Development of type I genetic markers from expressed sequence tags in highly polymorphic species
Expressed sequence tag (EST) databases provide a primary source of nuclear DNA sequences for genetic marker development in non-model organisms. To date, the process has been relatively inefficient for several reasons: - 1) priming site polymorphism in the template leads to inferior or erratic amplif...
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ftqueensland:oai:eprints.qut.edu.au:92882 2024-02-04T09:59:53+01:00 Development of type I genetic markers from expressed sequence tags in highly polymorphic species Kim, Woo-Jin Jung, Hyungtaek Gaffney, Patrick 2011 https://eprints.qut.edu.au/92882/ unknown Springer New York doi:10.1007/s10126-010-9280-4 Kim, Woo-Jin, Jung, Hyungtaek, & Gaffney, Patrick (2011) Development of type I genetic markers from expressed sequence tags in highly polymorphic species. Marine Biotechnology, 13(2), pp. 127-132. https://eprints.qut.edu.au/92882/ Institute for Future Environments; Science & Engineering Faculty; Centre for Tropical Crops and Biocommodities Consult author(s) regarding copyright matters This work is covered by copyright. Unless the document is being made available under a Creative Commons Licence, you must assume that re-use is limited to personal use and that permission from the copyright owner must be obtained for all other uses. If the document is available under a Creative Commons License (or other specified license) then refer to the Licence for details of permitted re-use. It is a condition of access that users recognise and abide by the legal requirements associated with these rights. If you believe that this work infringes copyright please provide details by email to qut.copyright@qut.edu.au Marine Biotechnology EST Indel Marker SNP UTR Contribution to Journal 2011 ftqueensland https://doi.org/10.1007/s10126-010-9280-4 2024-01-08T23:37:23Z Expressed sequence tag (EST) databases provide a primary source of nuclear DNA sequences for genetic marker development in non-model organisms. To date, the process has been relatively inefficient for several reasons: - 1) priming site polymorphism in the template leads to inferior or erratic amplification; - 2) introns in the target amplicon are too large and/or numerous to allow effective amplification under standard screening conditions, and; - 3) at least occasionally, a PCR primer straddles an exon–intron junction and is unable to bind to genomic DNA template. The first is only a minor issue for species or strains with low heterozygosity but becomes a significant problem for species with high genomic variation, such as marine organisms with extremely large effective population sizes. Problems arising from unanticipated introns are unavoidable but are most pronounced in intron-rich species, such as vertebrates and lophotrochozoans. We present an approach to marker development in the Pacific oyster Crassostrea gigas, a highly polymorphic and intron-rich species, which minimizes these problems, and should be applicable to other non-model species for which EST databases are available. Placement of PCR primers in the 3′ end of coding sequence and 3′ UTR improved PCR success rate from 51% to 97%. Almost all (37 of 39) markers developed for the Pacific oyster were polymorphic in a small test panel of wild and domesticated oysters. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Queensland University of Technology: QUT ePrints Pacific Indel’ ENVELOPE(35.282,35.282,66.963,66.963) Marine Biotechnology 13 2 127 132 |
institution |
Open Polar |
collection |
Queensland University of Technology: QUT ePrints |
op_collection_id |
ftqueensland |
language |
unknown |
topic |
EST Indel Marker SNP UTR |
spellingShingle |
EST Indel Marker SNP UTR Kim, Woo-Jin Jung, Hyungtaek Gaffney, Patrick Development of type I genetic markers from expressed sequence tags in highly polymorphic species |
topic_facet |
EST Indel Marker SNP UTR |
description |
Expressed sequence tag (EST) databases provide a primary source of nuclear DNA sequences for genetic marker development in non-model organisms. To date, the process has been relatively inefficient for several reasons: - 1) priming site polymorphism in the template leads to inferior or erratic amplification; - 2) introns in the target amplicon are too large and/or numerous to allow effective amplification under standard screening conditions, and; - 3) at least occasionally, a PCR primer straddles an exon–intron junction and is unable to bind to genomic DNA template. The first is only a minor issue for species or strains with low heterozygosity but becomes a significant problem for species with high genomic variation, such as marine organisms with extremely large effective population sizes. Problems arising from unanticipated introns are unavoidable but are most pronounced in intron-rich species, such as vertebrates and lophotrochozoans. We present an approach to marker development in the Pacific oyster Crassostrea gigas, a highly polymorphic and intron-rich species, which minimizes these problems, and should be applicable to other non-model species for which EST databases are available. Placement of PCR primers in the 3′ end of coding sequence and 3′ UTR improved PCR success rate from 51% to 97%. Almost all (37 of 39) markers developed for the Pacific oyster were polymorphic in a small test panel of wild and domesticated oysters. |
format |
Article in Journal/Newspaper |
author |
Kim, Woo-Jin Jung, Hyungtaek Gaffney, Patrick |
author_facet |
Kim, Woo-Jin Jung, Hyungtaek Gaffney, Patrick |
author_sort |
Kim, Woo-Jin |
title |
Development of type I genetic markers from expressed sequence tags in highly polymorphic species |
title_short |
Development of type I genetic markers from expressed sequence tags in highly polymorphic species |
title_full |
Development of type I genetic markers from expressed sequence tags in highly polymorphic species |
title_fullStr |
Development of type I genetic markers from expressed sequence tags in highly polymorphic species |
title_full_unstemmed |
Development of type I genetic markers from expressed sequence tags in highly polymorphic species |
title_sort |
development of type i genetic markers from expressed sequence tags in highly polymorphic species |
publisher |
Springer New York |
publishDate |
2011 |
url |
https://eprints.qut.edu.au/92882/ |
long_lat |
ENVELOPE(35.282,35.282,66.963,66.963) |
geographic |
Pacific Indel’ |
geographic_facet |
Pacific Indel’ |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Marine Biotechnology |
op_relation |
doi:10.1007/s10126-010-9280-4 Kim, Woo-Jin, Jung, Hyungtaek, & Gaffney, Patrick (2011) Development of type I genetic markers from expressed sequence tags in highly polymorphic species. Marine Biotechnology, 13(2), pp. 127-132. https://eprints.qut.edu.au/92882/ Institute for Future Environments; Science & Engineering Faculty; Centre for Tropical Crops and Biocommodities |
op_rights |
Consult author(s) regarding copyright matters This work is covered by copyright. Unless the document is being made available under a Creative Commons Licence, you must assume that re-use is limited to personal use and that permission from the copyright owner must be obtained for all other uses. If the document is available under a Creative Commons License (or other specified license) then refer to the Licence for details of permitted re-use. It is a condition of access that users recognise and abide by the legal requirements associated with these rights. If you believe that this work infringes copyright please provide details by email to qut.copyright@qut.edu.au |
op_doi |
https://doi.org/10.1007/s10126-010-9280-4 |
container_title |
Marine Biotechnology |
container_volume |
13 |
container_issue |
2 |
container_start_page |
127 |
op_container_end_page |
132 |
_version_ |
1789964922837270528 |