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Genetics and Genomics of Salmonid Fishes
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Genetics and Genomics of Salmonid Fishes

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 26568

Special Issue Editors

Dr. Daniel Macqueen

E-Mail Website
Guest Editor
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK
Interests: cross-cut genomes; evolution; physiology; phylogenetics; fish biology; aquaculture; salmonids
Dr. Manu Kumar Gundappa

E-Mail Website
Guest Editor
The Royal (Dick) School of Veterinary Studies and The Roslin Institute Easter Bush Campus, The University of Edinburgh, Midlothian, Edinburgh EH25 9RG, UK
Interests: salmonidae; aquaculture; wild salmonids; whole genome duplication; genetic variation; tetraploidy; genome sequencing; selective breeding; functional ggenomics; genome editing; genome evolution; phylogenetics; immunogenomics; nutrigenomics
Dr. Diego Robledo

E-Mail Website
Guest Editor
The Royal (Dick) School of Veterinary Studies and The Roslin Institute Easter Bush Campus, The University of Edinburgh, Midlothian, Edinburgh EH25 9RG, UK
Interests: salmonidae; aquaculture; wild salmonids; whole genome duplication; genetic variation; tetraploidy; genome sequencing; selective breeding; functional ggenomics; genome editing; genome evolution; phylogenetics; immunogenomics; nutrigenomics

Special Issue Information

Dear Colleagues,

Salmonids are one of the most iconic fish lineages. In addition to playing a crucial role in global food and economic security, this family attracts the attention of conservation efforts and of scientists keen to understand its interesting life history and genome biology. This interest has driven forward impressive recent advancements in salmonid genetics and genomics, including reference genome sequences and high-resolution genotyping tools for many key species. Genomics is proving central to the improvement of farmed salmonid traits (e.g., disease resistance) through modern breeding programmes, leading to increased animal welfare and industrial stability, and is equally vital to investigate genetic structuring and adaptation of wild populations, guiding stock management decisions. While genome-wide SNP markers remain the current state of the art for salmonid genetic analyses, there is a growing recognition of the crucial role that larger structural variants can play in population differentiation. Functional genomics—including fast-developing approaches to probe epigenetic features—is further shedding light onto different aspects of salmonid biology and health, including immunity and host–pathogen interactions, nutrition, sexual maturation and smoltification. A genomic perspective is also vital to interrogate the genome rediploidization process following the salmonid whole-genome duplication event (‘Ss4R’), including the evolution of duplicated gene networks. Excitingly, precise genome editing methods in salmonids are maturing rapidly, opening up new avenues to rapidly study the genetic basis of salmonid phenotypes. This Special Issue aims to gather leading articles that advance our understanding of salmonid biology by exploiting genetics and genomics across the full breadth of interest areas.

Dr. Daniel Macqueen
Dr Manu Kumar Gundappa
Dr Diego Robledo
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Salmonidae
  • Aquaculture
  • Wild Salmonids
  • Whole Genome Duplication
  • Genetic variation
  • Tetraploidy
  • Genome Sequencing
  • Selective Breeding
  • Functional Genomics
  • Genome Editing
  • Genome Evolution
  • Phylogenetics
  • Immunogenomics
  • Nutrigenomics

Published Papers (7 papers)

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Research

17 pages, 2656 KiB  
Article
Evolution of the IRF Family in Salmonids
by Thomas C. Clark, Pierre Boudinot and Bertrand Collet
Genes 2021, 12(2), 238; https://doi.org/10.3390/genes12020238 - 8 Feb 2021
Cited by 9 | Viewed by 2632
Abstract
Interferon regulatory factors (IRFs) as a family, are major regulators of the innate antiviral response in vertebrates principally involved in regulating the expression of interferons (IFNs) and interferon-stimulated genes (ISGs). To date, nine IRFs have been identified in mammals with a 10th member [...] Read more.
Interferon regulatory factors (IRFs) as a family, are major regulators of the innate antiviral response in vertebrates principally involved in regulating the expression of interferons (IFNs) and interferon-stimulated genes (ISGs). To date, nine IRFs have been identified in mammals with a 10th member also found in several avian and fish species. Through genome mining and phylogenetic analysis, we identified and characterised 23 irf genes in 6 salmonid species. This larger repertoire of IRF in salmonids results from two additional whole-genome duplications which occurred in early teleosts and salmonids, respectively. Synteny analysis was then used to identify and confirm which paralogues belonged to each subgroup and a new nomenclature was assigned to the salmonid IRFs. Furthermore, we present a full set of Real-Time PCR primers for all rainbow trout IRFs, confirmed by sequencing to ensure paralogue specificity. RT PCR was then used to examine the response of all trout irf genes in vivo, following Vibrio anguillarum and poly I:C stimulation, indicating potential functional divergence between paralogues. Overall, this study presents a comprehensive overview of the IRF family in salmonids and highlights some novel roles for the salmonid-specific IRFs in immunity. Full article
(This article belongs to the Special Issue Genetics and Genomics of Salmonid Fishes)
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30 pages, 13469 KiB  
Article
The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead (Oncorhynchus mykiss) Populations across the Elwha River Watershed
by Alexandra K. Fraik, John R. McMillan, Martin Liermann, Todd Bennett, Michael L. McHenry, Garrett J. McKinney, Abigail H. Wells, Gary Winans, Joanna L. Kelley, George R. Pess and Krista M. Nichols
Genes 2021, 12(1), 89; https://doi.org/10.3390/genes12010089 - 13 Jan 2021
Cited by 24 | Viewed by 6509 | Correction
Abstract
Dam construction and longitudinal river habitat fragmentation disrupt important life histories and movement of aquatic species. This is especially true for Oncorhynchus mykiss that exhibits both migratory (steelhead) and non-migratory (resident rainbow) forms. While the negative effects of dams on salmonids have been [...] Read more.
Dam construction and longitudinal river habitat fragmentation disrupt important life histories and movement of aquatic species. This is especially true for Oncorhynchus mykiss that exhibits both migratory (steelhead) and non-migratory (resident rainbow) forms. While the negative effects of dams on salmonids have been extensively documented, few studies have had the opportunity to compare population genetic diversity and structure prior to and following dam removal. Here we examine the impacts of the removal of two dams on the Elwha River on the population genetics of O. mykiss. Genetic data were produced from >1200 samples collected prior to dam removal from both life history forms, and post-dam removal from steelhead. We identified three genetic clusters prior to dam removal primarily explained by isolation due to dams and natural barriers. Following dam removal, genetic structure decreased and admixture increased. Despite large O. mykiss population declines after dam construction, we did not detect shifts in population genetic diversity or allele frequencies of loci putatively involved in migratory phenotypic variation. Steelhead descendants from formerly below and above dammed populations recolonized the river rapidly after dam removal, suggesting that dam construction did not significantly reduce genetic diversity underlying O. mykiss life history strategies. These results have significant evolutionary implications for the conservation of migratory adaptive potential in O. mykiss populations above current anthropogenic barriers. Full article
(This article belongs to the Special Issue Genetics and Genomics of Salmonid Fishes)
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18 pages, 2536 KiB  
Article
Compensatory Response of the Somatotropic Axis from IGFBP-2b Gene Editing in Rainbow Trout (Oncorhynchus mykiss)
by Beth M. Cleveland, Shiori Habara, Jin Oikawa, Lisa M. Radler and Munetaka Shimizu
Genes 2020, 11(12), 1488; https://doi.org/10.3390/genes11121488 - 10 Dec 2020
Cited by 11 | Viewed by 2157
Abstract
Rainbow trout with gene editing-induced reductions in serum insulin-like growth factor binding protein (IGFBP)-2b exhibit similar growth performance compared to fish without IGFBP-2b gene disruption. The objective of this study is to determine how the components of the insulin-like growth factor (IGF)/IGFBP system [...] Read more.
Rainbow trout with gene editing-induced reductions in serum insulin-like growth factor binding protein (IGFBP)-2b exhibit similar growth performance compared to fish without IGFBP-2b gene disruption. The objective of this study is to determine how the components of the insulin-like growth factor (IGF)/IGFBP system respond to a reduction in serum IGFBP-2b abundance. Editing the IGFBP-2b genes in rainbow trout resulted in an 83% decrease in serum IGFBP-2b in mutants. This resulted in a 35% reduction in serum IGF-I, which was offset by reduced expression of hepatic igfbp-1a2 and increased muscle igfr-1a; these responses suggest that an increased IGF-I signaling capacity offset reductions in serum IGF-I. During feed deprivation, the differential expression of igfbp genes supports the attenuation of the growth inhibitory response, likely due to the further reduction in serum IGF-I that alleviated the need for an IGF-inhibitory response. Unique igfbp expression patterns occurred during refeeding, suggesting an enhanced IGF-I signaling capacity in controls. Collectively, these findings support that the role of IGFBP-2b is to regulate serum IGF-I concentrations. The compensatory regulation of IGF/IGFBP system genes indicates that adjustments in other IGFBP, both circulating and at the local level, maintain IGF-I signaling at a level appropriate for the nutritional state of the fish. Full article
(This article belongs to the Special Issue Genetics and Genomics of Salmonid Fishes)
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19 pages, 1055 KiB  
Article
Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon
by Alice Shwe, Tone-Kari Knutsdatter Østbye, Aleksei Krasnov, Sigmund Ramberg and Rune Andreassen
Genes 2020, 11(9), 1059; https://doi.org/10.3390/genes11091059 - 8 Sep 2020
Cited by 13 | Viewed by 3547
Abstract
Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression [...] Read more.
Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression during smoltification and the adaption to seawater is largely unknown. Here, small RNA sequencing of materials from head kidney before, during smoltification and post seawater transfer were used to study expression dynamics of miRNAs, while microarray analysis was applied to study mRNA expression dynamics. Comparing all timepoints, 71 miRNAs and 2709 mRNAs were identified as differentially expressed (DE). Hierarchical clustering analysis of the DE miRNAs showed three major clusters with characteristic expression changes. Eighty-one DE mRNAs revealed negatively correlated expression patterns to DE miRNAs in Cluster I and III. Furthermore, 42 of these mRNAs were predicted as DE miRNA targets. Gene enrichment analysis of negatively correlated target genes showed they were enriched in gene ontology groups hormone biosynthesis, stress management, immune response, and ion transport. The results strongly indicate that post-transcriptional regulation of gene expression by miRNAs is important in smoltification and sea water adaption, and this study identifies several putative miRNA-target pairs for further functional studies. Full article
(This article belongs to the Special Issue Genetics and Genomics of Salmonid Fishes)
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9 pages, 1242 KiB  
Communication
Genome-Wide Association Study Confirms Previous Findings of Major Loci Affecting Resistance to Piscine myocarditis virus in Atlantic Salmon (Salmo salar L.)
by Borghild Hillestad, Ólafur H. Kristjánsson, Shokouh Makvandi-Nejad and Hooman K. Moghadam
Genes 2020, 11(6), 608; https://doi.org/10.3390/genes11060608 - 30 May 2020
Cited by 13 | Viewed by 2986
Abstract
Cardiomyopathy syndrome is a viral disease of Atlantic salmon, mostly affecting fish during the late stages of production, resulting in significant losses to the industry. It has been shown that resistance to this disease has a strong genetic component, with quantitative trait loci [...] Read more.
Cardiomyopathy syndrome is a viral disease of Atlantic salmon, mostly affecting fish during the late stages of production, resulting in significant losses to the industry. It has been shown that resistance to this disease has a strong genetic component, with quantitative trait loci (QTL) on chromosomes 27 (Ssa27) and Ssa12 to explain most of the additive genetic variance. Here, by analysing animals from a different year-class and a different population, we further aimed to confirm and narrow down the locations of these QTL. The data support the existence of the two QTL and suggest that the causative mutation on Ssa27 is most likely within the 10–10.5 Mbp segment of this chromosome. This region contains a cluster of major histocompatibility complex class I (MHC I) genes with the most strongly associated marker mapped to one of these loci. On Ssa12, the data confirmed the previous finding that the location of the causative mutation is within the 61.3 to 61.7 Mbp region. This segment contains several immune-related genes, but of particular interest are genes related to MHC II. Together, these findings highlight the likely key role of MHC genes in Atlantic salmon following infection with Piscine myocarditis virus (PMCV) and their potential impact on influencing the trajectory of this disease. Full article
(This article belongs to the Special Issue Genetics and Genomics of Salmonid Fishes)
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14 pages, 1585 KiB  
Article
Estimates of Autozygosity Through Runs of Homozygosity in Farmed Coho Salmon
by Grazyella M. Yoshida, Pablo Cáceres, Rodrigo Marín-Nahuelpi, Ben F. Koop and José M. Yáñez
Genes 2020, 11(5), 490; https://doi.org/10.3390/genes11050490 - 30 Apr 2020
Cited by 12 | Viewed by 3423
Abstract
The characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze [...] Read more.
The characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze and characterize ROH patterns and compare different genomic and pedigree-based methods to estimate the inbreeding coefficient in two pure lines (POP A and B) and one recently admixed line (POP C) of coho salmon (Oncorhynchus kisutch) breeding nuclei, genotyped using a 200 K Affymetrix Axiom® myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two “pure” lines and the recently admixed line (POP C) showed the lowest number and smaller mean length of ROH. The ROH analysis for different length classes suggests that all three coho salmon lines the genome is largely composed of a high number of short segments (<4 Mb), and for POP C no segment >16 Mb was found. A high variable number of ROH, mean length and inbreeding values across chromosomes; positively the consequence of artificial selection. Pedigree-based inbreeding values tended to underestimate genomic-based inbreeding levels, which in turn varied depending on the method used for estimation. The high positive correlations between different genomic-based inbreeding coefficients suggest that they are consistent and may be more accurate than pedigree-based methods, given that they capture information from past and more recent demographic events, even when there are no pedigree records available. Full article
(This article belongs to the Special Issue Genetics and Genomics of Salmonid Fishes)
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22 pages, 7018 KiB  
Article
Gene Profiling in the Adipose Fin of Salmonid Fishes Supports Its Function as a Flow Sensor
by Raphael Koll, Joan Martorell Ribera, Ronald M. Brunner, Alexander Rebl and Tom Goldammer
Genes 2020, 11(1), 21; https://doi.org/10.3390/genes11010021 - 23 Dec 2019
Cited by 4 | Viewed by 4279
Abstract
In stock enhancement and sea-ranching procedures, the adipose fin of hundreds of millions of salmonids is removed for marking purposes annually. However, recent studies proved the significance of the adipose fin as a flow sensor and attraction feature. In the present study, we [...] Read more.
In stock enhancement and sea-ranching procedures, the adipose fin of hundreds of millions of salmonids is removed for marking purposes annually. However, recent studies proved the significance of the adipose fin as a flow sensor and attraction feature. In the present study, we profiled the specific expression of 20 neuron- and glial cell-marker genes in the adipose fin and seven other tissues (including dorsal and pectoral fin, brain, skin, muscle, head kidney, and liver) of the salmonid species rainbow trout Oncorhynchus mykiss and maraena whitefish Coregonus maraena. Moreover, we measured the transcript abundance of genes coding for 15 mechanoreceptive channel proteins from a variety of mechanoreceptors known in vertebrates. The overall expression patterns indicate the presence of the entire repertoire of neurons, glial cells and receptor proteins on the RNA level. This quantification suggests that the adipose fin contains considerable amounts of small nerve fibers with unmyelinated or slightly myelinated axons and most likely mechanoreceptive potential. The findings are consistent for both rainbow trout and maraena whitefish and support a previous hypothesis about the innervation and potential flow sensory function of the adipose fin. Moreover, our data suggest that the resection of the adipose fin has a stronger impact on the welfare of salmonid fish than previously assumed. Full article
(This article belongs to the Special Issue Genetics and Genomics of Salmonid Fishes)
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