Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon

2005 ◽  
Vol 14 (13) ◽  
pp. 4193-4203 ◽  
Author(s):  
CHRISTIAN T. SMITH ◽  
CARITA M. ELFSTROM ◽  
LISA W. SEEB ◽  
JAMES E. SEEB
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Pacific Salmon ◽  
Sequence Data ◽  
Snp Detection

Sequence of Sockeye Salmon Type 1 and 2 Growth Hormone Genes and the Relationship of Rainbow Trout with Atlantic and Pacific Salmon

1993 ◽  
Vol 50 (8) ◽  
pp. 1738-1748 ◽  
Author(s):  
Robert H. Devlin
Keyword(s):  
Growth Hormone ◽  
Rainbow Trout ◽  
Gene Duplication ◽  
Atlantic Salmon ◽  
Sockeye Salmon ◽  
Pacific Salmon ◽  
Duplication Event ◽  
Breeding Population ◽  
Gene Duplication Event ◽  
Relationship Of

Two types of growth hormone genes have been isolated from sockeye salmon (Oncorhynchus nerka) and their complete nucleotide sequence determined. The genes encode proteins of 210 amino acids and show considerable similarity to growth hormones characterized in other salmonids and fishes. The two genes presumably arose from a gene duplication event that generated the tetraploid condition in salmonids and are highly conserved in their coding regions. The sequences have diverged approximately 18% in noncoding regions since the gene duplication event and show numerous deletions and/or insertions. Isolation of these two genes from a Pacific salmon allows comparison of their sequences to growth hormone genes characterized from rainbow trout and from Atlantic salmon. The results indicate that rainbow trout is more similar to Pacific than to Atlantic salmon and suggest that Atlantic salmon diverged from Pacific salmonids at a time when sockeye and rainbow trout were part of a common breeding population. These results support the recent reclassification of rainbow trout from the genus Salmo to Oncorhynchus.

scholarly journals Discriminating Among Pacific Salmon, Rainbow Trout, and Atlantic Salmon Species Using Common Genetic Screening Methods

2019 ◽  
Vol 10 (1) ◽  
pp. 228-240 ◽  
Author(s):  
Christopher Habicht ◽  
Christian T. Smith ◽  
Andrew Barclay ◽  
Heather A. Hoyt ◽  
Keith Turnquist ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Pacific Salmon ◽  
North Pacific Ocean ◽  
Genotyping By Sequencing ◽  
Population Monitoring ◽  
Common Species ◽  
Screening Methods ◽  
Life History Stage ◽  
The North

Abstract The five most common species of Pacific salmon, Rainbow Trout (steelhead) Oncorhynchus spp., and Atlantic Salmon Salmo salar intermingle in the North Pacific Ocean and its freshwater tributaries. Efficient morphological methods for distinguishing among these species are sometimes limited by condition of the specimen (degraded or missing morphology), life history stage, or training of the observer. Researchers have successfully applied various genetic methods to distinguish among these species when morphological analyses are not possible, but they cannot easily incorporate these methods into standard fish and wildlife population monitoring analysis workflows. Here we test five 5′–3′ exonuclease (TaqMan) assays developed from mitochondrial genes and provide novel methods that take advantage of TaqMan output to distinguish among these species. We found that combinations of as few as two of the five assays were adequate to distinguish all species. TaqMan chemistry is designed to interrogate a single nucleotide locus. We also explore the basis for the variation in the observed scatter plot distributions (variation in florescent signals) and show that this variation is due to nucleotide diversity in and near the probe site. Because the SNPs underlying the assays developed here are all physically close to one another along the mitochondrial genome, the potential exists to develop a single DNA sequence-based assay to discriminate among salmon species. This single assay can be added to a genotyping-by-sequencing panel to identify and exclude nontarget species from analyses.

scholarly journals Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pablo Cáceres ◽  
Agustín Barría ◽  
Kris A. Christensen ◽  
Liane N. Bassini ◽  
Katharina Correa ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Candidate Genes ◽  
Protein Phosphatase ◽  
Sea Lice ◽  
Genome Wide Association Studies ◽  
Dual Specificity ◽  
Dual Specificity Protein Phosphatase ◽  
Genomic Regions ◽  
Specificity Protein

AbstractSea lice (Caligus rogercresseyi) is an ectoparasite which causes major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The objectives of this study were to: (1) identify genomic regions associated with resistance to Caligus rogercresseyi in Atlantic salmon and rainbow trout by performing single-step Genome-Wide Association studies (ssGWAS), and (2) identify candidate genes related to trait variation based on exploring orthologous genes within the associated regions across species. A total of 2626 Atlantic salmon and 2643 rainbow trout were challenged and genotyped with 50 K and 57 K SNP panels, respectively. We ran two independent ssGWAS for sea lice resistance on each species and identified 7 and 13 regions explaining more than 1% of the genetic variance for the trait, with the most important regions explaining 3% and 2.7% for Atlantic salmon and rainbow trout, respectively. We identified genes associated with immune response, cytoskeleton function, and cell migration when focusing on important genomic regions for each species. Moreover, we found 15 common orthogroups which were present in more than one associated genomic region, within- or between-species; however, only one orthogroup showed a clear potential biological relevance in the response against sea lice. For instance, dual-specificity protein phosphatase 10-like (dusp10) and dual-specificity protein phosphatase 8 (dusp8) were found in genomic regions associated with lice density in Atlantic salmon and rainbow trout, respectively. Dusp10 and dusp8 are modulators of the MAPK pathway and might be involved in the differences of the inflammation response between lice resistant and susceptible fish from both species. Our results provide further knowledge on candidate genes related to sea lice resistance and may help establish better control for sea lice in fish populations.

scholarly journals A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

2021 ◽  
Author(s):  
Guangtu Gao ◽  
Susana Magadan ◽  
Geoffrey C Waldbieser ◽  
Ramey C Youngblood ◽  
Paul A Wheeler ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Chromosome Number ◽  
Genome Assembly ◽  
De Novo Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Structural Variations ◽  
High Coverage ◽  
Haploid Chromosome Number ◽  
Long Reads

Abstract 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 originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.

Thermal Acclimation and Temperature Selection in Atlantic Salmon, Salmo salar, and Rainbow Trout, S. gairdneri

1967 ◽  
Vol 24 (7) ◽  
pp. 1507-1513 ◽  
Author(s):  
M. Yaqub Javaid ◽  
John M. Anderson
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Salmo Salar ◽  
Thermal Acclimation ◽  
Acclimation Temperature ◽  
Horizontal Gradient ◽  
Temperature Selection ◽  
Marked Influence ◽  
Atlantic Salmon Salmo Salar

The selected temperature for Atlantic salmon and rainbow trout, as determined in a horizontal gradient, increases with acclimation temperature over the acclimation range 5–20 C for salmon and 10–20 C for trout. The final preferendum for salmon is about 17 C. The results for rainbow trout suggest that the type of gradient used, i.e. vertical or horizontal, has a marked influence on the experimentally determined relation between acclimation temperature and selected temperature.

scholarly journals Oral Administration of Lactococcus lactis Producing Interferon Type II, Enhances the Immune Response Against Bacterial Pathogens in Rainbow Trout

2021 ◽  
Vol 12 ◽  
Author(s):  
Alvaro Santibañez ◽  
Diego Paine ◽  
Mick Parra ◽  
Carlos Muñoz ◽  
Natalia Valdes ◽  
...  
Keyword(s):  
Immune Response ◽  
Lactic Acid ◽  
Rainbow Trout ◽  
Lactic Acid Bacteria ◽  
Atlantic Salmon ◽  
Oral Administration ◽  
Bacterial Infection ◽  
Type Ii ◽  
Recombinant Interferon

Lactic acid bacteria are a powerful vehicle for releasing of cytokines and immunostimulant peptides at the gastrointestinal level after oral administration. However, its therapeutic application against pathogens that affect rainbow trout and Atlantic salmon has been little explored. Type II interferon in Atlantic salmon activates the antiviral response, protecting against viral infection, but its role against bacterial infection has not been tested in vivo. In this work, through the design of a recombinant lactic acid bacterium capable of producing Interferon gamma from Atlantic salmon, we explore its role against bacterial infection and the ability to stimulate systemic immune response after oral administration of the recombinant probiotic. Recombinant interferon was active in vitro, mainly stimulating IL-6 expression in SHK-1 cells. In vivo, oral administration of the recombinant probiotic produced an increase in IL-6, IFNγ and IL-12 in the spleen and kidney, in addition to stimulating the activity of lysozyme in serum. The challenge trials indicated that the administration of the IFNγ-producing probiotic doubled the survival in fish infected with F. psychrophilum. In conclusion, our results showed that the oral administration of lactic acid bacteria producing IFNγ managed to stimulate the immune response at a systemic level, conferring protection against pathogens, showing a biotechnological potential for its application in aquaculture.

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