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Howard C, Taggart JB, Bradley CR, Gutierrez AP, Taylor JF, Prodöhl PA, Migaud H, Bekaert M. DNA extraction from recently fertilised Atlantic salmon embryos for use in microsatellite validation of triploidy. PLoS One 2023; 18:e0292319. [PMID: 37792726 PMCID: PMC10550122 DOI: 10.1371/journal.pone.0292319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
The current methods used for producing triploid Atlantic salmon are generally reliable but not infallible, and each batch of triploids must be validated to ensure consumer trust and licensing compliance. Microsatellites have recently been shown to offer a cheaper and more convenient alternative to traditional flow cytometry for triploidy validation in a commercial setting. However, incubating eggs to at least the eyed stage for microsatellite validation poses challenges, such as reduced quality and performance of triploids produced from later eggs in the stripping season. To address these issues, we propose another option: extracting DNA from recently fertilised eggs for use in conjunction with microsatellite validation. To achieve this, we have developed an optimized protocol for HotSHOT extraction that can rapidly and cheaply extract DNA from Atlantic salmon eggs, which can then be used for triploidy validation through microsatellites. Our approach offers a simpler and more cost-effective way to validate triploidy, without the need for skilled dissection or expensive kits.
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Affiliation(s)
- Callum Howard
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - John B. Taggart
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Caroline R. Bradley
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | | | - John F. Taylor
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Paulo A. Prodöhl
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Herve Migaud
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
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2
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Delomas TA, Willis SC, Parker BL, Miller D, Anders P, Schreier A, Narum S. Genotyping single nucleotide polymorphisms and inferring ploidy by amplicon sequencing for polyploid, ploidy-variable organisms. Mol Ecol Resour 2021; 21:2288-2298. [PMID: 34008918 DOI: 10.1111/1755-0998.13431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022]
Abstract
Whole genome duplication is hypothesized to have played a critical role in the evolution of several major taxa, including vertebrates, and while many lineages have rediploidized, some retain polyploid genomes. Additionally, variation in ploidy can occur naturally or be artificially induced within select plant and animal species. Modern genetic techniques have not been widely applied to polyploid or ploidy-variable species, in part due to the difficulty of obtaining genotype data from polyploids. In this study, we demonstrate a strategy for developing an amplicon sequencing panel of single nucleotide polymorphisms for high-throughput genotyping of polyploid organisms. We then develop a method to infer ploidy of individuals from amplicon sequencing data that is generalized to apply to any ploidy and does not require prior identification of heterozygous genotypes. Combining these two techniques will allow researchers to both infer ploidy and generate ploidy-aware genotypes with the same amplicon sequencing panel. We demonstrate this approach with white sturgeon Acipenser transmontanus, a ploidy-variable (octoploid, decaploid and dodecaploid) imperiled species under conservation management in the Pacific Northwest and obtained a panel of 325 loci. These loci were validated by examining inheritance in known-cross families, and the ploidy inference method was validated with known ploidy samples. We provide scripts that adapt existing pipelines to genotype polyploids and an R package for application of the ploidy inference method. We expect that these techniques will empower studies of genetic variation and inheritance in polyploid organisms that vary in ploidy level, either naturally or as a result of artificial propagation practices.
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Affiliation(s)
- Thomas A Delomas
- Pacific States Marine Fisheries Commission/Idaho Department of Fish and Game, Eagle Fish Genetics Laboratory, Eagle, ID, USA
| | - Stuart C Willis
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Blaine L Parker
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | | | | | - Andrea Schreier
- Genomic Variation Laboratory, Department of Animal Science, University of California Davis, Davis, CA, USA
| | - Shawn Narum
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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3
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Fraser TWK, Hansen TJ, Sambraus F, Fjelldal PG. Vertebral deformities in interspecific diploid and triploid salmonid hybrids. J Fish Biol 2021; 98:1059-1070. [PMID: 32307707 DOI: 10.1111/jfb.14353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 02/21/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Vertebral deformities in salmonid interspecific hybrids, some of which were triploidised, were assessed across three separate year classes during the freshwater life stage. Initially, eggs from a farmed Atlantic salmon Salmo salar were crossed with the sperm from a S. salar, arctic char Salvelinus alpinus or brown trout Salmo trutta. For S. salar × S. trutta, half the eggs were triploidised. In a second- and third-year class, the eggs from a farmed S. salar were crossed with the sperm from either a S. salar or a S. trutta, and half of each group was triploidised. In the two initial-year classes, all hybrids were larger than the S. salar controls, and triploid S. salar × S. trutta were larger than diploid counterparts. In the third-year class, the S. salar × S. trutta were smaller than the S. salar, in contrast to the initial 2 year classes, although the triploid hybrids were still larger than the diploids. In the third-year class, a high degree of spontaneous triploidy was also observed in the putative diploid groups (between 16 and 39%). Vertebral deformities were consistently higher in pressure-shocked triploids than diploids, irrespective of hybridisation, but there was no consistent effect of hybridisation among experiments. Although this study was not able to explain the contrasting results for vertebral deformities between year classes, triploid S. salar × S. trutta can demonstrate impressive freshwater growth that could be of interest for future farming programmes.
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Affiliation(s)
- Thomas W K Fraser
- Reproduction and Developmental Biology Group, Institute of Marine Research (IMR), Matre Aquaculture Research Station, Matredal, Norway
| | - Tom J Hansen
- Reproduction and Developmental Biology Group, Institute of Marine Research (IMR), Matre Aquaculture Research Station, Matredal, Norway
| | - Florian Sambraus
- Reproduction and Developmental Biology Group, Institute of Marine Research (IMR), Matre Aquaculture Research Station, Matredal, Norway
| | - Per Gunnar Fjelldal
- Reproduction and Developmental Biology Group, Institute of Marine Research (IMR), Matre Aquaculture Research Station, Matredal, Norway
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Fjelldal PG, Hansen TJ, Wargelius A, Ayllon F, Glover KA, Schulz RW, Fraser TWK. Development of supermale and all-male Atlantic salmon to research the vgll3 allele - puberty link. BMC Genet 2020; 21:123. [PMID: 33183224 PMCID: PMC7664053 DOI: 10.1186/s12863-020-00927-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Farmed Atlantic salmon are one of the most economically significant global aquaculture products. Early sexual maturation of farmed males represents a significant challenge to this industry and has been linked with the vgll3 genotype. However, tools to aid research of this topic, such as all-male and clonal fish, are still lacking. The present 6-year study examined if all-male production is possible in Atlantic salmon, a species with heteromorphic sex chromosomes (males being XY, females XX), and if all-male fish can be applied to further explore the vgll3 contribution on the likelihood of early maturation. RESULTS Estrogen treatment of mixed sex yolk sac larvae gave rise to one sexually mature hermaphrodite with a male genotype (XY) that was used to produce both self-fertilized offspring and androgenetic double haploid (dh) offspring following egg activation with UV treated sperm and pressure shock to block the first mitotic division. There were YY supermales among both offspring types, which were crossed with dh females. Between 1 and 8% of the putative all-male offspring from the eight crosses with self-fertilized supermales were found to have ovaries, and 95% of these phenotypic females were also genetically female. None of the offspring from the one dh supermale cross had ovaries. When assessing the general contribution of the vgll3 locus on the likelihood of early post-smolt sexual maturation (jacking) in the all-male populations we found individuals that were homozygous for the early maturing genotype (97%) were more likely to enter puberty than individuals that were homozygous for the late maturing genotype (26%). However, the likelihood of jacking within individuals with an early/late heterozygous genotype was higher when the early allele came from the dam (94%) compared to the sire (45%). CONCLUSIONS The present results show that supermale Atlantic salmon are viable and fertile and can be used as a research tool to study important aspects of sexual maturation, such as to further explore the sex dependent parental genetic contribution to age at puberty in Atlantic salmon. In addition, we report the production of viable double haploid supermale fish.
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Affiliation(s)
- Per Gunnar Fjelldal
- Institute of Marine Research (IMR), Matre Aquaculture Research Station, 5984 Matredal, Norway
| | - Tom J. Hansen
- Institute of Marine Research (IMR), Matre Aquaculture Research Station, 5984 Matredal, Norway
| | - Anna Wargelius
- Institute of Marine Research (IMR), PO Box 1870, Nordnes, 5817 Bergen, Norway
| | - Fernando Ayllon
- Institute of Marine Research (IMR), PO Box 1870, Nordnes, 5817 Bergen, Norway
| | - Kevin A. Glover
- Institute of Marine Research (IMR), PO Box 1870, Nordnes, 5817 Bergen, Norway
| | - Rüdiger W. Schulz
- Reproductive Biology Group, Division Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, The Netherlands
| | - Thomas W. K. Fraser
- Institute of Marine Research (IMR), Matre Aquaculture Research Station, 5984 Matredal, Norway
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Pomianowski K, Ocalewicz K. Cytogenetic investigation of Arctic char × brook trout F 1, F 2 and backcross hybrids revealed remnants of the chromosomal rearrangements. J Appl Genet 2020; 62:151-164. [PMID: 33128700 PMCID: PMC7822801 DOI: 10.1007/s13353-020-00584-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 11/25/2022]
Abstract
Arctic char (Salvelinus alpinus) and brook trout (Salvelinus fontinalis) hybridize and their offspring is viable and fertile. This may be a real treat for the native European stocks of Arctic char which gene pools might be unintendedly contaminated with the genetic elements of brook trout. On the other hand, hybrids of these two species are appreciated by customers and have some potential for the aquaculture. Moreover, Salvelinus hybrids and backcross individuals are interesting models in the research focused on influence of hybridization on the genomic organization and chromosome rearrangements. Thus, the main goal of the present study was to examine chromosomes of Arctic char × brook trout F1, F2 hybrids and backcross individuals and compare with genomic information concerning parental species to recognize karyotypic changes provoked by the hybridization events. Application of conventional and molecular (FISH) techniques allow to identify characteristic chromosomes for both parental species in the hybrid progeny and show multiplicity of cytotypes among different types of crosses with variability in structure and number of chromosome (81–85) and chromosome arm (99–101). Chromosome fragment was detected in the karyotype of one F1 and one backcross individual and the presence of one triploid (3n) fish was documented. Occurrence of chromosomes containing internally located telomeric sequences (ITS) inherited after brook trout or both parental species was shown in F1 and backcross progeny. Moreover, additional CMA3-positive signal on chromosome from Arctic char pair no. 2 in F1 fish and interstitially located active NOR visible on subtelo-acrocentric (F2 hybrid) and acrocentric (Sf × H individual) chromosomes were detected. Described polymorphic chromosomes together with specific, interstitial location of CMA3-positive found in F2 and Sf × H hybrids and DAPI-positive regions observed in H × Sa fish at different uniarmed chromosomes pair presumably are remnants of chromosomal rearrangements. Provided results strongly indicate that the hybridization process influenced the genome organization in the Salvelinus hybrid progeny.
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Affiliation(s)
- Konrad Pomianowski
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, ul. Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Faculty of Oceanography and Geography, Institute of Oceanography University of Gdansk, al. Marszalka Józefa Pilsudskiego 46, 81-378 Gdynia, Poland
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Shivaramu S, Lebeda I, Vuong DT, Rodina M, Gela D, Flajšhans M. Ploidy Levels and Fitness-Related Traits in Purebreds and Hybrids Originating from Sterlet ( Acipenser ruthenus) and Unusual Ploidy Levels of Siberian Sturgeon ( A. baerii). Genes (Basel) 2020; 11:E1164. [PMID: 33023081 PMCID: PMC7600540 DOI: 10.3390/genes11101164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/24/2020] [Accepted: 09/30/2020] [Indexed: 11/20/2022] Open
Abstract
The present study aimed to investigate and compare fitness-related traits and ploidy levels of purebreds and hybrids produced from sturgeon broodstock with both normal and abnormal ploidy levels. We used diploid Acipenser ruthenus and tetraploid A. baerii males and females to produce purebreds and reciprocal hybrids of normal ploidy levels. Likewise, we used diploid A. ruthenus and tetraploid A. baerii females mated to pentaploid and hexaploid A. baerii males to produce hybrids of abnormal ploidy levels. Fertilization of ova of A. ruthenus and A. baerii of normal ploidy with the sperm of pentaploid and hexaploid A. baerii produced fully viable progeny with ploidy levels that were intermediate between those of the parents as was also found in crosses of purebreds and reciprocal hybrids of normal ploidy levels. The A. ruthenus × pentaploid A. baerii and A. ruthenus × hexaploid A. baerii hybrids did not survive after 22 days post-hatch (dph). Mean body weight and cumulative survival were periodically checked at seven-time intervals. The recorded values of mean body weight were significantly higher in A. baerii × pentaploid A. baerii hybrids than other groups at three sampling points (160, 252 and 330 dph). In contrast, the highest cumulative survival was observed in A. baerii × A. ruthenus hybrids at all sampling points (14.47 ± 5.70 at 497 dph). Overall, most of the studied sturgeon hybrids displayed higher mean BW and cumulative survival compared to the purebreds. The utilization of sturgeon hybrids should be restricted to aquaculture purposes because they can pose a significant genetic threat to native populations through ecological interactions.
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Affiliation(s)
- Sahana Shivaramu
- South Bohemian Research Center for Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic; (I.L.); (D.T.V.); (M.R.); (D.G.); (M.F.)
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7
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Hansen TJ, Penman D, Glover KA, Fraser TWK, Vågseth T, Thorsen A, Sørvik AGE, Fjelldal PG. Production and verification of the first Atlantic salmon (Salmo salar L.) clonal lines. BMC Genet 2020; 21:71. [PMID: 32641046 PMCID: PMC7346428 DOI: 10.1186/s12863-020-00878-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/28/2020] [Indexed: 11/10/2022] Open
Abstract
Background In several fish species homozygous and heterozygous clonal lines have been produced using gynogenetic and androgenetic techniques. These lines are standardized and can be reproduced over generations. In rainbow trout such lines have existed for decades and has become important research tools in genome studies as well as in studies of commercially important traits. The Atlantic salmon is one of the best studied fish species globally, but all experiments are done on fish of wild or domesticated origin and access to standardized immortal fish lines would be of great benefit. Here, we describe the protocols developed to produce mitotic gynogenes, and from these the first clonal lines in Atlantic salmon. Results Atlantic salmon eggs fertilized with UV irradiated sperm combined with a pressure shock applied at 4700–4800 minC at 8 °C gave all homozygous (doubled haploid) gynogenetic progeny with high survival. From the six first maturing females, five all homozygous clonal lines were produced by meiotic gynogenesis and were verified as clonal and identical to their mother with microsatellite markers. Conclusions We have now produced the first documented cloned Atlantic salmon lines. This work demonstrates the potential for production of further Atlantic salmon clonal lines, potentially with distinct characteristics. Such lines will provide an important resource for further elucidation of phenotypic and genetic traits in this globally important species.
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Affiliation(s)
| | - David Penman
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Kevin Alan Glover
- Institute of Marine Research, 5817, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | | | - Tone Vågseth
- Institute of Marine Research, 5984, Matredal, Norway
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Glover KA, Harvey AC, Hansen TJ, Fjelldal PG, Besnier FN, Bos JB, Ayllon F, Taggart JB, Solberg MF. Chromosome aberrations in pressure-induced triploid Atlantic salmon. BMC Genet 2020; 21:59. [PMID: 32505176 PMCID: PMC7276064 DOI: 10.1186/s12863-020-00864-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Triploid organisms have three sets of chromosomes. In Atlantic salmon, hydrostatic pressure treatment of newly fertilized eggs has been extensively used to produce triploids which are functionally sterile due to their unpaired chromosomes. These fish often perform poorly on commercial farms, sometimes without explanation. Inheritance patterns in individuals subjected to pressure treatment have not been investigated in Atlantic salmon thus far. However, work on other species suggests that this treatment can result in aberrant inheritance. We therefore studied this in Atlantic salmon by genotyping 16 polymorphic microsatellites in eyed eggs and juveniles which had been subjected to pressure-induction of triploidy. Communally reared juveniles including fish subjected to pressure-induction of triploidy and their diploid siblings were included as a control. RESULTS No diploid offspring were detected in any of the eggs or juveniles which were subjected to hydrostatic pressure; therefore, the induction of triploidy was highly successful. Aberrant inheritance was nevertheless observed in 0.9% of the eggs and 0.9% of the juveniles that had been subjected to pressure treatment. In the communally reared fish, 0.3% of the fish subjected to pressure treatment displayed aberrant inheritance, while their diploid controls displayed 0% aberrant inheritance. Inheritance errors included two eyed eggs lacking maternal DNA across all microsatellites, and, examples in both eggs and juveniles of either the maternal or paternal allele lacking in one of the microsatellites. All individuals displaying chromosome aberrations were otherwise triploid. CONCLUSIONS This is the first study to document aberrant inheritance in Atlantic salmon that have been subjected to pressure-induction of triploidy. Our experiments unequivocally demonstrate that even when induction of triploidy is highly successful, this treatment can cause chromosome aberrations in this species. Based upon our novel data, and earlier studies in other organisms, we hypothesize that in batches of Atlantic salmon where low to modest triploid induction rates have been reported, aberrant inheritance is likely to be higher than the rates observed here. Therefore, we tentatively suggest that this could contribute to the unexplained poor performance of triploid salmon that is occasionally reported in commercial aquaculture. These hypotheses require further investigation.
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Affiliation(s)
- K A Glover
- Institute of Marine Research, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - A C Harvey
- Institute of Marine Research, Bergen, Norway.
| | - T J Hansen
- Institute of Marine Research, Bergen, Norway
| | | | - F N Besnier
- Institute of Marine Research, Bergen, Norway
| | - J B Bos
- ZEBCARE, Nederweert, The Netherlands
| | - F Ayllon
- Institute of Marine Research, Bergen, Norway
| | | | - M F Solberg
- Institute of Marine Research, Bergen, Norway
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Delomas TA. Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon sequencing. Mol Ecol Resour 2019; 19:1545-1551. [DOI: 10.1111/1755-0998.13073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Thomas A. Delomas
- Pacific States Marine Fisheries Commission Eagle Fish Genetics Laboratory Eagle ID USA
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10
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Vogt G, Dorn NJ, Pfeiffer M, Lukhaup C, Williams BW, Schulz R, Schrimpf A. The dimension of biological change caused by autotriploidy: A meta-analysis with triploid crayfish Procambarus virginalis and its diploid parent Procambarus fallax. ZOOL ANZ 2019. [DOI: 10.1016/j.jcz.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Jørgensen KM, Wennevik V, Eide Sørvik AG, Unneland L, Prusov S, Ayllon F, Glover KA. Investigating the frequency of triploid Atlantic salmon in wild Norwegian and Russian populations. BMC Genet 2018; 19:90. [PMID: 30285613 PMCID: PMC6171226 DOI: 10.1186/s12863-018-0676-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/19/2018] [Indexed: 12/18/2022] Open
Abstract
Background Fish may display variations in ploidy, including three sets of chromosomes, known as triploidy. A recent study revealed a frequency of ~ 2% spontaneous (i.e., non-intentional) triploidy in domesticated Atlantic salmon produced in Norwegian aquaculture in the period 2007–2014. In contrast, the frequency of triploidy in wild salmon populations has not been studied thus far, and in wild populations of other organisms, it has been very rarely studied. In population genetic data sets, individuals that potentially display chromosome abnormalities, such as triploids with three alleles, are typically excluded on the premise that they may reflect polluted or otherwise compromised samples. Here, we critically re-investigated the microsatellite genetic profile of ~ 6000 wild Atlantic salmon sampled from 80 rivers in Norway and Russia, to investigate the frequency of triploid individuals in wild salmon populations for the first time. Results We detected a single triploid salmon, and five individuals displaying three alleles at one of the loci, thus regarded as putatively trisomic. This gave an overall frequency of triploid and putatively trisomic individuals in the data set of 0.017 and 0.083% respectively. The triploid salmon was an adult female, and had spent 2 years in freshwater and 2 years in the sea. Conclusions We conclude that the frequency of naturally-occurring triploid Atlantic salmon in wild Norwegian and Russian populations is very low, and many-fold lower than the frequency of spontaneous triploids observed in aquaculture. Our results suggest that aquaculture rearing conditions substantially increase the probability of triploidy to develop, and/or permits greater survival of triploid individuals, in comparison to the wild. Electronic supplementary material The online version of this article (10.1186/s12863-018-0676-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Vidar Wennevik
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | | | - Laila Unneland
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO), Murmansk, 183038, Russia
| | - Fernando Ayllon
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway.,Sea lice Research Centre, Department of Biology, University of Bergen, N-5020, Bergen, Norway
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Murray DS, Kainz MJ, Hebberecht L, Sales KR, Hindar K, Gage MJG. Comparisons of reproductive function and fatty acid fillet quality between triploid and diploid farm Atlantic salmon ( Salmo salar). R Soc Open Sci 2018; 5:180493. [PMID: 30225039 PMCID: PMC6124059 DOI: 10.1098/rsos.180493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
Triploidy could prevent escaped farm salmon breeding in the wild, while also improving nutrient quality within farmed fillets. Despite these potential advantages, triploid Atlantic salmon have not been widely used in aquaculture, and their reproductive function has yet to be fully evaluated. Here, we compare reproductive function and fillet composition between triploid and diploid farm salmon under standard aquaculture rearing conditions. We show that female triploids are sterile and do not develop gonads. By contrast, males produce large numbers of motile spermatozoa capable of fertilizing wild salmon eggs. However, compared with diploids, reproductive development and survival rates of eggs fertilized by triploid males were significantly reduced, with less than 1% of eggs sired by triploid males reaching late-eyed stages of development. Analyses of fillets showed that total lipid and fatty acid quantities were significantly lower in triploid than in diploid Atlantic salmon fillets. However, when fatty acids were normalized to total lipid content, triploid fillets had significantly higher relative levels of important omega-3 long-chain polyunsaturated fatty acids. Our results show that: (i) escaped triploid farm salmon are very unlikely to reproduce in the wild and (ii) if able to match diploid fillet lipid content, triploid farm salmon could achieve better fillet quality in terms of essential fatty acids.
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Affiliation(s)
- D. S. Murray
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - M. J. Kainz
- WasserCluster – Biologische Station Lunz, 3929 Lunz am See, Austria
| | - L. Hebberecht
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - K. R. Sales
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - K. Hindar
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - M. J. G. Gage
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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Vogt G. Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives. J Biosci 2018; 43:189-223. [PMID: 29485126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of ''big'' biological questions. Genome mining is expected to reveal new insights into the genetic specificities of decapod crustaceans, the genetic basis of arthropod reproduction, moulting and immunity, and more general topics such as the genetic underpinning of adaptation to fresh water, omnivory, biomineralization, sexual system change, behavioural variation, clonal genome evolution, and resistance to cancer. Epigenetic investigations with the marbled crayfish can help clarifying the role of epigenetic mechanisms in gene regulation, tissue specification, adult stem cell regulation, cell ageing, organ regeneration and disease susceptibility. Marbled crayfish is further suitable to elucidate the relationship between genetic and epigenetic variation, the transgenerational inheritance of epigenetic signatures and the contribution of epigenetic phenotype variation to the establishment of social hierarchies, environmental adaptation and speciation. These issues can be tackled by experiments with highly standardized laboratory lineages, comparison of differently adapted wild populations and the generation of genetically and epigenetically edited strains.
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Affiliation(s)
- Gunter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany,
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15
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Vogt G. Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives. J Biosci 2018. [DOI: 10.1007/s12038-018-9741-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Moore LJ, Nilsen TO, Jarungsriapisit J, Fjelldal PG, Stefansson SO, Taranger GL, Patel S. Triploid atlantic salmon (Salmo salar L.) post-smolts accumulate prevalence more slowly than diploid salmon following bath challenge with salmonid alphavirus subtype 3. PLoS One 2017; 12:e0175468. [PMID: 28403165 DOI: 10.1371/journal.pone.0175468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 03/27/2017] [Indexed: 01/15/2023] Open
Abstract
Triploid Atlantic salmon (Salmo salar L.) may play an important role in the sustainable expansion of the Norwegian aquaculture industry. Therefore, the susceptibility of triploid salmon to common infections such as salmonid alphavirus (SAV), the causative agent of pancreas disease (PD), requires investigation. In this study, shortly after seawater transfer, diploid and triploid post-smolts were exposed to SAV type 3 (SAV3) using a bath challenge model where the infectious dose was 48 TCID50 ml-1 of tank water. Copy number analysis of SAV3 RNA in heart tissue showed that there was no difference in viral loads between the diploids and triploids. Prevalence reached 100% by the end of the 35-day experimental period in both infected groups. However, prevalence accumulated more slowly in the triploid group reaching 19% and 56% at 14 and 21 days post exposure (dpe) respectively. Whereas prevalence in the diploid group was 82% and 100% at the same time points indicating some differences between diploid and triploid fish. Both heart and pancreas from infected groups at 14 dpe showed typical histopathological changes associated with pancreas disease. Observation of this slower accumulation of prevalence following a natural infection route was possible due to the early sampling points and the exposure to a relatively low dose of virus. The triploid salmon in this study were not more susceptible to SAV3 than diploid salmon indicating that they could be used commercially to reduce the environmental impact of escaped farmed fish interbreeding with wild salmon. This is important information regarding the future use of triploid fish in large scale aquaculture where SAV3 is a financial threat to increased production.
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Harvey AC, Fjelldal PG, Solberg MF, Hansen T, Glover KA. Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set. BMC Genet 2017; 18:34. [PMID: 28399816 PMCID: PMC5387229 DOI: 10.1186/s12863-017-0502-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/06/2017] [Indexed: 12/30/2022] Open
Abstract
Background The Atlantic salmon aquaculture industry is investigating the feasibility of using sterile triploids to mitigate genetic interactions with wild conspecifics, however, studies investigating diploid and triploid performance often show contrasting results. Studies have identified dosage and dosage-compensation effects for gene expression between triploid and diploid salmonids, but no study has investigated how ploidy and parent-origin effects interact on a polygenic trait in divergent lines of Atlantic salmon (i.e. slow growing wild versus fast growing domesticated phenotype). This study utilised two experiments relating to the freshwater growth of diploid and triploid groups of pure wild (0% domesticated genome), pure domesticated (100% domesticated genome), and F1 reciprocal hybrid (33%, 50% or 66% domesticated genome) salmon where triploidy was either artificially induced (experiment 1) or naturally developed/spontaneous (experiment 2). Results In both experiments, reciprocal hybrid growth was influenced by the dosage effect of the second maternal chromosome, with growth increasing as ploidy level increased in individuals with a domesticated dam (from 50% to 66% domesticated genome), and the inverse in individuals with a wild dam (from 50% to 33% domesticated genome). Conclusions We demonstrate that the combined effect of ploidy and parent-origin on growth, a polygenic trait, is regulated in an additive pattern. Therefore, in order to maximise growth potential, the aquaculture industry should consider placing more emphasis on the breeding value of the dam than the sire when producing triploid families for commercial production. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0502-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A C Harvey
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - P G Fjelldal
- Institute of Marine Research (IMR), Matre Research Station, NO-5984, Matredal, Norway
| | - M F Solberg
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - T Hansen
- Institute of Marine Research (IMR), Matre Research Station, NO-5984, Matredal, Norway
| | - K A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Department of Biology, University of Bergen, P. O. Box 7803, N-5020, Bergen, Norway
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Fjelldal PG, Solberg MF, Hansen T, Vågseth T, Glover KA, Kryvi H. Salmonid fish: model organisms to study cardiovascular morphogenesis in conjoined twins? BMC Dev Biol 2016; 16:25. [PMID: 27422058 PMCID: PMC4947332 DOI: 10.1186/s12861-016-0125-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 07/08/2016] [Indexed: 11/13/2022]
Abstract
Background There is a gap in knowledge regarding the cardiovascular system in fish conjoined twins, and regarding the cardiovascular morphogenesis of conjoined twins in general. We examined the cardiovascular system in a pair of fully developed ventrally conjoined salmonid twins (45.5 g body weight), and the arrangement of the blood vessels during early development in ventrally conjoined yolk sac larvae salmonid twins (<0.5 g body weight). Results In the fully developed twins, one twin was normal, while the other was small and severely malformed. The mouth of the small twin was blocked, inhibiting respiration and feeding. Both twins had hearts, but these were connected through a common circulatory system. They were joined by the following blood vessels: (i) arteria iliaca running from arteria caudalis of the large twin to the kidney of the small twin; (ii) arteria subclavia running from aorta dorsalis of the large twin to aorta dorsalis of the small twin; (iii) vena hepatica running from the liver of the small twin into the sinus venosus of the large twin. Among the yolk sac larvae twins investigated, distinct vascular connections were found in some individuals through a joined v. vitellina hepatica. Conclusions Ventrally conjoined fish twins can develop cardiovascular connections during early development, enabling a normal superior twin to supply a malfunctioning twin with oxygen and nutrients. Since the yolk sac in salmonids is transparent, twinning in salmonids may be a useful model in which to study cardiovascular morphogenesis in conjoined twins. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0125-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Per Gunnar Fjelldal
- Institute of Marine research (IMR), Matre Aquaculture Research Station, Matredal, Norway. .,Havforskningsinstituttet, Matre, Matre 5, 5984, Matredal, Norway.
| | | | - Tom Hansen
- Institute of Marine research (IMR), Matre Aquaculture Research Station, Matredal, Norway
| | - Tone Vågseth
- Institute of Marine research (IMR), Matre Aquaculture Research Station, Matredal, Norway
| | - Kevin Alan Glover
- Institute of Marine research (IMR), Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Harald Kryvi
- Department of Biology, University of Bergen, Bergen, Norway
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Havelka M, Bytyutskyy D, Symonová R, Ráb P, Flajšhans M. The second highest chromosome count among vertebrates is observed in cultured sturgeon and is associated with genome plasticity. Genet Sel Evol 2016; 48:12. [PMID: 26867760 PMCID: PMC4751722 DOI: 10.1186/s12711-016-0194-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 02/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the five basal actinopterygian lineages, the Chondrostei, including sturgeon, shovelnose, and paddlefish (Order Acipenseriformes) show extraordinary ploidy diversity associated with three rounds of lineage-specific whole-genome duplication, resulting in three levels of ploidy in sturgeon. Recently, incidence of spontaneous polyploidization has been reported among cultured sturgeon and it could have serious negative implications for the economics of sturgeon farming. We report the occurrence of seven spontaneous heptaploid (7n) Siberian sturgeon Acipenser baerii, which is a functional tetraploid species (4n) with ~245 chromosomes. Our aims were to assess ploidy level and chromosome number of the analysed specimens and to identify the possible mechanism that underlies the occurrence of spontaneous additional chromosome sets in their genome. RESULTS Among 150 specimens resulting from the mating of a tetraploid (4n) A. baerii (~245 chromosomes) dam with a hexaploid (6n) A. baerii (~368 chromosomes) sire, 143 displayed a relative DNA content that corresponds to pentaploidy (5n) with an absolute DNA content of 8.98 ± 0.03 pg DNA per nucleus and nuclear area of 35.3 ± 4.3 μm(2) and seven specimens exhibited a relative DNA content that corresponds to heptaploidy (7n), with an absolute DNA content of 15.02 ± 0.04 pg DNA per nucleus and nuclear area of 48.4 ± 5.1 μm(2). Chromosome analyses confirmed a modal number of ~437 chromosomes in these heptaploid (7n) individuals. DNA genotyping of eight microsatellite loci followed by parental assignment confirmed spontaneous duplication of the maternal chromosome sets via retention of the second polar body in meiosis II as the mechanism for the formation of this unusual chromosome number and ploidy level in a functional tetraploid A. baerii. CONCLUSIONS We report the second highest chromosome count among vertebrates in cultured sturgeon (~437) after the schizothoracine cyprinid Ptychobarbus dipogon with ~446 chromosomes. The finding also represents the highest documented chromosome count in Acipenseriformes, and the first report of a functional heptaploid (7n) genome composition in sturgeon. To our knowledge, this study provides the first clear evidence of a maternal origin for spontaneous polyploidization in cultured A. baerii. To date, all available data indicate that spontaneous polyploidization occurs frequently among cultured sturgeons.
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Affiliation(s)
- Miloš Havelka
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in Ceske Budejovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic.
- Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate, Hokkaido, 041-8611, Japan.
| | - Dmytro Bytyutskyy
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in Ceske Budejovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic.
| | - Radka Symonová
- Research Institute for Limnology, University of Innsbruck, Mondseestraße 9, 5310, Mondsee, Austria.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 277 21, Liběchov, Czech Republic.
| | - Martin Flajšhans
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in Ceske Budejovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic.
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