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View article: <i>De novo</i> Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference
<i>De novo</i> Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference Open
Rainbow trout ( Oncorhynchus mykiss ) exhibit extensive genomic diversity shaped by domestication, life history, and geographic origin. To advance the development of a comprehensive pangenome reference, we present new de novo genome assemb…
View article: public mid-density genotyping platform for North American Atlantic salmon (Salmo salar L.)
public mid-density genotyping platform for North American Atlantic salmon (Salmo salar L.) Open
Genomics-enabled selective animal breeding has become common in recent years, prompting a growing need for diverse genotyping tools that facilitate collaboration among research groups while meeting specific programme needs and objectives. …
View article: Genome-wide association analysis of resistance to bacterial cold-water disease in an important rainbow trout aquaculture breeding population
Genome-wide association analysis of resistance to bacterial cold-water disease in an important rainbow trout aquaculture breeding population Open
Bacterial cold-water disease (BCWD) outbreaks in salmonid aquaculture have resulted in significant losses in commercial populations. Currently, there is no commercially available vaccine for the disease caused by Flavobacterium psychrophil…
View article: The genome assembly of the westslope cutthroat trout, <i>Oncorhynchus lewisi</i>, reveals interspecific chromosomal rearrangements with the rainbow trout, <i>Oncorhynchus mykiss</i>
The genome assembly of the westslope cutthroat trout, <i>Oncorhynchus lewisi</i>, reveals interspecific chromosomal rearrangements with the rainbow trout, <i>Oncorhynchus mykiss</i> Open
Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genet…
View article: Advancing genetic improvement in the omics era: status and priorities for United States aquaculture
Advancing genetic improvement in the omics era: status and priorities for United States aquaculture Open
Background The innovations of the “Omics Era” have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements we…
View article: Transcriptomic Response of the Ovarian Follicle Complex in Post-Vitellogenic Rainbow Trout to 17α,20β-Dihdroxy-4-pregnen-3-one In Vitro
Transcriptomic Response of the Ovarian Follicle Complex in Post-Vitellogenic Rainbow Trout to 17α,20β-Dihdroxy-4-pregnen-3-one In Vitro Open
Gonadotropins and progestins are the primary regulators of follicle maturation and ovulation in fish, and they require complex communication among the oocyte and somatic cells of the follicle. The major progestin and the maturation-inducin…
View article: The genome assembly of the westslope cutthroat trout,<i>Oncorhynchus lewisi</i>, reveals interspecific chromosomal rearrangements with the rainbow trout
The genome assembly of the westslope cutthroat trout,<i>Oncorhynchus lewisi</i>, reveals interspecific chromosomal rearrangements with the rainbow trout Open
Cutthroat trout ( Oncorhynchus clarkii ) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several gen…
View article: Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout
Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout Open
With the rapid and significant cost reduction of next-generation sequencing, low-coverage whole-genome sequencing (lcWGS), followed by genotype imputation, is becoming a cost-effective alternative to single-nucleotide polymorphism (SNP)-ar…
View article: Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci
Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci Open
Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV), which can cause substantial mortality and economic losses in rainbow trout aquaculture and fisheries enhancement hatchery program…
View article: The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon
The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon Open
Atlantic salmon (Salmo salar) in Northeastern US and Eastern Canada has high economic value for the sport fishing and aquaculture industries. Large differences exist between the genomes of Atlantic salmon of European origin and North Ameri…
View article: The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for North American Atlantic salmon
The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for North American Atlantic salmon Open
Given the genetic and genomic differences between Atlantic salmon of European origin and North American (N.A.) origin, it is crucial to develop unique genomic resources for each lineage. Here we describe the resources that we recently deve…
View article: Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping
Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping Open
Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USD…
View article: Identification of Haplotypes Associated With Resistance to Bacterial Cold Water Disease in Rainbow Trout Using Whole-Genome Resequencing
Identification of Haplotypes Associated With Resistance to Bacterial Cold Water Disease in Rainbow Trout Using Whole-Genome Resequencing Open
Bacterial cold water disease (BCWD) is an important disease in rainbow trout aquaculture. Previously, we have identified and validated two major QTL (quantitative trait loci) for BCWD resistance, located on chromosomes Omy08 and Omy25, in …
View article: Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Supplemental VCF file
Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Supplemental VCF file Open
Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USD…
View article: Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Supplemental VCF file
Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Supplemental VCF file Open
Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USD…
View article: Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping
Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping Open
Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USD…
View article: A long reads-based <i>de-novo</i> assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout
A long reads-based <i>de-novo</i> assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout Open
Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originat…
View article: A long reads-based <i>de-novo</i> assembly of the genome of the Arlee homozygous line reveals structural genome variation in rainbow trout
A long reads-based <i>de-novo</i> assembly of the genome of the Arlee homozygous line reveals structural genome variation in rainbow trout Open
Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originat…
View article: Assessing Accuracy of Genomic Predictions for Resistance to Infectious Hematopoietic Necrosis Virus With Progeny Testing of Selection Candidates in a Commercial Rainbow Trout Breeding Population
Assessing Accuracy of Genomic Predictions for Resistance to Infectious Hematopoietic Necrosis Virus With Progeny Testing of Selection Candidates in a Commercial Rainbow Trout Breeding Population Open
Infectious hematopoietic necrosis (IHN) is an economically important disease of salmonid fish caused by the IHN virus (IHNV). Under industrial aquaculture settings, IHNV can cause substantial mortality and losses. Actually, there is no con…
View article: A New Single Nucleotide Polymorphism Database for North American Atlantic Salmon Generated Through Whole Genome Resequencing
A New Single Nucleotide Polymorphism Database for North American Atlantic Salmon Generated Through Whole Genome Resequencing Open
DATA REPORT article Front. Genet., 21 February 2020Sec. Livestock Genomics Volume 11 - 2020 | https://doi.org/10.3389/fgene.2020.00085
View article: Additional file of Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes
Additional file of Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes Open
Additional file of Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes
View article: Additional file of A first generation integrated map of the rainbow trout genome
Additional file of A first generation integrated map of the rainbow trout genome Open
Additional file of A first generation integrated map of the rainbow trout genome
View article: Additional file 3 of Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes
Additional file 3 of Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes Open
Additional file 3:An example of multiple gene hits corresponding to odorant receptor gene family (sheet 1) or protocadherin gene family (sheet 2) in zebrafish. (XLS 43 KB)
View article: Additional file of A first generation integrated map of the rainbow trout genome
Additional file of A first generation integrated map of the rainbow trout genome Open
Additional file of A first generation integrated map of the rainbow trout genome
View article: Additional file 5 of Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes
Additional file 5 of Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes Open
Additional file 5:Summary of conserved microsyntenies identified by BlastX analysis with medaka (sheet 1), stickleback (sheet 2) and zebrafish (sheet 3) gene hits. Putative identities of mate paired genes were provided as ENSEMBL protein I…