Insights into isogenic clonal fish line development using high-throughput sequencing technologies
Isogenic clonal fish lines are a powerful resource for aquaculture-related research. Fully inbred individuals, clone founders, can be produced either through mitotic gynogenesis or androgenesis and a further generation from those propagates fully inbred clonal lines. Despite rapid generation, as opp...
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University of Stirling
2016
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Online Access: | http://hdl.handle.net/1893/24909 http://dspace.stir.ac.uk/bitstream/1893/24909/1/M_ORAL_PhD_thesis_final.pdf |
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ftunivstirling:oai:dspace.stir.ac.uk:1893/24909 2024-06-02T08:03:38+00:00 Insights into isogenic clonal fish line development using high-throughput sequencing technologies Oral, Munevver Penman, David Turkish Government (law: 1416) - Ministry of Education dept, AQUAEXCEL project (FP7 and follow up Horizon2020) 2016-10-31 application/pdf http://hdl.handle.net/1893/24909 http://dspace.stir.ac.uk/bitstream/1893/24909/1/M_ORAL_PhD_thesis_final.pdf en eng University of Stirling Institute of Aquaculture http://hdl.handle.net/1893/24909 http://dspace.stir.ac.uk/bitstream/1893/24909/1/M_ORAL_PhD_thesis_final.pdf Isogenic fish lines High Throughput Sequencing Aquaculture Meiotic Gynogenetics European seabass Atlantic salmon Nile tilapia Aquaculture Research Fishes Molecular aspects Molecular biology Research Thesis or Dissertation Doctoral Doctor of Philosophy 2016 ftunivstirling 2024-05-07T04:30:11Z Isogenic clonal fish lines are a powerful resource for aquaculture-related research. Fully inbred individuals, clone founders, can be produced either through mitotic gynogenesis or androgenesis and a further generation from those propagates fully inbred clonal lines. Despite rapid generation, as opposed to successive generation of sibling mating as in mice, the production of such lines may be hampered due to (i) potential residual contribution from irradiated gametes associated with poorly optimised protocols, (ii) reduced survival of clone founders and (iii) spontaneous arisal of meiotic gynogenetics with varying degree of heterozygosity, contaminating fully homozygous progenies. This research set out to address challenges and gain insights into isogenic clonal fish lines development by using double-digest RADseq (ddRADseq) to generate large numbers of genetic markers covering the genome of interest. Analysis of potential contribution from irradiated sperm indicated successful uniparental inheritance in meiotic and mitotic gynogenetics European seabass. Exclusive transmission of maternal alleles was detected in G1 progeny of Atlantic salmon (with a duplicated genome), while G2 progenies presented varying levels of sire contribution suggesting sub-optimal UV irradiation which was undetected previously with 27 microsatellite markers. Identification of telomeric markers in European seabass, with higher recombination frequencies for efficient differentiation of meiotic and mitotic gynogenetics was successful, and a genetic linkage map was generated from this data. One clear case of a spontaneous meiotic gynogenetic fish was detected among 18 putative DH fish in European seabass, despite earlier screening for isogenicity using 11 microsatellite markers. An unidentified larval DNA restriction digestion inhibition mechanism observed in Nile tilapia prevented the construction of SNP-based genetic linkage map. In summary, this study provides strong evidence on efficacy of NGS technologies for the development and ... Doctoral or Postdoctoral Thesis Atlantic salmon University of Stirling: Stirling Digital Research Repository |
institution |
Open Polar |
collection |
University of Stirling: Stirling Digital Research Repository |
op_collection_id |
ftunivstirling |
language |
English |
topic |
Isogenic fish lines High Throughput Sequencing Aquaculture Meiotic Gynogenetics European seabass Atlantic salmon Nile tilapia Aquaculture Research Fishes Molecular aspects Molecular biology Research |
spellingShingle |
Isogenic fish lines High Throughput Sequencing Aquaculture Meiotic Gynogenetics European seabass Atlantic salmon Nile tilapia Aquaculture Research Fishes Molecular aspects Molecular biology Research Oral, Munevver Insights into isogenic clonal fish line development using high-throughput sequencing technologies |
topic_facet |
Isogenic fish lines High Throughput Sequencing Aquaculture Meiotic Gynogenetics European seabass Atlantic salmon Nile tilapia Aquaculture Research Fishes Molecular aspects Molecular biology Research |
description |
Isogenic clonal fish lines are a powerful resource for aquaculture-related research. Fully inbred individuals, clone founders, can be produced either through mitotic gynogenesis or androgenesis and a further generation from those propagates fully inbred clonal lines. Despite rapid generation, as opposed to successive generation of sibling mating as in mice, the production of such lines may be hampered due to (i) potential residual contribution from irradiated gametes associated with poorly optimised protocols, (ii) reduced survival of clone founders and (iii) spontaneous arisal of meiotic gynogenetics with varying degree of heterozygosity, contaminating fully homozygous progenies. This research set out to address challenges and gain insights into isogenic clonal fish lines development by using double-digest RADseq (ddRADseq) to generate large numbers of genetic markers covering the genome of interest. Analysis of potential contribution from irradiated sperm indicated successful uniparental inheritance in meiotic and mitotic gynogenetics European seabass. Exclusive transmission of maternal alleles was detected in G1 progeny of Atlantic salmon (with a duplicated genome), while G2 progenies presented varying levels of sire contribution suggesting sub-optimal UV irradiation which was undetected previously with 27 microsatellite markers. Identification of telomeric markers in European seabass, with higher recombination frequencies for efficient differentiation of meiotic and mitotic gynogenetics was successful, and a genetic linkage map was generated from this data. One clear case of a spontaneous meiotic gynogenetic fish was detected among 18 putative DH fish in European seabass, despite earlier screening for isogenicity using 11 microsatellite markers. An unidentified larval DNA restriction digestion inhibition mechanism observed in Nile tilapia prevented the construction of SNP-based genetic linkage map. In summary, this study provides strong evidence on efficacy of NGS technologies for the development and ... |
author2 |
Penman, David Turkish Government (law: 1416) - Ministry of Education dept, AQUAEXCEL project (FP7 and follow up Horizon2020) |
format |
Doctoral or Postdoctoral Thesis |
author |
Oral, Munevver |
author_facet |
Oral, Munevver |
author_sort |
Oral, Munevver |
title |
Insights into isogenic clonal fish line development using high-throughput sequencing technologies |
title_short |
Insights into isogenic clonal fish line development using high-throughput sequencing technologies |
title_full |
Insights into isogenic clonal fish line development using high-throughput sequencing technologies |
title_fullStr |
Insights into isogenic clonal fish line development using high-throughput sequencing technologies |
title_full_unstemmed |
Insights into isogenic clonal fish line development using high-throughput sequencing technologies |
title_sort |
insights into isogenic clonal fish line development using high-throughput sequencing technologies |
publisher |
University of Stirling |
publishDate |
2016 |
url |
http://hdl.handle.net/1893/24909 http://dspace.stir.ac.uk/bitstream/1893/24909/1/M_ORAL_PhD_thesis_final.pdf |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://hdl.handle.net/1893/24909 http://dspace.stir.ac.uk/bitstream/1893/24909/1/M_ORAL_PhD_thesis_final.pdf |
_version_ |
1800748213376909312 |