Renault, Jean-Baptiste Lamy

Frontiers in Microbiology

 

2020

 

Development of a SNP linkage map and genome-wide association study for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus)

Vito A Mastrochirico-Filho, Carolina HS Borges, Milena V Freitas, Raquel B Ariede, Fabiana Pilarski, Ricardo Utsunomia, Roberto Carvalheiro, Alejandro P Gutierrez, Carolina Peñaloza, José M Yáñez, Ross D Houston, Diogo T Hashimoto

BMC Genomics 21 (1), 1-13

 

From FAANG to Fork: application of highly annotated genomes to improved farmed animal production

Emily L Clark, Alan L Archibald, Hans D Daetwyler, Martien AM Groenen, Peter W Harrison, Ross D Houston, Christa Kühn, Sigbjørn Lien, Daniel J Macqueen, James M Reecy, Diego Robledo, Mick Watson, Christopher K Tuggle, Elisabetta Giuffra

Genome Biology 21 (1), 1-9

 

Evaluation of interactive effects of phosphorus-32 and copper on marine and freshwater bivalve mollusks

Emily L Vernon, Michael N Moore, Tim P Bean, Awadhesh N Jha

International Journal of Radiation Biology, 1-14

 

Insights into the development of hepatocellular fibrillar inclusions in European flounder (Platichthys flesus) from UK estuaries

John P Bignell, Jon Barber, Kelly S Bateman, Mark Etherton, Stephen W Feist, Tamara S Galloway, Ioanna Katsiadaki, Marion Sebire, Alexander P Scott, Grant D Stentiford, Tim P Bean

Chemosphere 256, 12956

 

Genomic epidemiology of domestic and travel-associated Vibrio parahaemolyticus infections in the UK, 2008–2018

Craig Baker-Austin, Claire Jenkins, Jerome Dadzie, Orson Mestanza, Erick Delgado, Andy Powell, Tim Bean, Jaime Martinez-Urtaza

Food Control 115, 107244

 

The structural variation landscape in 492 Atlantic salmon genomes

Alicia C Bertolotti, Ryan M Layer, Manu Kumar Gundappa, Michael D Gallagher, Ege Pehlivanoglu, Torfinn Nome, Diego Robledo, Matthew P Kent, Line L Røsæg, Matilde M Holen, Teshome D Mulugeta, Thomas J Ashton, Kjetil Hindar, Harald Sægrov, Bjørn Florø-Larsen, Jaakko Erkinaro, Craig R Primmer, Louis Bernatchez, Samuel AM Martin, Ian A Johnston, Simen R Sandve, Sigbjørn Lien, Daniel J Macqueen

Nature Communications 11-1, 1-16

 

Genome-wide target enriched viral sequencing reveals extensive ‘hidden’ salmonid alphavirus diversity in farmed and wild fish populations 

Michael D Gallagher, Iveta Matejusova, Neil M Ruane, Daniel J Macqueen

Aquaculture 522, 735117

 

Genome sequencing of SAV3 reveals repeated seeding events of viral strains in Norwegian aquaculture

Michael D Gallagher, Marius Karlsen, Elin Petterson, Øyvind Haugland, Iveta Matejusova, Daniel J Macqueen

Frontiers in microbiology 11, 740

 

Arginine, ornithine and citrulline supplementation in rainbow trout: Free amino acid dynamics and gene expression responses to bacterial infection

TC Clark, J Tinsley, T Sigholt, DJ Macqueen, SAM Martin

Fish & Shellfish Immunology 98, 374-390

 

Supplementation of arginine, ornithine and citrulline in rainbow trout (Oncorhynchus mykiss): Effects on growth, amino acid levels in plasma and gene expression responses in liver tissue

TC Clark, J Tinsley, T Sigholt, DJ Macqueen, SAM Martin

Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology

 

Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing

Diego Robledo, Alastair Hamilton, Alejandro P. Gutiérrez, James E. Bron, Ross D. Houston

BMC Genomics 21, Article 271

 

QTL affecting morphometric traits and stress response in the gilthead seabream (Sparus aurata)

Kay Boulton, Cecile Massault, Ross D. Houston, Dirk Jande Koning, Chris S. Haley, Henk Bovenhuis, Costas Batargias, Adelino V.M. Canario, Giorgios Kotoulas, Costas S. Tsigenopoulos

Volume 319, Issues 1-2, 58-66

 

Quantitative trait loci and genes associated with salmonid alphavirus load in Atlantic salmon: implications for pancreas disease resistance and tolerance

M. L. Aslam, Diego Robledo, A. Krasnov, H. K. Moghadam, B. Hillestad, Ross D. Houston, M. Baranski, S. Boison, N. A. Robinson

Scientific Reports 10, 10393

 

Ephemeral detection of Bonamia exitiosa (Haplosporida) in adult and larval European flat oysters Ostrea edulis in the Solent, United Kingdom

Luke Helmer, Chris Hauton, Tim Bean, David Bass, Ian Hendy, Eric Harris-Scott, Joanne Preston

Journal of Invertebrate Pathology, Volume 174, 107421

 

Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system

Remi L. Gratacap, Tim Regan, Carola E. Dehler, Samuel A. M. Martin, Pierre Boudinot, Bertrand Collet, Ross D. Houston

BMC Biotechnology 20, 35

 

Development and Validation of an Open Access SNP Array for Nile Tilapia (Oreochromis niloticus)

Carolina Peñaloza, Diego Robledo, Agustin Barría, Trọng Q. Trịnh, Mahirah Mahmuddin, Pamela Wiener, John A.H. Benzie, Ross D. Houston

G3: Genes, Genomes, Genetics 120.401343

 

Developments in marine invertebrate primary culture reveal novel cell morphologies in the model bivalve Crassotrea gigas

Robert W.A. Potts​, Alejandro P. Gutierrez, Yennifer Cortés-Araya, Ross D. Houston, Tim P. Bean

PubMed eCollection 32547861

 

Harnessing genomics to fast-track genetic improvement in aquaculture

Ross D. Houston, Tim P. Bean, Daniel J. Macqueen, Manu Kumar Gundappa, Ye Hwa Jin, Tom L. Jenkins, Sarah Louise C. Selly, Samuel A. M. Martin, Jamie R. Stevens, Eduarda M. Santos, Andrew Davie, Diego Robledo

Nature Reviews Genetics 21, 389-409

 

Genetic parameters for resistance to Tilapia Lake Virus (TiLV) in Nile tilapia (Oreochromis niloticus)

A. Barria, T. Q. Trinh, M. Mahmuddin, J.A.H. Benzie, V. M. Chadag, R. D. Houston

Aquaculture 522, 735126

 

Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing

D. Robledo, A. Hamilton, A. P. Gutierrez, J.E. Bron, R. D. Houston

BMC Genomics 21 (271)

 

Arginine, ornithine and citrulline supplementation in rainbow trout: Free amino acid dynamics and gene expression responses to bacterial infection

T. C. Clark, J. Tinsley, T. Sigholt, D. J. Macqueen, S. A. M. Martin

Fish & Shellfish Immunology  97, 374-390

 

Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon

M. Naval-Sanchez, S. McWilliam, B. Evans, J. M. Yáñez, R. D. Houston, J. W. Kijas

Frontiers in genetics 10

 

De novo transcriptome assembly of the Qatari pearl oyster (Pinctada imbricata radiata)

Tim P Bean, Zenaba Khatir, Brett P Lyons, Ronny van Aerle, Diana Minardi, John P Bignell, David Smyth, Bruno Welter Giraldes, Alexandra Leitão

Marine genomics 51, 100734

 

The application of nanopore sequencing technology to the study of dinoflagellates: a proof of concept study for rapid sequence-based discrimination of potentially harmful algae

Robert G Hatfield, Frederico M Batista, Timothy P Bean, Vera G Fonseca, Andres Santos, Andrew D Turner, Adam Lewis, Karl J Dean, Jaime Martinez-Urtaza

Frontiers in Microbiology 11, 844

 

Genomic prediction using low density marker panels in aquaculture: performance across species, traits, and genotyping platforms

C. KriaridouS. Tsairidou, R. D. Houston, D. Robledo

Frontiers in genetics 10

 

Assessing relative biomarker responses in marine and freshwater bivalve molluscs following exposure to phosphorus 32: application of genotoxicological and molecular biomarkers

Emily L Vernon, Tim P Bean, Awadhesh N Jha

Journal of environmental radioactivity 213, 106120

 

Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

A. P. Gutierrez, J. Symonds, N. King, K. Steiner, T.P. Bean, R. D. Houston

Animal Genetics 522, 735126

 

Pearl Oyster: from national icon to guardian of Qatar's marine environment

Alexandra Leitao BenHamadou, Zenaba Khatir, Noora Al-Shamary, Hassan Hassan, Zainab Hizan, Aisha Al-Ashwal, Mark Chatting, Shafeeq Hamza, Bruno Giraldes, Diana Minardi, Tim Bean, Stephane Bayen, Brett Lyons

Qatar University Press

 

A Single-Tube HNB-Based Loop-Mediated Isothermal Amplification for the Robust Detection of the Ostreid herpesvirus 1

Maja A Zaczek-Moczydłowska, Letitia Mohamed-Smith, Anna Toldrà, Chantelle Hooper, Mònica Campàs, M Dolors Furones, Tim P Bean, Katrina Campbell

International journal of molecular sciences 21.18, 6605

 

Genome-wide target enriched viral sequencing reveals extensive 'hidden' salmonid alphavirus diversity in farmed and wild fish populations

M. D. Gallagher, I. Matejusova, N. M. Ruane, D. J. Macqueen

Aquaculture 422, 735117

 

Optimising low-cost genotyping and imputation strategies for genomic selection in Atlantic salmon

S. Tsairidou, A. Hamilton, D. Robledo, J. E. Bron, R. D. Houston

G3: Genes, Genomes, Genetics 10 (2) 181-590

 

2019

 

Effect of growth rate on transcriptomic responses to immune stimulation in wild-type, domesticated, and GH-transgenic coho salmon

Jin-Hyoung Kim, Daniel J Macqueen, James R Winton, John D Hansen, Hyun Park, Robert H Devlin

BMC Genomics 20.1, 1-16

 

SalMotifDB: a tool for analyzing putative transcription factor binding sites in Salmonid genomes

Teshome Dagne Mulugeta, Torfinn Nome, Thu-Hien To, Manu Kumar Gundappa, Daniel J Macqueen, Dag Inge Våge, Simen Rød Sandve, Torgeir R Hvidsten

BMC Genomics 20.1, 1-8

 

Characterizing the genetic structure of introduced Nile tilapia (Oreochromis niloticus) strains in Tanzania using double digest RAD sequencing

M. Moses, M. Mtolera, L. J. Chauk, F. A. L. Pinto, D. J. De Koning, R. D. Houston, C. Palaiokostas

Aquaculture International 28, 477-492

 

Assessment of genetic diversity and population structure in culture Australian Pacific oysters

J. W. Kijas, A. P. Gutierrez, R. D. Houston, S. McWilliam, T. P. Bean, K. Soyano, J. E. Symonds, N. King, C. Lind, P. Kube

Animal Genetics 50 (6), 686-694

 

Potential of Genome Editing to Improve Aquaculture Breeding and Production

R. Gratacap, A. Wargelius, R. B. Edvardsen, R. D. Houston

Trends in Genetics 35 (9), 672-684

 

Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon

Diego Robledo, Alejandro P. Gutierrez, A. Barria, J. P. Lhorente, Ross D Houston, J. M. Yáñez

Frontiers in genetics 10

 

Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): New genomic tools for breeding programs and management of natural resources

Manuel Vera, Belén G Pardo, Asunción Cao, Román Vilas, Carlos Fernández, Andrés Blanco, Alejandro P Gutierrez, Tim P Bean, Ross D Houston, Antonio Villalba, Paulino Martínez

Evolutionary Applications 12.9, 1781-1796

 

Expanding the miRNA Repertoire in Atlantic Salmon; Discovery of IsomiRs and miRNAs Highly Expressed in Different Tissues and Developmental Stages

Nardos Tesfaye Woldemariam, Oleg Agafonov, Bjørn Høyheim, Ross D. Houston, John B. Taggart, Rune Andreassen

Cells 8 (1), 42

 

Optimizing genomic prediction of host resistance to koi herpesvirus disease in carp

Christos Palaiokostas, Tomas Vesely, Martin Kocour, Martin Prchal, Dagmar Pokorova, Veronika Piackova, Lubomir Pojezdal, Ross D. Houston

BioRxiv, 609784

 

Balancing selection at a premature stop mutation in the myostatin gene underlies a recessive leg weakness syndrome in pigs

Oswald Matika, Diego Robledo, Ricardo Pong-Wong, Stephen C. Bishop, Valentina Riggio, Heather Finlayson, Natalie R. Lowe, Annabelle E. Hoste, Grant A. Walling, Jorge del Pozo, Alan L. Archibald, John A. Woolliams, Ross D. Houston

PLoS genetics 15 (1), e1007759

 

Development of a TaqMan qPCR assay for detection of Alexandrium spp and application to harmful algal bloom monitoring

Robert G Hatfield, Timothy Bean, Andrew D Turner, David N Lees, James Lowther, Adam Lewis, Craig Baker-Austin

Toxicon: X 2, 100011

 

Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

Ross D. Houston, Daniel J. Macqueen

Animal genetics 50 (1), 3-14

 

Detailed insights into pan‐European population structure and inbreeding in wild and hatchery Pacific oysters (Crassostrea gigas) revealed by genome‐wide SNP data

David L. J. Vendrami, Ross D. Houston, Karim Gharbi, Luca Telesca, Alejandro P. Gutierrez, Helen Gurney‐Smith, Natsuki Hasegawa, Pierre Boudry, Joseph I. Hoffman

Evolutionary Applications 12 (3), 519-534

 

Genetic differences in host infectivity affect disease spread and survival in epidemics

Osvaldo Anacleto, Santiago Cabaleiro, Beatriz Villanueva, Maria Saura, Ross D. Houston, John A. Woolliams, Andrea B. Doeschl-Wilson

Scientific reports 9 (1), 4924

 

Novel insights into the genetic relationship between growth and disease resistance in an aquaculture strain of Coho salmon (Oncorhynchus kisutch)

A Barría, A. B. Doeschl-Wilson, J. P. Lhorente, Ross D. Houston, J. M. Yáñez

Aquaculture, 734207

 

Development of a TaqMan qPCR assay for detection of Alexandrium spp and application to Harmful Algal Bloom monitoring

Robert G. Hatfield, Timothy Bean, Andrew D. Turner, David N. Lees, James Lowther, Adam Lewis, Craig Baker-Austin

Toxicon: X, 100011

 

Proteomic comparison of selective breeding and growth hormone transgenesis in fish: Unique pathways to enhanced growth

D. R. Causey, J. H. Kim, D. A. Stead, S. A. M. Martin, R. H. Devlin, Daniel J Macqueen

Journal of proteomics 192, 114-124

 

Rainbow trout (Oncorhynchus mykiss) urea cycle and polyamine synthesis gene families show dynamic expression responses to inflammation

T. C. Clark, J. Tinsley, Daniel J. Macqueen, S. A. M. Martin

Fish & Shellfish Immunology 89, 290-300

 

Integrating Genomic and Morphological Approaches in Fish Pathology Research: The Case of Turbot (Scophthalmus maximus) Enteromyxosis

Paolo Ronza, Diego Robledo, Roberto Bermúdez, Ana Paula Losada, Belén G Pardo, Paulino Martínez, María Isabel Quiroga

Frontiers in genetics 10, 26

 

Enhancing genetic disease control by selecting for lower host infectivity and susceptibility

S. Tsairidou, O. Anacleto, J. A. Wooliams,  A. Doeschl-Wilson

Heredity 122, 742-758

 

Discovery of all three types in cartilaginous fishes enables phylogenetic resolution of the origins and evolution of interferons

AK Redmond, J Zou, CJ Secombes, DJ Macqueen, H Dooley

Frontiers in immunology 10, 1558

 

The AMPK system of salmonid fishes was expanded through genome duplication and is regulated by growth and immune status in muscle

DR Causey, JH Kim, RH Devlin, SAM Martin, DJ Macqueen

Scientific reports 9 (1), 1-11

 

Rainbow trout (Oncorhynchus mykiss) urea cycle and polyamine synthesis gene families show dynamic expression responses to inflammation

TC Clark, J Tinsley, DJ Macqueen, SAM Martin

Fish & shellfish immunology 89, 290-300

 

Atlantic Salmon (Salmon salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

RD Houston, DJ Macqueen

Animal genetics 50 (1), 3-14