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Dissertation•

Towards the development of clonal lines in the European sea bass (Dicentrarchus labrax L) : application of uniparental reproduction techniques with an insight into sea bass eggs

Julie Colleter
13 Feb 2015-
TL;DR: Gynogenesis was reported successful to produce clonal founders in the sea bass, but high numbers of meiotic individuals contaminating fully homozygous progenies highlighted the need for efficient DNA markers to distinguish mitotic gynogenetic individuals.
Abstract: Clonal lines are a powerful scientific tool for improved genetic characterization of organisms used in research. Inbred fish lines can be produced in only two generations using uniparental reproduction techniques. Androgenesis, achieved with variable success in several freshwater species, has been attempted in the European sea bass (Dicentrarchus labrax L), a marine fish of commercial and scientific interest. The low yields of progenies inheriting only the paternal genome after UV-irradiation of eggs led to considerations on the occurrence of UV screening compounds in pelagic eggs. Mycosporine-like amino acids and gadusol were found in many marine and freshwater organisms, but their occurrence in fish eggs was not clearly related to a behavioral pattern and while gadusol appeared in higher proportions in pelagic marine eggs compared to benthic species, this statement did not apply in freshwater, and moreover the kind of compounds was related to phylogeny. Further studies on DNA photorepair could enlighten hypotheses to understand the mechanisms underlying the disparate results obtained in inducing androgenesis in different fish species. Gynogenesis was reported successful to produce clonal founders in the sea bass, but high numbers of meiotic individuals contaminating fully homozygous progenies highlighted the need for efficient DNA markers to distinguish mitotic gynogenetic individuals. Furthermore, gonad development was highly delayed in gynogenetic progenies enhancing the difficulties to produce clonal lines. A high variability between individuals in the success of uniparental reproduction brought out gamete characterization and quality as a prerequisite.
Citations
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Journal Article•
An experimental study of the reproductive behaviour and success of farmed and wild Atlantic salmon (Salmo salar)

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Ian A. Fleming, Bror Jonsson, Mart R. Gross, Anders Lamberg
01 Jan 1997-Oceanographic Literature Review
TL;DR: In this article, the authors report experiments to assess the competitive and reproductive abilities of fifth-generation farmed salmon and their potential impacts upon wild salmon and conclude that farmed females had less than one-third of the reproductive success of wild females.
Abstract: 1. Escape of cultured organisms into natural ecosystems may threaten wild populations both ecologically and genetically. In the aquaculture industry, farmed Atlantic salmon (Salmo salar L.) often escape and enter the spawning grounds of wild salmon. We report experiments to assess the competitive and reproductive abilities of fifth-generation farmed salmon and their potential impacts upon wild salmon. 2. The farmed and wild females had similar levels of competitive behaviour; however, they differed in reproductive behaviour and success. Farmed females displayed less breeding behaviour, constructed fewer nests, retained a greater weight of eggs unspawned, were less efficient at nest covering, incurred more nest destruction, and suffered greater egg mortality than wild females. As a result, farmed females had less than one-third of the reproductive success of wild females. 3. The farmed males were even less successful than the farmed females in competition with the wild fish. They were less aggressive, courted less, partook in fewer spawnings, and achieved only an estimated one to three percentage of the reproductive success of the wild males. 4. The farmed males exhibited inappropriate mating behaviour, that led to poor fertilization success, even in the absence of competition with wild males. 5. Adult farmed fish are thus likely to be relatively unsuccessful in natural environments due to a competitive and reproductive inferiority apparently resulting from domestication.

301 citations

Journal Article•DOI•
Gene-centromere mapping in meiotic gynogenetic European seabass.

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Münevver Oral1, Julie Colléter2, Michaël Bekaert1, John B. Taggart1, Christos Palaiokostas1, Brendan McAndrew1, Marc Vandeputte3, Marc Vandeputte2, Béatrice Chatain2, Heiner Kuhl4, Richard Reinhardt5, Stefano Peruzzi6, David J. Penman1 •
University of Stirling1, IFREMER2, Université Paris-Saclay3, Leibniz Association4, Max Planck Society5, University of Tromsø6
07 Jun 2017-BMC Genomics
TL;DR: Genome-wide screening enabled substantive verification of the production of the gynogenetic family used in this study, and the large number of telomeric and subtelomeric markers with high heterozygosity values in the meiotic gynagenetic family indicate that such markers could be used to clearly distinguish between meiotic and mitotic gwnogenetics.
Abstract: Fully isogenic lines in fish can be developed using “mitotic” gynogenesis (suppression of first zygotic mitosis following inactivation of the sperm genome). However, genome-wide verification of the steps in this process has seldom been applied. We used ddRADseq to generate SNP markers in a meiotic gynogenetic family of European seabass (Dicentrarchus labrax): (i) to verify the lack of paternal contribution in a meiotic gynogenetic family; (ii) to generate a gene-centromere map from this family; (iii) to identify telomeric markers that could distinguish mitotic gynogenetics from meiotic gynogenetics, which sometimes arise spontaneously in mitotic gynogenetic families. From a single meiotic gynogenetic family consisting of 79 progeny, 42 million sequencing reads (Illumina, trimmed to 148 bases) resolved 6866 unique RAD-tags. The 340 male-informative SNP markers that were identified confirmed the lack of paternal contribution. A gene-centromere map was constructed based on 804 female-informative SNPs in 24 linkage groups (2n = 48) with a total length of 1251.02 cM (initial LG assignment was based on the seabass genome assembly, dicLab v1). Chromosome arm structure could be clearly discerned from the pattern of heterozygosity in each linkage group in 18 out of 24 LGs: the other six showed anomalies that appeared to be related to issues in the genome assembly. Genome-wide screening enabled substantive verification of the production of the gynogenetic family used in this study. The large number of telomeric and subtelomeric markers with high heterozygosity values in the meiotic gynogenetic family indicate that such markers could be used to clearly distinguish between meiotic and mitotic gynogenetics.

10 citations

Dissertation•
Insights into isogenic clonal fish line development using high-throughput sequencing technologies

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Munevver Oral
31 Oct 2016

4 citations

Cites background or methods from "Towards the development of clonal l..."

  • ...Although 11 microsatellites (Chistiakov et al., 2005; García De León et al., 1995; Colléter, 2015) that are currently in use (positioned on physical map, Fig 3....

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  • ..., 2005) that have been used to differentiate between meiotic and mitotic gynogenetic sea bass (Colléter, 2015) were also assigned to the physical map once the genomic positions in basepairs were identified using Blastn (1E -20 and lower)....

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  • ...were produced alongside fully homozygous progeny in many families, as detected by the microsatellite panel, highlighting the need for a large number of DNA markers to distinguish mitotic gynogenetic individuals more reliably (Colléter 2015)....

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  • ...of completely homozygous putative mitotic gynogenetics (Colléter, 2015)....

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DNA Content in Eurasian Sturgeon Species Determined by flow cytomery

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Vadim J. Birstein
13 Jul 2016
TL;DR: The nuclear DNA content in 10 species of chondrostean fishes was measured by flow cytometry and the sterlet Acipenser ruthenus blood cells were used as an internal standard.
Abstract: DNA Content in Eurasian Sturgeon Species Determined by flow cytomery , DNA Content in Eurasian Sturgeon Species Determined by flow cytomery , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی

2 citations

Genetic manipulations and gene banking in tilapia

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J.M. Myers, D.J. Penman, B.J. McAndrew, K.J. Rana
01 Jan 1993

2 citations

References
More filters
Journal Article•DOI•
Micro-Checker: Software for identifying and correcting genotyping errors in microsatellite data

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Cock van Oosterhout, William F. Hutchinson, D. Wills1, Peter Shipley1•
University of Hull1
01 Sep 2004-Molecular Ecology Notes
TL;DR: MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
Abstract: DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO - CHECKER is WINDOWS ®-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis. MICRO CHECKER can be freely downloaded from http://www.microchecker.hull.ac.uk/.

9,953 citations

"Towards the development of clonal l..." refers methods in this paper

  • ...Presence of null alleles in the PCR products was analyzed using Microchecker software version 2.2.3 (Van Oosterhout et al., 2004)....

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Introduction to quantitative genetics. 1. ed.

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D S Falconer
01 Jan 1984

2,473 citations

"Towards the development of clonal l..." refers background in this paper

  • ...Genetic variance is also divided into an additive genetic component (VA), a dominance component (VD) and an interaction component (VI) (Falconer and Mackay, 1996)....

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  • ...…the formula for genetic variance between and within families applied therefore is: VA-tot = VA-between families + VA- within families = 2fVA + (1+F-2f)VA = (1+F)VA where f is the coefficient of coancestry (Malécot relationship) among individuals of the same family (Falconer and Mackay, 1996)....

    [...]

  • ...In the case of fish, fully inbred individuals are obtained in only one generation, the formula for genetic variance between and within families applied therefore is: VA-tot = VA-between families + VA- within families = 2fVA + (1+F-2f)VA = (1+F)VA where f is the coefficient of coancestry (Malécot relationship) among individuals of the same family (Falconer and Mackay, 1996)....

    [...]

Journal Article•DOI•
UV-induced DNA damage and repair: a review

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Rajeshwar P. Sinha1, Donat-P. Häder1•
University of Erlangen-Nuremberg1
10 Apr 2002-Photochemical and Photobiological Sciences
TL;DR: This review deals with UV-induced DNA damage and the associated repair mechanisms as well as methods of detectingDNA damage and its future perspectives.
Abstract: Increases in ultraviolet radiation at the Earth's surface due to the depletion of the stratospheric ozone layer have recently fuelled interest in the mechanisms of various effects it might have on organisms. DNA is certainly one of the key targets for UV-induced damage in a variety of organisms ranging from bacteria to humans. UV radiation induces two of the most abundant mutagenic and cytotoxic DNA lesions such as cyclobutane–pyrimidine dimers (CPDs) and 6–4 photoproducts (6–4PPs) and their Dewar valence isomers. However, cells have developed a number of repair or tolerance mechanisms to counteract the DNA damage caused by UV or any other stressors. Photoreactivation with the help of the enzyme photolyase is one of the most important and frequently occurring repair mechanisms in a variety of organisms. Excision repair, which can be distinguished into base excision repair (BER) and nucleotide excision repair (NER), also plays an important role in DNA repair in several organisms with the help of a number of glycosylases and polymerases, respectively. In addition, mechanisms such as mutagenic repair or dimer bypass, recombinational repair, cell-cycle checkpoints, apoptosis and certain alternative repair pathways are also operative in various organisms. This review deals with UV-induced DNA damage and the associated repair mechanisms as well as methods of detecting DNA damage and its future perspectives.

1,655 citations

"Towards the development of clonal l..." refers background or methods in this paper

  • ...Several methods have been used to detect DNA damage (see review by Sinha and Hader, 2002), but one of the most sensitive to detect UV effects in single cells is comet assay (electrophoretic technique) combined with T4 endonuclease V (an enzyme that specifically repairs UV-induced cyclobutane…...

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  • ...Les mécanismes de photoréparation de l’ADN, basés sur l’activité enzymatique de la photolyase, sont présents chez de nombreux organismes d’origines phylogénétiques variées (Sinha and Hader, 2002)....

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  • ...After UV irradiation, the CPDs are the most abundant DNA damage products (Sinha and Hader, 2002)....

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  • ...Screening compounds are known to provide a first line of defense in fish eggs (Cockell and Knowland, 1999; Sinha et al., 2007) while active DNA repair processes may be used by eggs to deal with damage caused by UV (Sinha and Hader, 2002)....

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  • ...Photolyases have been reported in many species in many taxa as bacteria, fungi, plants, invertebrates and many vertebrates (Sinha and Hader, 2002)....

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Journal Article•DOI•
Evidence for a lack of DNA double-strand break repair in human cells exposed to very low x-ray doses

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Kai Rothkamm1, Markus Löbrich•
Saarland University1
29 Apr 2003-Proceedings of the National Academy of Sciences of the United States of America
TL;DR: Evidence is presented that foci of γ-H2AX (a phosphorylated histone), detected by immunofluorescence, are quantitatively the same as DSBs and are capable of quantifying the repair of individual D SBs, allowing the investigation of DSB repair after radiation doses as low as 1 mGy, an improvement by several orders of magnitude over current methods.
Abstract: DNA double-strand breaks (DSBs) are generally accepted to be the most biologically significant lesion by which ionizing radiation causes cancer and hereditary disease. However, no information on the induction and processing of DSBs after physiologically relevant radiation doses is available. Many of the methods used to measure DSB repair inadvertently introduce this form of damage as part of the methodology, and hence are limited in their sensitivity. Here we present evidence that foci of γ-H2AX (a phosphorylated histone), detected by immunofluorescence, are quantitatively the same as DSBs and are capable of quantifying the repair of individual DSBs. This finding allows the investigation of DSB repair after radiation doses as low as 1 mGy, an improvement by several orders of magnitude over current methods. Surprisingly, DSBs induced in cultures of nondividing primary human fibroblasts by very low radiation doses (≈1 mGy) remain unrepaired for many days, in strong contrast to efficient DSB repair that is observed at higher doses. However, the level of DSBs in irradiated cultures decreases to that of unirradiated cell cultures if the cells are allowed to proliferate after irradiation, and we present evidence that this effect may be caused by an elimination of the cells carrying unrepaired DSBs. The results presented are in contrast to current models of risk assessment that assume that cellular responses are equally efficient at low and high doses, and provide the opportunity to employ γ-H2AX foci formation as a direct biomarker for human exposure to low quantities of ionizing radiation.

1,604 citations

"Towards the development of clonal l..." refers background in this paper

  • ...The most biologically significant lesion caused by ionizing irradiation (gamma or Xray) is double-strand breaks (DSBs) that shatter DNA (Rothkamm and Lobrich, 2003)....

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  • ...…dimers, UV-irradiation also causes the formation of DNA-DNA or RNA-RNA cross-links (Friedberg, 1985; Komen and Thorgaard, 2007) The most biologically significant lesion caused by ionizing irradiation (gamma or Xray) is double-strand breaks (DSBs) that shatter DNA (Rothkamm and Lobrich, 2003)....

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Journal Article•DOI•
Production of clones of homozygous diploid zebra fish ( Brachydanio rerio )

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George Streisinger1, Charline Walker1, Nancy A. Dower1, Donna Knauber1, Fred Singer1 •
University of Oregon1
28 May 1981-Nature
TL;DR: Clones of homozygous fish have been produced from individual homozygotes and associated genetic methods facilitate genetic analyses of this vertebrate.
Abstract: Homozygous diploid zebra fish have been produced on a large scale by the application of simple physical treatments. Clones of homozygous fish have been produced from individual homozygotes. These clones and associated genetic methods will facilitate genetic analyses of this vertebrate.

1,203 citations

"Towards the development of clonal l..." refers background in this paper

  • ...The F1 hybrids are more vigorous and interesting for the isolation of mutants because they are more likely to be free of recessive lethal genes (Streisinger et al., 1981)....

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  • ...…produced by retention of the second polar body (or inhibition of the second meiotic division) and depending on the frequency of recombination events, the individuals produced are more or less homozygous and can be used to estimate gene-centromere distances (Purdom, 1993; Streisinger et al., 1981)....

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  • ...29 Meiotic gynogenetic diploids are produced by retention of the second polar body (or inhibition of the second meiotic division) and depending on the frequency of recombination events, the individuals produced are more or less homozygous and can be used to estimate gene-centromere distances (Purdom, 1993; Streisinger et al., 1981)....

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