A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon
Abstract A multistage testing strategy to detect QTL for resistance to infectious salmon anemia (ISA) in Atlantic salmon is proposed. First, genotyping of amplified fragment length polymorphisms (AFLP) and a transmission disequilibrium test (TDT) were carried out using dead offspring from a disease...
Published in: | Genetics |
---|---|
Main Authors: | , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Oxford University Press (OUP)
2004
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1534/genetics.103.013227 https://academic.oup.com/genetics/article-pdf/167/2/851/42059226/genetics0851.pdf |
id |
croxfordunivpr:10.1534/genetics.103.013227 |
---|---|
record_format |
openpolar |
spelling |
croxfordunivpr:10.1534/genetics.103.013227 2023-12-31T10:04:42+01:00 A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon Moen, Thomas Fjalestad, Kjersti T Munck, Hege Gomez-Raya, Luis 2004 http://dx.doi.org/10.1534/genetics.103.013227 https://academic.oup.com/genetics/article-pdf/167/2/851/42059226/genetics0851.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model Genetics volume 167, issue 2, page 851-858 ISSN 1943-2631 Genetics journal-article 2004 croxfordunivpr https://doi.org/10.1534/genetics.103.013227 2023-12-06T08:45:34Z Abstract A multistage testing strategy to detect QTL for resistance to infectious salmon anemia (ISA) in Atlantic salmon is proposed. First, genotyping of amplified fragment length polymorphisms (AFLP) and a transmission disequilibrium test (TDT) were carried out using dead offspring from a disease resistance challenge test. Second, AFLP genotyping among survivors followed by a Mendelian segregation test was performed. Third, within-family survival analyses using all offspring were developed and applied to significant TDT markers with Mendelian inheritance. Maximum-likelihood methodology was developed for TDT with dominant markers to exploit linkage disequilibrium within families. The strategy was tested with two full-sib families of Atlantic salmon sired by the same male and consisting of 79 offspring in total. All dead offspring from the two families were typed for 64 primer combinations, resulting in 340 scored markers. There were 26 significant results out of 401 TDTs using dead offspring. In the second stage, only 17 marker families showed Mendelian segregation and were tested in survival analysis. A permutation test was performed for all survival analyses to compute experimentwise P-values. Two markers, aaccac356 and agccta150, were significant at P < 0.05 when accounting for multiple testing in the survival analyses. The proposed strategy might be more powerful than current mapping strategies because it reduces the number of tests to be performed in the last testing stage. Article in Journal/Newspaper Atlantic salmon Oxford University Press (via Crossref) Genetics 167 2 851 858 |
institution |
Open Polar |
collection |
Oxford University Press (via Crossref) |
op_collection_id |
croxfordunivpr |
language |
English |
topic |
Genetics |
spellingShingle |
Genetics Moen, Thomas Fjalestad, Kjersti T Munck, Hege Gomez-Raya, Luis A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon |
topic_facet |
Genetics |
description |
Abstract A multistage testing strategy to detect QTL for resistance to infectious salmon anemia (ISA) in Atlantic salmon is proposed. First, genotyping of amplified fragment length polymorphisms (AFLP) and a transmission disequilibrium test (TDT) were carried out using dead offspring from a disease resistance challenge test. Second, AFLP genotyping among survivors followed by a Mendelian segregation test was performed. Third, within-family survival analyses using all offspring were developed and applied to significant TDT markers with Mendelian inheritance. Maximum-likelihood methodology was developed for TDT with dominant markers to exploit linkage disequilibrium within families. The strategy was tested with two full-sib families of Atlantic salmon sired by the same male and consisting of 79 offspring in total. All dead offspring from the two families were typed for 64 primer combinations, resulting in 340 scored markers. There were 26 significant results out of 401 TDTs using dead offspring. In the second stage, only 17 marker families showed Mendelian segregation and were tested in survival analysis. A permutation test was performed for all survival analyses to compute experimentwise P-values. Two markers, aaccac356 and agccta150, were significant at P < 0.05 when accounting for multiple testing in the survival analyses. The proposed strategy might be more powerful than current mapping strategies because it reduces the number of tests to be performed in the last testing stage. |
format |
Article in Journal/Newspaper |
author |
Moen, Thomas Fjalestad, Kjersti T Munck, Hege Gomez-Raya, Luis |
author_facet |
Moen, Thomas Fjalestad, Kjersti T Munck, Hege Gomez-Raya, Luis |
author_sort |
Moen, Thomas |
title |
A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon |
title_short |
A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon |
title_full |
A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon |
title_fullStr |
A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon |
title_full_unstemmed |
A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon |
title_sort |
multistage testing strategy for detection of quantitative trait loci affecting disease resistance in atlantic salmon |
publisher |
Oxford University Press (OUP) |
publishDate |
2004 |
url |
http://dx.doi.org/10.1534/genetics.103.013227 https://academic.oup.com/genetics/article-pdf/167/2/851/42059226/genetics0851.pdf |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Genetics volume 167, issue 2, page 851-858 ISSN 1943-2631 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1534/genetics.103.013227 |
container_title |
Genetics |
container_volume |
167 |
container_issue |
2 |
container_start_page |
851 |
op_container_end_page |
858 |
_version_ |
1786836020942077952 |