Use of sequence data from rainbow trout and Atlantic Blackwell Publishing, Ltd. salmon for SNP detection in Pacific salmon
Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecolo...
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ftciteseerx:oai:CiteSeerX.psu:10.1.1.327.1436 2023-05-15T18:09:58+02:00 Use of sequence data from rainbow trout and Atlantic Blackwell Publishing, Ltd. salmon for SNP detection in Pacific salmon Christian T. Smith Carita M. Elfstrom Lisa W. Seeb James E. Seeb The Pennsylvania State University CiteSeerX Archives 2005 application/pdf http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.327.1436 http://doc.nprb.org/web/publication/project_0205-0303_seeb_mol_ecol_2005.pdf en eng http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.327.1436 http://doc.nprb.org/web/publication/project_0205-0303_seeb_mol_ecol_2005.pdf Metadata may be used without restrictions as long as the oai identifier remains attached to it. http://doc.nprb.org/web/publication/project_0205-0303_seeb_mol_ecol_2005.pdf 5′-nuclease reaction chinook salmon chum salmon Oncorhynchus SNP sockeye salmon text 2005 ftciteseerx 2016-09-04T00:31:41Z Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large-scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus-only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing ∼89 kb we observed a frequency of 4.30 × 10 −3 SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high-throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application. Text Salmo salar Unknown Keta ENVELOPE(-19.455,-19.455,65.656,65.656) Pacific Sockeye ENVELOPE(-130.143,-130.143,54.160,54.160) |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
ftciteseerx |
language |
English |
topic |
5′-nuclease reaction chinook salmon chum salmon Oncorhynchus SNP sockeye salmon |
spellingShingle |
5′-nuclease reaction chinook salmon chum salmon Oncorhynchus SNP sockeye salmon Christian T. Smith Carita M. Elfstrom Lisa W. Seeb James E. Seeb Use of sequence data from rainbow trout and Atlantic Blackwell Publishing, Ltd. salmon for SNP detection in Pacific salmon |
topic_facet |
5′-nuclease reaction chinook salmon chum salmon Oncorhynchus SNP sockeye salmon |
description |
Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large-scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus-only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing ∼89 kb we observed a frequency of 4.30 × 10 −3 SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high-throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application. |
author2 |
The Pennsylvania State University CiteSeerX Archives |
format |
Text |
author |
Christian T. Smith Carita M. Elfstrom Lisa W. Seeb James E. Seeb |
author_facet |
Christian T. Smith Carita M. Elfstrom Lisa W. Seeb James E. Seeb |
author_sort |
Christian T. Smith |
title |
Use of sequence data from rainbow trout and Atlantic Blackwell Publishing, Ltd. salmon for SNP detection in Pacific salmon |
title_short |
Use of sequence data from rainbow trout and Atlantic Blackwell Publishing, Ltd. salmon for SNP detection in Pacific salmon |
title_full |
Use of sequence data from rainbow trout and Atlantic Blackwell Publishing, Ltd. salmon for SNP detection in Pacific salmon |
title_fullStr |
Use of sequence data from rainbow trout and Atlantic Blackwell Publishing, Ltd. salmon for SNP detection in Pacific salmon |
title_full_unstemmed |
Use of sequence data from rainbow trout and Atlantic Blackwell Publishing, Ltd. salmon for SNP detection in Pacific salmon |
title_sort |
use of sequence data from rainbow trout and atlantic blackwell publishing, ltd. salmon for snp detection in pacific salmon |
publishDate |
2005 |
url |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.327.1436 http://doc.nprb.org/web/publication/project_0205-0303_seeb_mol_ecol_2005.pdf |
long_lat |
ENVELOPE(-19.455,-19.455,65.656,65.656) ENVELOPE(-130.143,-130.143,54.160,54.160) |
geographic |
Keta Pacific Sockeye |
geographic_facet |
Keta Pacific Sockeye |
genre |
Salmo salar |
genre_facet |
Salmo salar |
op_source |
http://doc.nprb.org/web/publication/project_0205-0303_seeb_mol_ecol_2005.pdf |
op_relation |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.327.1436 http://doc.nprb.org/web/publication/project_0205-0303_seeb_mol_ecol_2005.pdf |
op_rights |
Metadata may be used without restrictions as long as the oai identifier remains attached to it. |
_version_ |
1766182685697376256 |