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Gao G, Waldbieser GC, Youngblood RC, Zhao D, Pietrak MR, Allen MS, Stannard JA, Buchanan JT, Long RL, Milligan M, Burr G, Mejía-Guerra K, Sheehan MJ, Scheffler BE, Rexroad CE, Peterson BC, Palti Y. 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. G3 (BETHESDA, MD.) 2023; 13:jkad138. [PMID: 37335943 PMCID: PMC10468304 DOI: 10.1093/g3journal/jkad138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/21/2023]
Abstract
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 American (N.A.) origin. Given the genetic and genomic differences between the 2 lineages, it is crucial to develop unique genomic resources for N.A. Atlantic salmon. Here, we describe the resources that we recently developed for genomic and genetic research in N.A. Atlantic salmon aquaculture. Firstly, a new single nucleotide polymorphism (SNP) database for N.A. Atlantic salmon consisting of 3.1 million putative SNPs was generated using data from whole-genome resequencing of 80 N.A. Atlantic salmon individuals. Secondly, a high-density 50K SNP array enriched for the genic regions of the genome and containing 3 sex determination and 61 putative continent of origin markers was developed and validated. Thirdly, a genetic map composed of 27 linkage groups with 36K SNP markers was generated from 2,512 individuals in 141 full-sib families. Finally, a chromosome-level de novo genome assembly from a male N.A. Atlantic salmon from the St. John River aquaculture strain was generated using PacBio long reads. Information from Hi-C proximity ligation sequences and Bionano optical mapping was used to concatenate the contigs into scaffolds. The assembly contains 1,755 scaffolds and only 1,253 gaps, with a total length of 2.83 Gb and N50 of 17.2 Mb. A BUSCO analysis detected 96.2% of the conserved Actinopterygii genes in the assembly, and the genetic linkage information was used to guide the formation of 27 chromosome sequences. Comparative analysis with the reference genome assembly of the European Atlantic salmon confirmed that the karyotype differences between the 2 lineages are caused by a fission in chromosome Ssa01 and 3 chromosome fusions including the p arm of chromosome Ssa01 with Ssa23, Ssa08 with Ssa29, and Ssa26 with Ssa28. The genomic resources we have generated for Atlantic salmon provide a crucial boost for genetic research and for management of farmed and wild populations in this highly valued species.
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Affiliation(s)
- Guangtu Gao
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430, USA
| | - Geoffrey C Waldbieser
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experimental Station Road, Stoneville, MS 38776, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Dongyan Zhao
- Breeding Insight, 119 CALS Surge Facility, Cornell University, 525 Tower Road, Ithaca, NY 14853, USA
| | - Michael R Pietrak
- USDA-ARS National Cold Water Marine Aquaculture Center, 25 Salmon Farm Road, Franklin, ME 04634, USA
| | - Melissa S Allen
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, San Diego, CA 92121, USA
| | - Jason A Stannard
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, San Diego, CA 92121, USA
| | - John T Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, San Diego, CA 92121, USA
| | - Roseanna L Long
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430, USA
| | - Melissa Milligan
- USDA-ARS National Cold Water Marine Aquaculture Center, 25 Salmon Farm Road, Franklin, ME 04634, USA
| | - Gary Burr
- USDA-ARS National Cold Water Marine Aquaculture Center, 25 Salmon Farm Road, Franklin, ME 04634, USA
| | - Katherine Mejía-Guerra
- Breeding Insight, 119 CALS Surge Facility, Cornell University, 525 Tower Road, Ithaca, NY 14853, USA
| | - Moira J Sheehan
- Breeding Insight, 119 CALS Surge Facility, Cornell University, 525 Tower Road, Ithaca, NY 14853, USA
| | - Brian E Scheffler
- USDA-ARS Genomics and Bioinformatics Research Unit, 141 Experimental Station Road, Stoneville, MS 38776, USA
| | - Caird E Rexroad
- USDA-ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA
| | - Brian C Peterson
- USDA-ARS National Cold Water Marine Aquaculture Center, 25 Salmon Farm Road, Franklin, ME 04634, USA
| | - Yniv Palti
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV 25430, USA
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Flynn JM, Hu KB, Clark AG. Three recent sex chromosome-to-autosome fusions in a Drosophila virilis strain with high satellite DNA content. Genetics 2023; 224:iyad062. [PMID: 37052958 PMCID: PMC10213488 DOI: 10.1093/genetics/iyad062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/02/2022] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
The karyotype, or number and arrangement of chromosomes, has varying levels of stability across both evolution and disease. Karyotype changes often originate from DNA breaks near the centromeres of chromosomes, which generally contain long arrays of tandem repeats or satellite DNA. Drosophila virilis possesses among the highest relative satellite abundances of studied species, with almost half its genome composed of three related 7 bp satellites. We discovered a strain of D. virilis that we infer recently underwent three independent chromosome fusion events involving the X and Y chromosomes, in addition to one subsequent fission event. Here, we isolate and characterize the four different karyotypes we discovered in this strain which we believe demonstrates remarkable genome instability. We discovered that one of the substrains with an X-autosome fusion has an X-to-Y chromosome nondisjunction rate 20 × higher than the D. virilis reference strain (21% vs 1%). Finally, we found an overall higher rate of DNA breakage in the substrain with higher satellite DNA compared to a genetically similar substrain with less satellite DNA. This suggests that satellite DNA abundance may play a role in the risk of genome instability. Overall, we introduce a novel system consisting of a single strain with four different karyotypes, which we believe will be useful for future studies of genome instability, centromere function, and sex chromosome evolution.
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Affiliation(s)
- Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building Room 227, Ithaca, NY 14853, USA
| | - Kevin B Hu
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building Room 227, Ithaca, NY 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building Room 227, Ithaca, NY 14853, USA
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3
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Bradbury IR, Lehnert SJ, Kess T, Van Wyngaarden M, Duffy S, Messmer AM, Wringe B, Karoliussen S, Dempson JB, Fleming IA, Solberg MF, Glover KA, Bentzen P. Genomic evidence of recent European introgression into North American farmed and wild Atlantic salmon. Evol Appl 2022; 15:1436-1448. [PMID: 36187183 PMCID: PMC9488674 DOI: 10.1111/eva.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/10/2022] [Accepted: 07/08/2022] [Indexed: 12/02/2022] Open
Abstract
Gene flow between wild and domestic populations has been repeatedly demonstrated across a diverse range of taxa. Ultimately, the genetic impacts of gene flow from domestic into wild populations depend both on the degree of domestication and the original source of the domesticated population. Atlantic salmon, Salmo salar, used in North American aquaculture are ostensibly of North American origin. However, evidence of European introgression into North American aquaculture salmon has accumulated in recent decades, even though the use of diploid European salmon has never been approved in Canada. The full extent of such introgression as well as the potential impacts on wild salmon in the Northwest Atlantic remains uncertain. Here, we extend previous work comparing North American and European wild salmon (n = 5799) using a 220 K SNP array to quantify levels of recent European introgression into samples of domestic salmon, aquaculture escapees, and wild salmon collected throughout Atlantic Canada. Analysis of North American farmed salmon (n = 403) and escapees (n = 289) displayed significantly elevated levels of European ancestry by comparison with wild individuals (p < 0.001). Of North American farmed salmon sampled between 2011 and 2018, ~17% had more than 10% European ancestry and several individuals exceeded 40% European ancestry. Samples of escaped farmed salmon similarly displayed elevated levels of European ancestry, with two individuals classified as 100% European. Analysis of juvenile salmon collected in rivers proximate to aquaculture locations also revealed evidence of elevated European ancestry and larger admixture tract in comparison to individuals collected at distance from aquaculture. Overall, our results demonstrate that even though diploid European salmon have never been approved for use in Canada, individuals of full and partial European ancestry have been in use over the last decade, and that some of these individuals have escaped and hybridized in the wild.
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Affiliation(s)
- Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Sarah Jean Lehnert
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Tony Kess
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | | | - Steven Duffy
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Amber M. Messmer
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Brendan Wringe
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | - Silje Karoliussen
- Centre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - J. Brian Dempson
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Ian A. Fleming
- Department of Ocean Sciences, Ocean Sciences CentreMemorial University of NewfoundlandSt John'sNLCanada
| | | | - Kevin A. Glover
- Population Genetics Research GroupInstitute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
| | - Paul Bentzen
- Biology DepartmentDalhousie UniversityHalifaxNSCanada
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Watson KB, Lehnert SJ, Bentzen P, Kess T, Einfeldt A, Duffy S, Perriman B, Lien S, Kent M, Bradbury IR. Environmentally associated chromosomal structural variation influences fine-scale population structure of Atlantic Salmon (Salmo salar). Mol Ecol 2021; 31:1057-1075. [PMID: 34862998 DOI: 10.1111/mec.16307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/25/2021] [Accepted: 11/19/2021] [Indexed: 01/17/2023]
Abstract
Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non-model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans-Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine-scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence.
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Affiliation(s)
- K Beth Watson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Sarah J Lehnert
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Antony Einfeldt
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Steven Duffy
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Ben Perriman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Matthew Kent
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ian R Bradbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
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5
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Islam SS, Wringe BF, Bradbury IR, Fleming IA. Behavioural variation among divergent European and North American farmed and wild Atlantic salmon (Salmo salar) populations. Appl Anim Behav Sci 2020. [DOI: 10.1016/j.applanim.2020.105029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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6
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Lehnert SJ, Kess T, Bentzen P, Clément M, Bradbury IR. Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar). Mol Ecol 2020; 29:2160-2175. [PMID: 32432380 DOI: 10.1111/mec.15480] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/17/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023]
Abstract
As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 single nucleotide polymorphisms (SNPs) and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and the processes shaping them. We found evidence of high (mean FST = 0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3 Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16 and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium, despite no significant reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near-fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.
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Affiliation(s)
- Sarah J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St. John's, NL, Canada.,Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Ian R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada.,Department of Biology, Dalhousie University, Halifax, NS, Canada
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7
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Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout. G3-GENES GENOMES GENETICS 2020; 10:1929-1947. [PMID: 32284313 PMCID: PMC7263693 DOI: 10.1534/g3.120.401184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char (Salvelinus alpinus) are likely differentiated by three or four chromosomal fissions, possibly one chromosomal fusion, and 6 or more large inversions. Combining centromere mapping information with putative inversion coordinates revealed that the majority of detected inversions differentiating lake trout from other salmonids are pericentric and located on acrocentric and telocentric linkage groups. Our results suggest that speciation and adaptive divergence within the genus Salvelinus may have been associated with multiple pericentric inversions occurring primarily on acrocentric and telocentric chromosomes. The linkage map presented here will be a critical resource for advancing conservation oriented genomic research on lake trout and exploring chromosomal evolution within and between salmonid species.
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Gao G, Pietrak MR, Burr GS, Rexroad CE, Peterson BC, Palti Y. A New Single Nucleotide Polymorphism Database for North American Atlantic Salmon Generated Through Whole Genome Resequencing. Front Genet 2020; 11:85. [PMID: 32153644 PMCID: PMC7046687 DOI: 10.3389/fgene.2020.00085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/27/2020] [Indexed: 12/30/2022] Open
Affiliation(s)
- Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, United States
| | - Michael R Pietrak
- National Cold Water Marine Aquaculture Center, ARS-USDA, Orono, ME, United States
| | - Gary S Burr
- National Cold Water Marine Aquaculture Center, ARS-USDA, Orono, ME, United States
| | - Caird E Rexroad
- USDA ARS Office of National Programs, George Washington Carver Center, Washington, D.C., United States
| | - Brian C Peterson
- National Cold Water Marine Aquaculture Center, ARS-USDA, Orono, ME, United States
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, United States
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9
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Bernaś R, Poćwierz-Kotus A, Árnyasi M, Kent MP, Lien S, Wenne R. Genetic Differentiation in Hatchery and Stocked Populations of Sea Trout in the Southern Baltic: Selection Evidence at SNP Loci. Genes (Basel) 2020; 11:genes11020184. [PMID: 32050680 PMCID: PMC7073890 DOI: 10.3390/genes11020184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/23/2020] [Accepted: 02/06/2020] [Indexed: 11/16/2022] Open
Abstract
The impacts and interactions between hatchery-bred fish and wild fish populations has been a topic of active investigation in recent decades. In some instances, the benefits of stocking can be overshadowed by negative effects such as genetic introgression with natural populations, loss of genetic diversity, and dilution of local adaptations. Methods that facilitate the identification of stocked fish enable us to estimate not only the effectiveness of stocking but also the level of natural reproduction and the degree of hybridization. The longest Baltic river, the Vistula, also has the second highest discharge. Historically, it hosted numerous populations of the anadromous form of brown trout (sea trout); however, dam construction has since interfered with and reduced spawning migration to a rate that is much lower than before. Reduced spawning has resulted in a population collapse and a negative flow-on effect on commercial catches. In response, Poland (along with many other Baltic countries) initiated an intensive stocking program which continues today and which sees the average annual release of 700,000 smolts. As a consequence, today’s main-river and inshore catches come from stock-enhanced populations. High-throughput single-nucleotide polymorphism (SNP) genotyping was performed on samples of sea trout from southern Baltic populations; results suggest that a significant portion of the sea trout catches in the Vistula mouth region have direct hatchery origin and indicate the presence of Pomeranian specimens. SNP loci identified as outliers indicate a potential selection pressure that may be related with effects of hatchery breeding and mixing with natural populations. The brown trout SNP array applied in this study showed high effectiveness not only for population differentiation, but more importantly, it emerged as a sensitive tool to provide evidence of detection selection.
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Affiliation(s)
- Rafał Bernaś
- Inland Fisheries Institute in Olsztyn, Department of Migratory Fishes, Rutki, 83-330 Żukowo, Poland
- Correspondence: ; Tel.: +48-585-507-704
| | - Anita Poćwierz-Kotus
- Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; (A.P.-K.); (R.W.)
| | - Mariann Árnyasi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Norwegian University of Life Sciences (NMBU), 5003 Ås, Norway; (M.Á.); (M.P.K.); (S.L.)
| | - Matthew Peter Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Norwegian University of Life Sciences (NMBU), 5003 Ås, Norway; (M.Á.); (M.P.K.); (S.L.)
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Norwegian University of Life Sciences (NMBU), 5003 Ås, Norway; (M.Á.); (M.P.K.); (S.L.)
| | - Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; (A.P.-K.); (R.W.)
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Gabián M, Morán P, Fernández AI, Villanueva B, Chtioui A, Kent MP, Covelo-Soto L, Fernández A, Saura M. Identification of genomic regions regulating sex determination in Atlantic salmon using high density SNP data. BMC Genomics 2019; 20:764. [PMID: 31640542 PMCID: PMC6805462 DOI: 10.1186/s12864-019-6104-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/13/2019] [Indexed: 02/07/2023] Open
Abstract
Background A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs to the family Salmonidae of fishes and represents a species of great commercial value. Although the species is assumed to be male heterogametic with XY sex determination, the precise genetic basis of sexual development remains unclear. The complexity is likely associated to the relatively recent salmonid specific whole genome duplication that may be responsible for certain genome instability. This instability together with the capacity of the sex-determining gene to move across the genome as reported by previous studies, may explain that sexual development genes are not circumscribed to the same chromosomes in all members of the species. In this study, we have used a 220 K SNP panel developed for Atlantic salmon to identify the chromosomes explaining the highest proportion of the genetic variance for sex as well as candidate regions and genes associated to sexual development in this species. Results Results from regional heritability analysis showed that the chromosomes explaining the highest proportion of variance in these populations were Ssa02 (heritability = 0.42, SE = 0.12) and Ssa21 (heritability = 0.26, SE = 0.11). After pruning by linkage disequilibrium, genome-wide association analyses revealed 114 SNPs that were significantly associated with sex, being Ssa02 the chromosome containing a greatest number of regions. Close examination of the candidate regions evidenced important genes related to sex in other species of Class Actinopterygii, including SDY, genes from family SOX, RSPO1, ESR1, U2AF2A, LMO7, GNRH-R, DND and FIGLA. Conclusions The combined results from regional heritability analysis and genome-wide association have provided new advances in the knowledge of the genetic regulation of sex determination in Atlantic salmon, supporting that Ssa02 is the candidate chromosome for sex in this species and suggesting an alternative population lineage in Spanish wild populations according to the results from Ssa21.
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Affiliation(s)
- María Gabián
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, 36310, Spain
| | - Paloma Morán
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, 36310, Spain
| | - Ana I Fernández
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain
| | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain
| | - Amel Chtioui
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain
| | - Matthew P Kent
- Center for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Bioscience, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway
| | - Lara Covelo-Soto
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, 36310, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7,5, 28040, Madrid, Spain.
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11
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Kurland S, Wheat CW, de la Paz Celorio Mancera M, Kutschera VE, Hill J, Andersson A, Rubin C, Andersson L, Ryman N, Laikre L. Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species. Ecol Evol 2019; 9:11448-11463. [PMID: 31641485 PMCID: PMC6802065 DOI: 10.1002/ece3.5646] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F ST) between the two introduced populations exceeds that of the naturally sympatric populations (F ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ ( π ¯ ≈ 0.002 and π ¯ ≈ 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.
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Affiliation(s)
- Sara Kurland
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Christopher W. Wheat
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | | | - Verena E. Kutschera
- Science for Life Laboratory and Department for Biochemistry and BiophysicsStockholm UniversitySolnaSweden
| | - Jason Hill
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Anastasia Andersson
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Carl‐Johan Rubin
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTXUSA
| | - Nils Ryman
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
| | - Linda Laikre
- Division of Population GeneticsDepartment of ZoologyStockholm UniversityStockholmSweden
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12
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Lehnert SJ, Kess T, Bentzen P, Kent MP, Lien S, Gilbey J, Clément M, Jeffery NW, Waples RS, Bradbury IR. Genomic signatures and correlates of widespread population declines in salmon. Nat Commun 2019; 10:2996. [PMID: 31278264 PMCID: PMC6611788 DOI: 10.1038/s41467-019-10972-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/11/2019] [Indexed: 12/27/2022] Open
Abstract
Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (Ne) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, Ne has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.
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Affiliation(s)
- S J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada.
| | - T Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada
| | - P Bentzen
- Biology Department, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| | - M P Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - S Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - J Gilbey
- Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, PH16 5LB, UK
| | - M Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial University of Newfoundland, 155 Ridge Rd, St. John's, NL, A1C 5R3, Canada
- Labrador Institute, Memorial University of Newfoundland, 219 Hamilton River Rd, Happy Valley-Goose Bay, NL, A0P 1E0, Canada
| | - N W Jeffery
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Dr, Dartmouth, NS, B2Y 4A2, Canada
| | - R S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, 98112, USA
| | - I R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada
- Biology Department, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
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13
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Wennevik V, Quintela M, Skaala Ø, Verspoor E, Prusov S, Glover KA. Population genetic analysis reveals a geographically limited transition zone between two genetically distinct Atlantic salmon lineages in Norway. Ecol Evol 2019; 9:6901-6921. [PMID: 31380023 PMCID: PMC6662299 DOI: 10.1002/ece3.5258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/17/2022] Open
Abstract
Atlantic salmon is characterized by a high degree of population genetic structure throughout its native range. However, while populations inhabiting rivers in Norway and Russia make up a significant proportion of salmon in the Atlantic, thus far, genetic studies in this region have only encompassed low to modest numbers of populations. Here, we provide the first "in-depth" investigation of population genetic structuring in the species in this region. Analysis of 18 microsatellites on >9,000 fish from 115 rivers revealed highly significant population genetic structure throughout, following a hierarchical pattern. The highest and clearest level of division separated populations north and south of the Lofoten region in northern Norway. In this region, only a few populations displayed intermediate genetic profiles, strongly indicating a geographically limited transition zone. This was further supported by a dedicated cline analysis. Population genetic structure was also characterized by a pattern of isolation by distance. A decline in overall genetic diversity was observed from the south to the north, and two of the microsatellites showed a clear decrease in number of alleles across the observed transition zone. Together, these analyses support results from previous studies, that salmon in Norway originate from two main genetic lineages, one from the Barents-White Sea refugium that recolonized northern Norwegian and adjacent Russian rivers, and one from the eastern Atlantic that recolonized the rest of Norway. Furthermore, our results indicate that local conditions in the limited geographic transition zone between the two observed lineages, characterized by open coastline with no obvious barriers to gene flow, are strong enough to maintain the genetic differentiation between them.
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Affiliation(s)
| | | | | | - Eric Verspoor
- Rivers and Lochs Institute, Inverness CollegeUniversity of the Highlands and IslandsInvernessUK
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO)MurmanskRussia
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14
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Lehnert SJ, Bentzen P, Kess T, Lien S, Horne JB, Clément M, Bradbury IR. Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon. Mol Ecol 2019; 28:2074-2087. [DOI: 10.1111/mec.15065] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/12/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Sarah J. Lehnert
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
| | - Paul Bentzen
- Biology Department Dalhousie University Halifax Nova Scotia Canada
| | - Tony Kess
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences Norwegian University of Life Sciences Ås Norway
| | - John B. Horne
- Gulf Coast Research Laboratory University of Southern Mississippi Ocean Springs Mississippi USA
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute Memorial University of Newfoundland St. John's Newfoundland Canada
- Labrador Institute Memorial University of Newfoundland Happy Valley‐Goose Bay Newfoundland Canada
| | - Ian R. Bradbury
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
- Biology Department Dalhousie University Halifax Nova Scotia Canada
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15
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López ME, Benestan L, Moore J, Perrier C, Gilbey J, Di Genova A, Maass A, Diaz D, Lhorente J, Correa K, Neira R, Bernatchez L, Yáñez JM. Comparing genomic signatures of domestication in two Atlantic salmon ( Salmo salar L.) populations with different geographical origins. Evol Appl 2019; 12:137-156. [PMID: 30622641 PMCID: PMC6304691 DOI: 10.1111/eva.12689] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.
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Affiliation(s)
- Maria E. López
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Laura Benestan
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Jean‐Sebastien Moore
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Charles Perrier
- Centre d’Écologie Fonctionnelle et ÉvolutiveUnité Mixte de Recherche CNRS 5175MontpellierFrance
| | - John Gilbey
- Marine Scotland ScienceFreshwater Fisheries LaboratoryFaskallyPitlochryUK
| | - Alex Di Genova
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Alejandro Maass
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Diego Diaz
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | | | | | - Roberto Neira
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Louis Bernatchez
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - José M. Yáñez
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- AquainnovoPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
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16
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Wellband K, Mérot C, Linnansaari T, Elliott JAK, Curry RA, Bernatchez L. Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon. Mol Ecol 2018; 28:1439-1459. [PMID: 30506831 DOI: 10.1111/mec.14965] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/30/2022]
Abstract
Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global FST = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (FST = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250-Kb region of chromosome 9, including the gene six6 that has previously been linked to age-at-maturity and run-timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.
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Affiliation(s)
- Kyle Wellband
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Tommi Linnansaari
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - J A K Elliott
- Cooke Aquaculture Inc, Oak Bay, New Brunswick, Canada
| | - R Allen Curry
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
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17
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Schaeffer LR, Ang KP, Elliott JAK, Herlin M, Powell F, Boulding EG. Genetic evaluation of Atlantic salmon for growth traits incorporating SNP markers. J Anim Breed Genet 2018; 135:349-356. [PMID: 30105811 DOI: 10.1111/jbg.12355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 11/28/2022]
Abstract
Genetic evaluations of individual fish were calculated for growth traits in North American Atlantic salmon with and without inclusion of genetic markers. The number of SNP markers was reduced to 6,000 and further to 270 in order to reduce the problem of overparameterization. SNP genotypes were predicted for all ungenotyped animals in the pedigree. Analysis of traits used a model with polygenic effects and SNP markers together. Polygenic effects refer to the additive genetic effects that remain after accounting for SNP genotypes. SNP marker genotypes were included as covariates to evaluate fish for growth traits (weight and length) in different environments (freshwater and seawater) with genders separated. Including regressions on SNP marker genotypes reduced the sum of squares of residuals by 2.7%-12.5% and increased the variability of Mendelian sampling effects (i.e., within-family variation) compared to traditional animal model evaluations. Genetic evaluations may be carried out with a few hundred markers which may be more affordable for genotyping large numbers of fish.
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Affiliation(s)
| | - Keng Pee Ang
- Cooke Aquaculture, Oak Bay Hatchery, St Andrews, New Brunswick, Canada
| | - Jake A K Elliott
- Cooke Aquaculture, Oak Bay Hatchery, St Andrews, New Brunswick, Canada
| | - Marine Herlin
- Cooke Aquaculture, Oak Bay Hatchery, St Andrews, New Brunswick, Canada
| | - Frank Powell
- Cooke Aquaculture, Oak Bay Hatchery, St Andrews, New Brunswick, Canada
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18
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Wringe BF, Jeffery NW, Stanley RRE, Hamilton LC, Anderson EC, Fleming IA, Grant C, Dempson JB, Veinott G, Duffy SJ, Bradbury IR. Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic. Commun Biol 2018; 1:108. [PMID: 30271988 PMCID: PMC6123692 DOI: 10.1038/s42003-018-0112-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 07/16/2018] [Indexed: 11/09/2022] Open
Abstract
Domestication is rife with episodes of interbreeding between cultured and wild populations, potentially challenging adaptive variation in the wild. In Atlantic salmon, Salmo salar, the number of domesticated individuals far exceeds wild individuals, and escape events occur regularly, yet evidence of the magnitude and geographic scale of interbreeding resulting from individual escape events is lacking. We screened juvenile Atlantic salmon using 95 single nucleotide polymorphisms following a single, large aquaculture escape in the Northwest Atlantic and report the landscape-scale detection of hybrid and feral salmon (27.1%, 17/18 rivers). Hybrids were reproductively viable, and observed at higher frequency in smaller wild populations. Repeated annual sampling of this cohort revealed decreases in the presence of hybrid and feral offspring over time. These results link previous observations of escaped salmon in rivers with reports of population genetic change, and demonstrate the potential negative consequences of escapes from net-pen aquaculture on wild populations.
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Affiliation(s)
- Brendan F Wringe
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, A1C 5S7, Canada
| | - Nicholas W Jeffery
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Ryan R E Stanley
- Science Branch, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, B2Y 4A2, Canada
| | - Lorraine C Hamilton
- Aquatic Biotechnology Laboratory, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, B2Y 4A2, Canada
| | - Eric C Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, 95060, USA
| | - Ian A Fleming
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, A1C 5S7, Canada
| | - Carole Grant
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - J Brian Dempson
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - Geoff Veinott
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - Steven J Duffy
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada
| | - Ian R Bradbury
- Science Branch, Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, Newfoundland, A1C 5X1, Canada.
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, A1C 5S7, Canada.
- Faculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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19
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Pedersen S, Liu L, Glebe B, Leadbeater S, Lien S, Boulding EG. Mapping of quantitative trait loci associated with size, shape, and parr mark traits using first- and second-generation backcrosses between European and North American Atlantic salmon (Salmo salar). Genome 2018; 61:33-42. [DOI: 10.1139/gen-2017-0026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Little is known about the genetic architecture of traits important for salmonid restoration ecology. We mapped quantitative trait loci (QTL) using single nucleotide polymorphisms (SNPs) for juvenile body length, weight, shape, and vertical skin pigmentation patterns (parr marks) within three hybrid backcross families between European and North American subspecies of Atlantic salmon. Amounts of variation in skin colour and pattern quantified in the two second-generation transAtlantic families exceeded the ranges seen in purebred populations. GridQTL analyses using low-density female-specific linkage maps detected QTL showing experiment-wide significance on Ssa02, Ssa03, Ssa09, Ssa11, Ssa19, and Ssa26/28 for both length and weight; on Ssa04 and Ssa23 for parr mark number; on Ssa09 and Ssa13 for parr mark contrast; and on Ssa05, Ssa07, Ssa10, Ssa11, Ssa18, Ssa23, and Ssa26/28 for geometric morphometric shape coordinates. Pleiotrophic QTL on Ssa11 affected length, weight, and shape. No QTL was found that explained more than 10% of the phenotypic variance in pigmentation or shape traits. Each QTL was approximately positioned on the physical map of the Atlantic salmon genome. Some QTL locations confirmed previous studies but many were new. Studies like ours may increase the success of salmon restoration projects by enabling better phenotypic and genetic matching between introduced and extirpated strains.
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Affiliation(s)
- Stephanie Pedersen
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Lei Liu
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Brian Glebe
- Department of Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, NB E5B 2L9, Canada
| | - Steven Leadbeater
- Department of Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, NB E5B 2L9, Canada
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
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20
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Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus Salvelinus. G3-GENES GENOMES GENETICS 2017; 7:3821-3830. [PMID: 28963166 PMCID: PMC5677171 DOI: 10.1534/g3.117.300317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from nonmodel organisms. This manuscript details the application of restriction site-associated DNA sequencing (RADseq) to generate a marker-dense genetic map for Brook Trout (Salvelinus fontinalis). The consensus map was constructed from three full-sib families totaling 176 F1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic Salmon for 38 linkage groups, with Rainbow Trout for 37 linkage groups, Arctic Char for 36 linkage groups, and with a previously published Brook Trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of 8 metacentric and 34 acrocentric chromosomes in Brook Trout. Six metacentric chromosomes seem to be conserved with Arctic Char suggesting there have been at least two species-specific fusion and fission events within the genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on the Y chromosome) was mapped to Brook Trout BC35, which is homologous with Atlantic Salmon Ssa09qa, Rainbow Trout Omy25, and Arctic Char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus, and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus.
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21
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Jeffery NW, Stanley RRE, Wringe BF, Guijarro-Sabaniel J, Bourret V, Bernatchez L, Bentzen P, Beiko RG, Gilbey J, Clément M, Bradbury IR. Range-wide parallel climate-associated genomic clines in Atlantic salmon. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171394. [PMID: 29291123 PMCID: PMC5717698 DOI: 10.1098/rsos.171394] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/13/2017] [Indexed: 05/02/2023]
Abstract
Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.
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Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland and Labrador, CanadaA1C 5X1
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
- Author for correspondence: Nicholas W. Jeffery e-mail:
| | - Ryan R. E. Stanley
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, CanadaB2Y 4A2
| | - Brendan F. Wringe
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland and Labrador, CanadaA1C 5X1
| | - Javier Guijarro-Sabaniel
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, CanadaB2Y 4A2
| | - Vincent Bourret
- Laboratoire d'expertise biolégale, MFFP, Québec, Québec, CanadaG1P 3W8
| | - Louis Bernatchez
- Department of Biology, Université Laval, Québec, Québec, CanadaG1 V 0A6
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
| | - John Gilbey
- Marine Scotland, Freshwater Fisheries Laboratory, Faskally, Pitlochry PH16 5LB, UK
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St John's, NL, Canada
- Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Ian R. Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland and Labrador, CanadaA1C 5X1
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
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A Dense Brown Trout ( Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity. G3-GENES GENOMES GENETICS 2017; 7:1365-1376. [PMID: 28235829 PMCID: PMC5386884 DOI: 10.1534/g3.116.038497] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout.
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Liu L, Ang KP, Elliott JAK, Kent MP, Lien S, MacDonald D, Boulding EG. 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. Evol Appl 2016; 10:276-296. [PMID: 28250812 PMCID: PMC5322405 DOI: 10.1111/eva.12450] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 11/16/2016] [Indexed: 01/08/2023] Open
Abstract
Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.
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Affiliation(s)
- Lei Liu
- Department of Integrative Biology University of Guelph Guelph ON Canada; Present address: School of Marine Sciences Ningbo University Ningbo China
| | | | | | - Matthew Peter Kent
- Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway
| | - Danielle MacDonald
- Saint Andrews Biological Station Department of Fisheries and Oceans Canada Saint Andrews NB Canada
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24
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Leitwein M, Gagnaire PA, Desmarais E, Guendouz S, Rohmer M, Berrebi P, Guinand B. Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations. JOURNAL OF FISH BIOLOGY 2016; 89:2717-2734. [PMID: 27666575 DOI: 10.1111/jfb.13131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/01/2016] [Indexed: 06/06/2023]
Abstract
A genome-wide assessment of diversity is provided for wild Mediterranean brown trout Salmo trutta populations from headwater tributaries of the Orb River and from Atlantic and Mediterranean hatchery-reared strains that have been used for stocking. Double-digest restriction-site-associated DNA sequencing (dd-RADseq) was performed and the efficiency of de novo and reference-mapping approaches to obtain individual genotypes was compared. Large numbers of single nucleotide polymorphism (SNP) markers with similar genome-wide distributions were discovered using both approaches (196 639 v. 121 016 SNPs, respectively), with c. 80% of the loci detected de novo being also found with reference mapping, using the Atlantic salmon Salmo salar genome as a reference. Lower mapping density but larger nucleotide diversity (π) was generally observed near extremities of linkage groups, consistent with regions of residual tetrasomic inheritance observed in salmonids. Genome-wide diversity estimates revealed reduced polymorphism in hatchery strains (π = 0·0040 and π = 0·0029 in Atlantic and Mediterranean strains, respectively) compared to wild populations (π = 0·0049), a pattern that was congruent with allelic richness estimated from microsatellite markers. Finally, pronounced heterozygote deficiency was found in hatchery strains (Atlantic FIS = 0·18; Mediterranean FIS = 0·42), indicating that stocking practices may affect the genetic diversity in wild populations. These new genomic resources will provide important tools to define better conservation strategies in S. trutta.
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Affiliation(s)
- M Leitwein
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
| | - P-A Gagnaire
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
- Station Biologique Marine, 2 Avenue des Chantiers, 34200, Sète, France
| | - E Desmarais
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
| | - S Guendouz
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, 141 rue de Cardonille, 34094, Montpellier Cedex 5, France
| | - M Rohmer
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, 141 rue de Cardonille, 34094, Montpellier Cedex 5, France
| | - P Berrebi
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
| | - B Guinand
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
- Département Biologie-Ecologie, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
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25
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Evidence of recent signatures of selection during domestication in an Atlantic salmon population. Mar Genomics 2016; 26:41-50. [DOI: 10.1016/j.margen.2015.12.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/25/2015] [Accepted: 12/16/2015] [Indexed: 11/17/2022]
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26
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Wenne R, Drywa A, Kent M, Sundsaasen KK, Lien S. SNP Arrays for Species Identification in Salmonids. Methods Mol Biol 2016; 1452:97-111. [PMID: 27460372 DOI: 10.1007/978-1-4939-3774-5_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The use of SNP genotyping microarrays, developed in one species to analyze a closely related species for which genomic sequence information is scarce, enables the rapid development of a genomic resource (SNP information) without the need to develop new species-specific markers. Using large numbers of microarray SNPs offers the best chance to detect informative markers in nontarget species, markers that can very often be assayed using a lower throughput platform as is described in this paper.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-712, Sopot, Poland.
| | - Agata Drywa
- Institute of Oceanology, Polish Academy of Sciences, Powstancow Warszawy 55, 81-712, Sopot, Poland
| | - Matthew Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
| | - Kristil Kindem Sundsaasen
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
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27
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Bradbury IR, Hamilton LC, Dempson B, Robertson MJ, Bourret V, Bernatchez L, Verspoor E. Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure. Mol Ecol 2015; 24:5130-44. [DOI: 10.1111/mec.13395] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Ian R. Bradbury
- Science Branch; Department of Fisheries and Oceans Canada; 80 East White Hills Road St. John's Newfoundland Canada A1C 5X1
| | - Lorraine C. Hamilton
- Aquatic Biotechnology Laboratory; Bedford Institute of Oceanography; Dartmouth Halifax Nova Scotia Canada B2Y 4A2
| | - Brian Dempson
- Science Branch; Department of Fisheries and Oceans Canada; 80 East White Hills Road St. John's Newfoundland Canada A1C 5X1
| | - Martha J. Robertson
- Science Branch; Department of Fisheries and Oceans Canada; 80 East White Hills Road St. John's Newfoundland Canada A1C 5X1
| | - Vincent Bourret
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec Canada G1V 0A6
- Direction de la faune aquatique; Ministère du Développement durable, de l'Environnement, de la Faune et des Parcs; Québec Québec Canada G1S 4X4
| | - Louis Bernatchez
- Direction de la faune aquatique; Ministère du Développement durable, de l'Environnement, de la Faune et des Parcs; Québec Québec Canada G1S 4X4
| | - Eric Verspoor
- Rivers and Lochs Institute; Inverness College University of the Highlands and Islands; Inverness IV2 5NA UK
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28
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Genomic Instability of the Sex-Determining Locus in Atlantic Salmon (Salmo salar). G3-GENES GENOMES GENETICS 2015; 5:2513-22. [PMID: 26401030 PMCID: PMC4632069 DOI: 10.1534/g3.115.020115] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Atlantic salmon and rainbow trout, like other members of the subfamily Salmoninae, are gonochoristic with male heterogamety. The finding that sex-linked genetic markers varied between species suggested that the sex-determining gene differs among salmonid species, or that there is one sex-determining gene that has the capacity to move around the genome. The discovery of sdY, the sex-determining gene in rainbow trout, and its presence in many male salmonids gave support to the latter. Additional evidence for a salmonid-specific, sex-determining jumping gene came from the mapping of the sex-determining locus to three different chromosomes in Tasmanian male Atlantic salmon lineages. To characterize the sex-determining region, we isolated three sdY containing BACs from an Atlantic salmon male library. Sequencing of these BACs yielded two contigs, one of which contained the sdY gene. Sequence analysis of the borders of male-specific and female/male common regions revealed highly repetitive sequences associated with mobile elements, which may allow an sdY cassette to jump around the genome. FISH analysis using a BAC or a plasmid containing the sdY gene showed that the sdY gene did indeed localize to the chromosomes where SEX had been mapped in different Tasmanian Atlantic salmon families. Moreover, the plasmid sdY gene probe hybridized primarily to one of the sex chromosomes as would be expected of a male-specific gene. Our results suggest that a common salmonid sex-determining gene (sdY) can move between three specific loci on chromosomes 2, 3, and 6, giving the impression that there are multiple SEX loci both within and between salmonid species.
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29
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Allendorf FW, Bassham S, Cresko WA, Limborg MT, Seeb LW, Seeb JE. Effects of crossovers between homeologs on inheritance and population genomics in polyploid-derived salmonid fishes. J Hered 2015; 106:217-27. [PMID: 25838153 DOI: 10.1093/jhered/esv015] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 02/19/2015] [Indexed: 01/24/2023] Open
Abstract
A whole genome duplication occurred in the ancestor of all salmonid fishes some 50-100 million years ago. Early inheritance studies with allozymes indicated that loci in the salmonid genome are inherited disomically in females. However, some pairs of duplicated loci showed patterns of inheritance in males indicating pairing and recombination between homeologous chromosomes. Nearly 20% of loci in the salmonid genome are duplicated and share the same alleles (isoloci), apparently due to homeologous recombination. Half-tetrad analysis revealed that isoloci tend to be telomeric. These results suggested that residual tetrasomic inheritance of isoloci results from homeologous recombination near chromosome ends and that continued disomic inheritance resulted from homologous pairing of centromeric regions. Many current genetic maps of salmonids are based on single nucleotide polymorphisms and microsatellites that are no longer duplicated. Therefore, long sections of chromosomes on these maps are poorly represented, especially telomeric regions. In addition, preferential multivalent pairing of homeologs from the same species in F1 hybrids results in an excess of nonparental gametes (so-called pseudolinkage). We consider how not including duplicated loci has affected our understanding of population and evolutionary genetics of salmonids, and we discuss how incorporating these loci will benefit our understanding of population genomics.
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Affiliation(s)
- Fred W Allendorf
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb).
| | - Susan Bassham
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - William A Cresko
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - Morten T Limborg
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - Lisa W Seeb
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
| | - James E Seeb
- From the University of Montana, Division of Biological Sciences, Missoula, MT 59812 (Allendorf); University of Oregon, Institute of Ecology and Evolution, Eugene, OR (Bassham and Cresko); and University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA (Limborg, L. Seeb, and J. Seeb)
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30
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Waples RK, Seeb LW, Seeb JE. Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta). Mol Ecol Resour 2015; 16:17-28. [DOI: 10.1111/1755-0998.12394] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/13/2015] [Accepted: 02/20/2015] [Indexed: 11/27/2022]
Affiliation(s)
- R. K. Waples
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle Washington 98195 USA
| | - L. W. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle Washington 98195 USA
| | - J. E. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street Box 355020 Seattle Washington 98195 USA
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31
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Comparative mapping for bighead carp (Aristichthys nobilis) against model and non-model fishes provides insights into the genomic evolution of cyprinids. Mol Genet Genomics 2015; 290:1313-26. [PMID: 25627158 DOI: 10.1007/s00438-015-0992-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 01/09/2015] [Indexed: 02/03/2023]
Abstract
Comparative mapping provides an efficient method to connect genomes of non-model and model fishes. In this study, we used flanking sequences of the 659 microsatellites on a genetic map of bighead carp (Aristichthys nobilis) to comprehensively study syntenic relationships between bighead carp and nine model and non-model fishes. Of the five model and two food fishes with whole genome data, Cyprinus carpio showed the highest rate of positive BLAST hits (95.3 %) with bighead carp map, followed by Danio rerio (70.9 %), Oreochromis niloticus (21.7 %), Tetraodon nigroviridis (6.4 %), Gasterosteus aculeatus (5.2 %), Oryzias latipes (4.7 %) and Fugu rubripes (3.5 %). Chromosomal syntenic analyses showed that inversion was the basic chromosomal rearrangement during genomic evolution of cyprinids, and the extent of inversions and translocations was found to be positively correlated with evolutionary relationships among fishes studied. Among the five investigated cyprinids, linkage groups (LGs) of bighead carp, Hypophthalmichthys molitrix and Ctenopharyngodon idella exhibited a one-to-one relationship. Besides, LG 9 of bighead carp and homologous LGs of silver carp and grass carp all corresponded to the chromosomes 10 and 22 of zebrafish, suggesting that chromosomal fission may have occurred in the ancestor of zebrafish. On the other hand, LGs of bighead carp and common carp showed an approximate one-to-two relationship with extensive translocations, confirming the occurrence of a 4th whole genome duplication in common carp. This study provides insights into the understanding of genome evolution among cyprinids and would aid in transferring positional and functional information of genes from model fish like zebrafish to non-model fish like bighead carp.
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32
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Moore JS, Bourret V, Dionne M, Bradbury I, O'Reilly P, Kent M, Chaput G, Bernatchez L. Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci. Mol Ecol 2014; 23:5680-97. [DOI: 10.1111/mec.12972] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Jean-Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
| | - Vincent Bourret
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
- Direction de la Protection de la Faune; Ministère des Forêts; de la Faune et des Parcs; Québec Québec G1S 4X4 Canada
| | - Mélanie Dionne
- Direction de la Faune Aquatique; Ministère des Forêts; de la Faune et des Parcs; Québec Québec G1S 4X4 Canada
| | - Ian Bradbury
- Science Branch; Fisheries and Oceans Canada; 80 East White Road St. John's Newfoundland A1C 5X1 Canada
| | - Patrick O'Reilly
- Science Branch; Fisheries and Oceans Canada; Bedford Institute of Oceanography; 1 Challenger Drive Dartmouth Nova Scotia B2Y 4A2 Canada
| | - Matthew Kent
- Centre for Integrative Genetics (CIGENE); Department of Animal and Aquacultural Sciences (IHA); Norwegian University of Life Sciences; PO Box 5003 1432 Aas Norway
| | - Gérald Chaput
- Fisheries and Oceans Canada; PO Box 5030 Moncton New Brunswick E1C 9B6 Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
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33
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Affiliation(s)
- William S Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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34
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Bourret V, Dionne M, Bernatchez L. Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multilocus analysis surpasses genome scan. Mol Ecol 2014; 23:4444-57. [DOI: 10.1111/mec.12798] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Vincent Bourret
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec Canada G1V 0A6
| | - Mélanie Dionne
- Service de la faune aquatique; Ministère des Forêts; de la Faune et des Parcs du Québec; Québec Canada G1S 4X4
| | - Louis Bernatchez
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec Canada G1V 0A6
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35
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Zueva KJ, Lumme J, Veselov AE, Kent MP, Lien S, Primmer CR. Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution? PLoS One 2014; 9:e91672. [PMID: 24670947 PMCID: PMC3966780 DOI: 10.1371/journal.pone.0091672] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 02/14/2014] [Indexed: 12/15/2022] Open
Abstract
Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved.
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Affiliation(s)
- Ksenia J. Zueva
- Department of Biology, University of Turku, Turku, Finland
- * E-mail:
| | - Jaakko Lumme
- Department of Biology, University of Oulu, Oulu, Finland
| | - Alexey E. Veselov
- Institute of Biology, Karelian Research Centre of RAS, Petrozavodsk, Russia
| | - Matthew P. Kent
- Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE) and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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36
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Gonen S, Lowe NR, Cezard T, Gharbi K, Bishop SC, Houston RD. Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing. BMC Genomics 2014; 15:166. [PMID: 24571138 PMCID: PMC4028894 DOI: 10.1186/1471-2164-15-166] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 02/18/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Genetic linkage maps are useful tools for mapping quantitative trait loci (QTL) influencing variation in traits of interest in a population. Genotyping-by-sequencing approaches such as Restriction-site Associated DNA sequencing (RAD-Seq) now enable the rapid discovery and genotyping of genome-wide SNP markers suitable for the development of dense SNP linkage maps, including in non-model organisms such as Atlantic salmon (Salmo salar). This paper describes the development and characterisation of a high density SNP linkage map based on SbfI RAD-Seq SNP markers from two Atlantic salmon reference families. RESULTS Approximately 6,000 SNPs were assigned to 29 linkage groups, utilising markers from known genomic locations as anchors. Linkage maps were then constructed for the four mapping parents separately. Overall map lengths were comparable between male and female parents, but the distribution of the SNPs showed sex-specific patterns with a greater degree of clustering of sire-segregating SNPs to single chromosome regions. The maps were integrated with the Atlantic salmon draft reference genome contigs, allowing the unique assignment of ~4,000 contigs to a linkage group. 112 genome contigs mapped to two or more linkage groups, highlighting regions of putative homeology within the salmon genome. A comparative genomics analysis with the stickleback reference genome identified putative genes closely linked to approximately half of the ordered SNPs and demonstrated blocks of orthology between the Atlantic salmon and stickleback genomes. A subset of 47 RAD-Seq SNPs were successfully validated using a high-throughput genotyping assay, with a correspondence of 97% between the two assays. CONCLUSIONS This Atlantic salmon RAD-Seq linkage map is a resource for salmonid genomics research as genotyping-by-sequencing becomes increasingly common. This is aided by the integration of the SbfI RAD-Seq SNPs with existing reference maps and the draft reference genome, as well as the identification of putative genes proximal to the SNPs. Differences in the distribution of recombination events between the sexes is evident, and regions of homeology have been identified which are reflective of the recent salmonid whole genome duplication.
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Affiliation(s)
- Serap Gonen
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, Scotland, UK
| | - Natalie R Lowe
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, Scotland, UK
| | - Timothé Cezard
- Edinburgh Genomics, Ashworth Laboratories, King’s Buildings, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, King’s Buildings, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
| | - Stephen C Bishop
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, Scotland, UK
| | - Ross D Houston
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, Scotland, UK
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Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones. Chromosoma 2014; 123:281-91. [PMID: 24473579 DOI: 10.1007/s00412-014-0452-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/09/2014] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
Bacterial artificial chromosomes (BAC) have been widely used for fluorescence in situ hybridization (FISH) mapping of chromosome landmarks in different organisms, including a few in teleosts. In this study, we used BAC-FISH to consolidate the previous genetic and cytogenetic maps of the turbot (Scophthalmus maximus), a commercially important pleuronectiform. The maps consisted of 24 linkage groups (LGs) but only 22 chromosomes. All turbot LGs were assigned to specific chromosomes using BAC probes obtained from a turbot 5× genomic BAC library. It consisted of 46,080 clones with inserts of at least 100 kb and <5 % empty vectors. These BAC probes contained gene-derived or anonymous markers, most of them linked to quantitative trait loci (QTL) related to productive traits. BAC clones were mapped by FISH to unique marker-specific chromosomal positions, which showed a notable concordance with previous genetic mapping data. The two metacentric pairs were cytogenetically assigned to LG2 and LG16, and the nucleolar organizer region (NOR)-bearing pair was assigned to LG15. Double-color FISH assays enabled the consolidation of the turbot genetic map into 22 linkage groups by merging LG8 with LG18 and LG21 with LG24. In this work, a first-generation probe panel of BAC clones anchored to the turbot linkage and cytogenetical map was developed. It is a useful tool for chromosome traceability in turbot, but also relevant in the context of pleuronectiform karyotypes, which often show small hardly identifiable chromosomes. This panel will also be valuable for further integrative genomics of turbot within Pleuronectiformes and teleosts, especially for fine QTL mapping for aquaculture traits, comparative genomics, and whole-genome assembly.
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Castro R, Bromage E, Abós B, Pignatelli J, González Granja A, Luque A, Tafalla C. CCR7 is mainly expressed in teleost gills, where it defines an IgD+IgM- B lymphocyte subset. THE JOURNAL OF IMMUNOLOGY 2013; 192:1257-66. [PMID: 24353268 DOI: 10.4049/jimmunol.1302471] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Chemokine receptor CCR7, the receptor for both CCL19 and CCL21 chemokines, regulates the recruitment and clustering of circulating leukocytes to secondary lymphoid tissues, such as lymph nodes and Peyer's patches. Even though teleost fish do not have either of these secondary lymphoid structures, we have recently reported a homolog to CCR7 in rainbow trout (Oncorhynchus mykiss). In the present work, we have studied the distribution of leukocytes bearing extracellular CCR7 in naive adult tissues by flow cytometry, observing that among the different leukocyte populations, the highest numbers of cells with membrane (mem)CCR7 were recorded in the gill (7.5 ± 2% CCR7(+) cells). In comparison, head kidney, spleen, thymus, intestine, and peripheral blood possessed <5% CCR7(+) cells. When CCR7 was studied at early developmental stages, we detected a progressive increase in gene expression and protein CCR7 levels in the gills throughout development. Surprisingly, the majority of the CCR7(+) cells in the gills were not myeloid cells and did not express membrane CD8, IgM, nor IgT, but expressed IgD on the cell surface. In fact, most IgD(+) cells in the gills expressed CCR7. Intriguingly, the IgD(+)CCR7(+) population did not coexpress memIgM. Finally, when trout were bath challenged with viral hemorrhagic septicemia virus, the number of CCR7(+) cells significantly decreased in the gills while significantly increased in head kidney. These results provide evidence of the presence of a novel memIgD(+)memIgM(-) B lymphocyte subset in trout that expresses memCCR7 and responds to viral infections. Similarities with IgD(+)IgM(-) subsets in mammals are discussed.
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Affiliation(s)
- Rosario Castro
- Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación Agraria y Alimentaria, Valdeolmos, Madrid 28130, Spain
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Perrier C, Bourret V, Kent MP, Bernatchez L. Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon. Mol Ecol 2013; 22:5577-93. [DOI: 10.1111/mec.12500] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Charles Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada G1V 0A6
| | - Vincent Bourret
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada G1V 0A6
| | - Matthew P. Kent
- Department of Animal and Aquaculture Sciences; Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; PO Box 5003 Aas 1432 Norway
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada G1V 0A6
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Evidence for multiple sex-determining loci in Tasmanian Atlantic salmon (Salmo salar). Heredity (Edinb) 2013; 113:86-92. [PMID: 23759729 PMCID: PMC4815647 DOI: 10.1038/hdy.2013.55] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 04/30/2013] [Accepted: 05/02/2013] [Indexed: 11/11/2022] Open
Abstract
Phenotypic sex in salmonids is determined primarily by a genetic male heterogametic system; yet, sex reversal can be accomplished via hormonal treatment. In Tasmanian Atlantic salmon aquaculture, to overcome problems associated with early sexual maturation in males, sex-reversed females are crossed with normal females to produce all female stock. However, phenotypic distinction of sex-reversed females (neo-males) from true males is problematic. We set out to identify genetic markers that could make this distinction. Microsatellite markers from chromosome 2 (Ssa02), to which the sex-determining locus (SEX) has been mapped in two Scottish Atlantic salmon families, did not predict sex in a pilot study of seven families. A TaqMan 64 SNP genome-wide scan suggested SEX was on Ssa06 in these families, and this was confirmed by microsatellite markers. A survey of 58 families in total representing 38 male lineages in the SALTAS breeding program found that 34 of the families had SEX on Ssa02, in 22 of the families SEX was on Ssa06, and two of the families had a third SEX locus, on Ssa03. A PCR test using primers designed from the recently published sdY gene is consistent with Tasmanian Atlantic salmon having a single sex-determining gene that may be located on at least three linkage groups.
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Vincent B, Dionne M, Kent MP, Lien S, Bernatchez L. LANDSCAPE GENOMICS IN ATLANTIC SALMON (SALMO SALAR): SEARCHING FOR GENE-ENVIRONMENT INTERACTIONS DRIVING LOCAL ADAPTATION. Evolution 2013; 67:3469-87. [DOI: 10.1111/evo.12139] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 03/27/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Bourret Vincent
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec G1V 0A6 Canada
| | - Mélanie Dionne
- Direction de la faune aquatique; Ministère du Développement durable; de l'Environnement; de la Faune et des Parcs; Québec G1S 4×4 Canada
| | - Matthew P. Kent
- Department of Animal and Aquacultural Sciences; Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; PO Box 5003, 1432 Aas Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences; Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; PO Box 5003, 1432 Aas Norway
| | - Louis Bernatchez
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec G1V 0A6 Canada
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Ulusoy S, Ozkan G, Alkanat M, Mungan S, Yuluğ E, Orem A. Perspective on rhabdomyolysis-induced acute kidney injury and new treatment options. Am J Nephrol 2013; 38:368-78. [PMID: 24158126 DOI: 10.1159/000355537] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/08/2013] [Indexed: 12/22/2022]
Abstract
AIM The purpose of this study was to assess the role of caspase-dependent apoptosis, caspase 1, calpain 1, inducible nitric oxide synthase (iNOS) and endothelial nitric oxide synthase (eNOS) and the protective effect of grape seed proanthocyanidin extract (GSPE) in the development of rhabdomyolysis-induced acute kidney injury (AKI). MATERIALS AND METHODS Twenty-one rats were divided into 3 groups - control, rhabdomyolysis and rhabdomyolysis + GSPE. Rhabdomyolysis was induced in the rhabdomyolysis and rhabdomyolysis + GSPE groups with the injection into both hind limbs of 10 ml/kg hypertonic (50%) glycerol following 24-hour dehydration on the 6th day. The rhabdomyolysis + GSPE group was given GSPE at 100 mg/kg by gavage for 7 days. The experiment was concluded 48 h after glycerol injection. Blood specimens were collected, and kidney tissues were extracted for histopathological examination. RESULTS We identified an increase in blood urea nitrogen, creatinine, histopathological score, iNOS, caspase 3, caspase 1 and calpain 1 expression in the rhabdomyolysis group compared to the controls and a decrease in eNOS expression. In the rhabdomyolysis + GSPE group, however, there was a decrease in these mediators, together with an increase in eNOS expression. CONCLUSION This study shows for the first time in the literature that calpain 1 is involved in the pathogenesis of rhabdomyolysis-induced AKI, and that GSPE may have a renoprotective effect.
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Affiliation(s)
- S Ulusoy
- Department of Nephrology, Karadeniz Technical University, Trabzon, Turkey
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Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon. Comp Funct Genomics 2012; 2012:628204. [PMID: 23326209 PMCID: PMC3544263 DOI: 10.1155/2012/628204] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/29/2012] [Accepted: 11/09/2012] [Indexed: 11/28/2022] Open
Abstract
Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.
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