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

Accuracy of genotype imputation and genomic predictions in a two-generation farmed Atlantic salmon population using high-density and low-density SNP panels

(2018) Grazyella M. Yoshida et al.   AQUACULTURE

Liver proteome response of pre-harvest Atlantic salmon following exposure to elevated temperature

(2018) Waldo G. Nuez-Ortín et al.   BMC GENOMICS

Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes

(2018) Carol Best et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

The demographic history of Atlantic salmon (Salmo salar ) across its distribution range reconstructed from approximate Bayesian computations*

(2018) Quentin Rougemont et al.   EVOLUTION

Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations

(2018) Timothy P. Bilton et al.   GENETICS

Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes

(2018) Victoria L. Pritchard et al.   MOLECULAR ECOLOGY

Life-stage-associated remodelling of lipid metabolism regulation in Atlantic salmon

(2018) Gareth Gillard et al.   MOLECULAR ECOLOGY

Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing

(2018) Laurène A. Lecaudey et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”

(2018) Lauryl M J Nutter et al.   NATURE METHODS

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

(2018) Kris A. Christensen et al.   PLoS One

Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon

(2018) Shawn R. Narum et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

(2018) Todd P. Michael et al.   Nature Communications

Vgll3 and the Hippo pathway are regulated in Sertoli cells upon entry and during puberty in Atlantic salmon testis

(2018) Erik Kjærner-Semb et al.   Scientific Reports

Transcriptome response of Atlantic salmon (Salmo salar ) to competition with ecologically similar non-native species

(2018) Xiaoping He et al.   Ecology and Evolution

Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations

(2018) Timothy P. Bilton et al.   GENETICS

Behavioral Fever Drives Epigenetic Modulation of the Immune Response in Fish

(2018) Sebastian Boltana et al.   Frontiers in Immunology

Insulin-Like Growth Factor-Binding Proteins of Teleost Fishes

(2018) Daniel Garcia de la Serrana et al.   Frontiers in Endocrinology

Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity

(2018) Tamsyn M. Uren Webster et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The grayling genome reveals selection on gene expression regulation after whole genome duplication

(2018) Srinidhi Varadharajan et al.   Genome Biology and Evolution

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

(2018) Dwight R. Causey et al.   Journal of Proteomics

CRISPR plants now subject to tough GM laws in European Union

(2018) Ewen Callaway   NATURE

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly

(2018) Kris A. Christensen et al.   PLoS One

Proteome analysis reveals a role of rainbow trout lymphoid organs during Yersinia ruckeri infection process

(2018) Gokhlesh Kumar et al.   Scientific Reports

Gene Expression Response to Sea Lice in Atlantic Salmon Skin: RNA Sequencing Comparison Between Resistant and Susceptible Animals

(2018) Diego Robledo et al.   Frontiers in Genetics

High-throughput proteomic profiling of the fish liver following bacterial infection

(2018) Dwight R Causey et al.   BMC GENOMICS

Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

(2017) Kevin A Glover et al.   FISH AND FISHERIES

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Application of genomics in salmon aquaculture breeding programs by Ashie Norris

(2017) Ashie Norris   Marine Genomics

First genetically engineered salmon sold in Canada

(2017) Emily Waltz   NATURE

Population genetics of sexual conflict in the genomic era

(2017) Judith E. Mank   NATURE REVIEWS GENETICS

Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon

(2017) Jérémy Le Luyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Future directions in breeding for disease resistance in aquaculture species

(2017) Ross D. Houston   REVISTA BRASILEIRA DE ZOOTECNIA-BRAZILIAN JOURNAL OF ANIMAL SCIENCE

Applications of genotyping by sequencing in aquaculture breeding and genetics

(2017) Diego Robledo et al.   Reviews in Aquaculture

Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system

(2017) Yihan Zhang et al.   Nature Communications

Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon

(2017) Hsin-Yuan Tsai et al.   G3-Genes Genomes Genetics

Precision engineering for PRRSV resistance in pigs: Macrophages from genome edited pigs lacking CD163 SRCR5 domain are fully resistant to both PRRSV genotypes while maintaining biological function

(2017) Christine Burkard et al.   PLoS Pathogens

Epigenetic considerations in aquaculture

(2017) Mackenzie R. Gavery et al.   PeerJ

Impacts of Early Life Stress on the Methylome and Transcriptome of Atlantic Salmon

(2017) Hooman K. Moghadam et al.   Scientific Reports

Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection

(2016) Erik Kjærner-Semb et al.   BMC GENOMICS

Differential responses of the gut transcriptome to plant protein diets in farmed Atlantic salmon

(2016) Elżbieta Król et al.   BMC GENOMICS

Gene expression comparison of resistant and susceptible Atlantic salmon fry challenged with Infectious Pancreatic Necrosis virus reveals a marked contrast in immune response

(2016) Diego Robledo et al.   BMC GENOMICS

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

(2016) Lei Liu et al.   Evolutionary Applications

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line

(2016) Carola E. Dehler et al.   MARINE BIOTECHNOLOGY

Evidence of recent signatures of selection during domestication in an Atlantic salmon population

(2016) A.P. Gutierrez et al.   Marine Genomics

Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing

(2016) Morten T. Limborg et al.   MOLECULAR ECOLOGY

Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations

(2016) J. M. Yáñez et al.   Molecular Ecology Resources

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Selection response in fish and shellfish: a review

(2016) Trygve Gjedrem et al.   Reviews in Aquaculture

Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon ( Salmo salar ) Genome

(2016) Hsin Y. Tsai et al.   G3-Genes Genomes Genetics

Dnd knockout ablates germ cells and demonstrates germ cell independent sex differentiation in Atlantic salmon

(2016) Anna Wargelius et al.   Scientific Reports

A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research

(2016) Karina Gajardo et al.   Scientific Reports

A new view of the fish gut microbiome: Advances from next-generation sequencing

(2015) Mahdi Ghanbari et al.   AQUACULTURE

The genetic architecture of growth and fillet traits in farmed Atlantic salmon (Salmo salar)

(2015) Hsin Yuan Tsai et al.   BMC GENETICS

Genome-wide association analysis reveals loci associated with resistance against Piscirickettsia salmonis in two Atlantic salmon (Salmo salar L.) chromosomes

(2015) Katharina Correa et al.   BMC GENOMICS

Genome wide association and genomic prediction for growth traits in juvenile farmed Atlantic salmon using a high density SNP array

(2015) Hsin-Yuan Tsai et al.   BMC GENOMICS

Epithelial Cadherin Determines Resistance to Infectious Pancreatic Necrosis Virus in Atlantic Salmon

(2015) Thomas Moen et al.   GENETICS

Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar)

(2015) S Gonen et al.   HEREDITY

Effects of Crossovers Between Homeologs on Inheritance and Population Genomics in Polyploid-Derived Salmonid Fishes

(2015) F. W. Allendorf et al.   JOURNAL OF HEREDITY

Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

(2015) R. K. Waples et al.   Molecular Ecology Resources

Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

(2015) Nicola J. Barson et al.   NATURE

The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males

(2015) Fernando Ayllon et al.   PLoS Genetics

Epithelial Cadherin Determines Resistance to Infectious Pancreatic Necrosis Virus in Atlantic Salmon

(2015) Thomas Moen et al.   GENETICS

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

(2015) Leif Andersson et al.   GENOME BIOLOGY

Using optical mapping data for the improvement of vertebrate genome assemblies

(2015) Kerstin Howe et al.   GigaScience

Sequencing millions of animals for genomic selection 2.0

(2015) J. M. Hickey   JOURNAL OF ANIMAL BREEDING AND GENETICS

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

(2014) Ross D Houston et al.   BMC GENOMICS

Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing

(2014) Serap Gonen et al.   BMC GENOMICS

Enigmatic Orthology Relationships between Hox Clusters of the African Butterfly Fish and Other Teleosts Following Ancient Whole-Genome Duplication

(2014) Kyle J. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci

(2014) Jean-Sébastien Moore et al.   MOLECULAR ECOLOGY

Whole-genome duplication in teleost fishes and its evolutionary consequences

(2014) Stella M. K. Glasauer et al.   MOLECULAR GENETICS AND GENOMICS

The emergence of proteome-wide technologies: systematic analysis of proteins comes of age

(2014) Michal Breker et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Targeted Mutagenesis in Atlantic Salmon (Salmo salar L.) Using the CRISPR/Cas9 System Induces Complete Knockout Individuals in the F0 Generation

(2014) Rolf B. Edvardsen et al.   PLoS One

A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

(2014) D. J. Macqueen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries

(2014) Martin S. Llewellyn et al.   Frontiers in Microbiology

Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae

(2013) Markos A. Alexandrou et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Accelerating Improvement of Livestock with Genomic Selection

(2013) Theo Meuwissen et al.   Annual Review of Animal Biosciences

Genetic mapping of quantitative trait loci (QTL) for body-weight in Atlantic salmon (Salmo salar) using a 6.5K SNP array

(2012) Alejandro P. Gutierrez et al.   AQUACULTURE

Genetic improvement for the development of efficient global aquaculture: A personal opinion review

(2012) Trygve Gjedrem   AQUACULTURE

Genomic arrangement of salinity tolerance QTLs in salmonids: A comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss)

(2012) Joseph D Norman et al.   BMC GENOMICS

Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon

(2012) Ross D Houston et al.   BMC GENOMICS

Asymmetrical viability in backcrosses between highly divergent populations of Atlantic salmon (Salmo salar): implications for conservation

(2012) Eef Cauwelier et al.   CONSERVATION GENETICS

SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

(2012) Vincent Bourret et al.   MOLECULAR ECOLOGY

A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

(2011) Sigbjørn Lien et al.   BMC GENOMICS

Extent and scale of local adaptation in salmonid fishes: review and meta-analysis

(2011) D J Fraser et al.   HEREDITY

Segregation of infectious pancreatic necrosis resistance QTL in the early life cycle of Atlantic Salmon (Salmo salar)

(2010) A. A. Gheyas et al.   ANIMAL GENETICS

Detection of QTL affecting harvest traits in a commercial Atlantic salmon population

(2009) R. D. Houston et al.   ANIMAL GENETICS

Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait

(2009) Thomas Moen et al.   BMC GENOMICS

The susceptibility of Atlantic salmon fry to freshwater infectious pancreatic necrosis is largely explained by a major QTL

(2009) R D Houston et al.   HEREDITY

Major Quantitative Trait Loci Affect Resistance to Infectious Pancreatic Necrosis in Atlantic Salmon (Salmo salar)

(2008) R. D. Houston et al.   GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Endocrine systems in juvenile anadromous and landlocked Atlantic salmon (Salmo salar): Seasonal development and seawater acclimation

(2007) Tom O. Nilsen et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY