A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects
Background As farming of Atlantic salmon is growing as an aquaculture enterprise, the need to identify the genomic mechanisms for specific traits is becoming more important in breeding and management of the animal. Traits of importance might be related to growth, disease resistance, food conversion...
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ftoslouniv:oai:www.duo.uio.no:10852/46593 2023-05-15T15:30:01+02:00 A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects Thorsen, Jim Zhu, Baoli Frengen, Eirik Osoegawa, Kazutoyo de Jong, Pieter J Koop, Ben F Davidson, William S Høyheim, Bjørn 2005 http://hdl.handle.net/10852/46593 http://urn.nb.no/URN:NBN:no-50774 https://doi.org/10.1186/1471-2164-6-50 eng eng http://urn.nb.no/URN:NBN:no-50774 BMC Genomics. 2005 Apr 04;6(1):50 http://hdl.handle.net/10852/46593 http://dx.doi.org/10.1186/1471-2164-6-50 URN:NBN:no-50774 Fulltext https://www.duo.uio.no/bitstream/handle/10852/46593/1/12864_2004_Article_251.pdf Thorsen et al. Attribution 2.0 Generic http://creativecommons.org/licenses/by/2.0/ CC-BY Journal article Tidsskriftartikkel Peer reviewed PublishedVersion 2005 ftoslouniv https://doi.org/10.1186/1471-2164-6-50 2020-06-21T08:48:53Z Background As farming of Atlantic salmon is growing as an aquaculture enterprise, the need to identify the genomic mechanisms for specific traits is becoming more important in breeding and management of the animal. Traits of importance might be related to growth, disease resistance, food conversion efficiency, color or taste. To identify genomic regions responsible for specific traits, genomic large insert libraries have previously proven to be of crucial importance. These large insert libraries can be screened using gene or genetic markers in order to identify and map regions of interest. Furthermore, large-scale mapping can utilize highly redundant libraries in genome projects, and hence provide valuable data on the genome structure. Results Here we report the construction and characterization of a highly redundant bacterial artificial chromosome (BAC) library constructed from a Norwegian aquaculture strain male of Atlantic salmon (Salmo salar). The library consists of a total number of 305 557 clones, in which approximately 299 000 are recombinants. The average insert size of the library is 188 kbp, representing 18-fold genome coverage. High-density filters each consisting of 18 432 clones spotted in duplicates have been produced for hybridization screening, and are publicly available [1]. To characterize the library, 15 expressed sequence tags (ESTs) derived overgos and 12 oligo sequences derived from microsatellite markers were used in hybridization screening of the complete BAC library. Secondary hybridizations with individual probes were performed for the clones detected. The BACs positive for the EST probes were fingerprinted and mapped into contigs, yielding an average of 3 contigs for each probe. Clones identified using genomic probes were PCR verified using microsatellite specific primers. Conclusion Identification of genes and genomic regions of interest is greatly aided by the availability of the CHORI-214 Atlantic salmon BAC library. We have demonstrated the library's ability to identify specific genes and genetic markers using hybridization, PCR and fingerprinting experiments. In addition, multiple fingerprinting contigs indicated a pseudo-tetraploidity of the Atlantic salmon genome. The highly redundant CHORI-214 BAC library is expected to be an important resource for mapping and sequencing of the Atlantic salmon genome. Article in Journal/Newspaper Atlantic salmon Salmo salar Universitet i Oslo: Digitale utgivelser ved UiO (DUO) BMC Genomics 6 1 |
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Open Polar |
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Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
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ftoslouniv |
language |
English |
description |
Background As farming of Atlantic salmon is growing as an aquaculture enterprise, the need to identify the genomic mechanisms for specific traits is becoming more important in breeding and management of the animal. Traits of importance might be related to growth, disease resistance, food conversion efficiency, color or taste. To identify genomic regions responsible for specific traits, genomic large insert libraries have previously proven to be of crucial importance. These large insert libraries can be screened using gene or genetic markers in order to identify and map regions of interest. Furthermore, large-scale mapping can utilize highly redundant libraries in genome projects, and hence provide valuable data on the genome structure. Results Here we report the construction and characterization of a highly redundant bacterial artificial chromosome (BAC) library constructed from a Norwegian aquaculture strain male of Atlantic salmon (Salmo salar). The library consists of a total number of 305 557 clones, in which approximately 299 000 are recombinants. The average insert size of the library is 188 kbp, representing 18-fold genome coverage. High-density filters each consisting of 18 432 clones spotted in duplicates have been produced for hybridization screening, and are publicly available [1]. To characterize the library, 15 expressed sequence tags (ESTs) derived overgos and 12 oligo sequences derived from microsatellite markers were used in hybridization screening of the complete BAC library. Secondary hybridizations with individual probes were performed for the clones detected. The BACs positive for the EST probes were fingerprinted and mapped into contigs, yielding an average of 3 contigs for each probe. Clones identified using genomic probes were PCR verified using microsatellite specific primers. Conclusion Identification of genes and genomic regions of interest is greatly aided by the availability of the CHORI-214 Atlantic salmon BAC library. We have demonstrated the library's ability to identify specific genes and genetic markers using hybridization, PCR and fingerprinting experiments. In addition, multiple fingerprinting contigs indicated a pseudo-tetraploidity of the Atlantic salmon genome. The highly redundant CHORI-214 BAC library is expected to be an important resource for mapping and sequencing of the Atlantic salmon genome. |
format |
Article in Journal/Newspaper |
author |
Thorsen, Jim Zhu, Baoli Frengen, Eirik Osoegawa, Kazutoyo de Jong, Pieter J Koop, Ben F Davidson, William S Høyheim, Bjørn |
spellingShingle |
Thorsen, Jim Zhu, Baoli Frengen, Eirik Osoegawa, Kazutoyo de Jong, Pieter J Koop, Ben F Davidson, William S Høyheim, Bjørn A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects |
author_facet |
Thorsen, Jim Zhu, Baoli Frengen, Eirik Osoegawa, Kazutoyo de Jong, Pieter J Koop, Ben F Davidson, William S Høyheim, Bjørn |
author_sort |
Thorsen, Jim |
title |
A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects |
title_short |
A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects |
title_full |
A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects |
title_fullStr |
A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects |
title_full_unstemmed |
A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects |
title_sort |
highly redundant bac library of atlantic salmon (salmo salar): an important tool for salmon projects |
publishDate |
2005 |
url |
http://hdl.handle.net/10852/46593 http://urn.nb.no/URN:NBN:no-50774 https://doi.org/10.1186/1471-2164-6-50 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
http://urn.nb.no/URN:NBN:no-50774 BMC Genomics. 2005 Apr 04;6(1):50 http://hdl.handle.net/10852/46593 http://dx.doi.org/10.1186/1471-2164-6-50 URN:NBN:no-50774 Fulltext https://www.duo.uio.no/bitstream/handle/10852/46593/1/12864_2004_Article_251.pdf |
op_rights |
Thorsen et al. Attribution 2.0 Generic http://creativecommons.org/licenses/by/2.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1186/1471-2164-6-50 |
container_title |
BMC Genomics |
container_volume |
6 |
container_issue |
1 |
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1766360469683044352 |