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Delaval A, Glover KA, Solberg MF, Taggart JB, Besnier F, Sørvik AGE, Øyro J, Garnes-Gutvik SN, Fjelldal PG, Hansen T, Harvey A. A genetic method to infer ploidy and aberrant inheritance in triploid organisms. Mol Ecol Resour 2024:e14004. [PMID: 39104309 DOI: 10.1111/1755-0998.14004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 05/22/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024]
Abstract
Polyploidy occurs naturally across eukaryotic lineages and has been harnessed in the domestication of many crops and vertebrates. In aquaculture, triploidy can be induced as a biocontainment strategy, as it creates a reproductive barrier preventing farm-to-wild introgression, which is currently a major conservation issue for the industry. However, recent work suggests that triploidisation protocols may, on occasion, produce 'failed triploids' displaying diploidy, aneuploidy and aberrant inheritance. The potentially negative consequences for conservation and animal welfare motivate the need for methods to evaluate the success of ploidy-manipulation protocols early in the production process. We developed a semi-automated version of the MAC-PR (microsatellite DNA allele counting - peak ratios) method to resolve the allelic configuration of large numbers of individuals across a panel of microsatellite markers that can be used to infer ploidy, pedigree and inheritance aberrations. We demonstrate an application of the approach using material from a series of Atlantic salmon (Salmo salar) breeding experiments where ploidy was manipulated using a hydrostatic pressure treatment. We validated the approach to infer ploidy against blood smears, finding a > 99% agreement between these methods, and demonstrate its potential utility to infer ploidy as early as the embryonic stage. Furthermore, we present tools to assign diploid and triploid progeny to families and to detect aberrant inheritance, which may be useful for breeding programmes that utilise ploidy manipulation techniques. The approach adds to the ploidy verification toolbox. The increased precision in detecting ploidy and inheritance aberrations will facilitate the ability of triploidisation programmes to prevent farm-to-wild introgression.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Tom Hansen
- Institute of Marine Research, Matre Research Station, Matredal, Norway
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Menezes WF, Alvarenga ÉR, Nóbrega RH, França LR, Luz MR, Manduca LG, da Costa FFB, Bezerra VM, Fernandes AFDA, Turra EM. Growth performance, reproductive status, and chromosomal instability in triploid Nile tilapias. Anim Reprod 2024; 21:e20230147. [PMID: 38803328 PMCID: PMC11129864 DOI: 10.1590/1984-3143-ar2023-0147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/18/2024] [Indexed: 05/29/2024] Open
Abstract
Reproductive control is one of the biggest challenges in tilapia production and triploidy was developed as an alternative to sterilization. In general, polyploids present chromosomal instability but for triploid Nile tilapia it has yet to be reported. This study evaluated the chromosomal instability from juveniles to adulthood, growth performance and gonadal status of tilapia hatched from eggs submitted or not to heat shock for triploid induction. Nile tilapia oocytes were fertilized (1,476 oocytes), half of the eggs were subjected to a four-minute shock in 41 °C water four minutes after fertilization and the other half were not (Control group). The eggs were incubated (at 27°C) and 160 larvae from the treated group hatched and survived after yolk sac absorption. The determination of ploidy was performed by flow cytometry at 85th (juveniles) and 301st (adults) days of age post yolk sac absorption. At the time of the first cytometry analysis there were 73 surviving juveniles from the treated group, and only 14 were confirmed triploid. However, at the analysis of adult ploidy, one out of 8 surviving adult tilapias from the 14 confirmed triploid juveniles remained triploid. Gonadal histology showed that the non-remaining triploids continued to produce gametes. The growth performance of triploid tilapia was initially superior to that of diploid tilapia during the juvenile phase, but similar in adults. Once the chromosome sets are lost and the tilapias become diploid again, at least in tissues with a high proliferation rate, such as the hematopoietic tissue that was analyzed (and possibly in gonads), all possible advantages of triploids are probably lost. Thus, our results suggest that, due to genomic instabilities, the triploid generation of tilapia has low efficiency.
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Affiliation(s)
- Williane Ferreira Menezes
- Departamento de Zootecnia, Escola de Veterinária, Laboratório de Aquacultura, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Érika Ramos Alvarenga
- Departamento de Zootecnia, Escola de Veterinária, Laboratório de Aquacultura, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Rafael Henrique Nóbrega
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista Júlio de Mesquita Filho, Botucatu, SP, Brasil
| | - Luiz Renato França
- Departamento de Zootecnia, Escola de Veterinária, Laboratório de Aquacultura, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Marcelo Rezende Luz
- Departamento de Zootecnia, Escola de Veterinária, Laboratório de Aquacultura, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Ludson Guimarães Manduca
- Departamento de Zootecnia, Escola de Veterinária, Laboratório de Aquacultura, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Franklin Fernando Batista da Costa
- Departamento de Zootecnia, Escola de Veterinária, Laboratório de Aquacultura, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Vinícius Monteiro Bezerra
- Departamento de Zootecnia, Escola de Veterinária, Laboratório de Aquacultura, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | | | - Eduardo Maldonado Turra
- Departamento de Zootecnia, Escola de Veterinária, Laboratório de Aquacultura, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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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] [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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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] [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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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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