Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males
Whereas detection and positioning of genes that affect quantitative traits (quantitative trait loci (QTL)) using linkage mapping uses only information from recombinants in the genotyped generations, linkage disequilibrium (LD) mapping uses historical recombinants. Thus, whereas linkage mapping requi...
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ftunivqespace:oai:espace.library.uq.edu.au:UQ:398749 2023-05-15T15:31:52+02:00 Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males Hayes, B. J. Gjuvsland, A. Omholt, S. 2006-07-03 https://espace.library.uq.edu.au/view/UQ:398749 eng eng Nature Publishing Group doi:10.1038/sj.hdy.6800827 issn:0018-067X issn:1365-2540 orcid:0000-0002-5606-3970 Commercial salmon populations Linkage disequilibrium mapping QTL 1100 Agricultural and Biological Sciences 1311 Genetics 2716 Genetics (clinical) Journal Article 2006 ftunivqespace https://doi.org/10.1038/sj.hdy.6800827 2020-08-18T02:46:27Z Whereas detection and positioning of genes that affect quantitative traits (quantitative trait loci (QTL)) using linkage mapping uses only information from recombinants in the genotyped generations, linkage disequilibrium (LD) mapping uses historical recombinants. Thus, whereas linkage mapping requires large family sizes to detect and accurately position QTL, LD mapping is more dependant on the number of families sampled from the population. In commercial Atlantic salmon breeding programmes, only a small number of individuals per family are routinely phenotyped for traits such as disease resistance and meat colour. In this paper, we assess the power and accuracy of combined linkage disequilibrium linkage analysis (LDLA) to detect QTL in the commercial population using simulation. When 15 half-sib sire families (each sire mated to 30 dams, each dam with 10 progeny) were sampled from the population for genotyping, we were able to detect a QTL explaining 10% of the phenotypic variance in 85% of replicates and position this QTL within 3 cM of the true position in 70% of replicates. When recombination was absent in males, a feature of the salmon genome, power to detect QTL increased; however, the accuracy of positioning the QTL was decreased. By increasing the number of sire families sampled from the population to be genotyped to 30, we were able to increase both the proportion of QTL detected and correctly positioned (even with no recombination in males). QTL with much smaller effect could also be detected. The results suggest that even with the existing recording structure in commercial salmon breeding programmes, there is considerable power to detect and accurately position QTL using LDLA. Article in Journal/Newspaper Atlantic salmon The University of Queensland: UQ eSpace Heredity 97 1 19 26 |
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The University of Queensland: UQ eSpace |
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ftunivqespace |
language |
English |
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Commercial salmon populations Linkage disequilibrium mapping QTL 1100 Agricultural and Biological Sciences 1311 Genetics 2716 Genetics (clinical) |
spellingShingle |
Commercial salmon populations Linkage disequilibrium mapping QTL 1100 Agricultural and Biological Sciences 1311 Genetics 2716 Genetics (clinical) Hayes, B. J. Gjuvsland, A. Omholt, S. Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males |
topic_facet |
Commercial salmon populations Linkage disequilibrium mapping QTL 1100 Agricultural and Biological Sciences 1311 Genetics 2716 Genetics (clinical) |
description |
Whereas detection and positioning of genes that affect quantitative traits (quantitative trait loci (QTL)) using linkage mapping uses only information from recombinants in the genotyped generations, linkage disequilibrium (LD) mapping uses historical recombinants. Thus, whereas linkage mapping requires large family sizes to detect and accurately position QTL, LD mapping is more dependant on the number of families sampled from the population. In commercial Atlantic salmon breeding programmes, only a small number of individuals per family are routinely phenotyped for traits such as disease resistance and meat colour. In this paper, we assess the power and accuracy of combined linkage disequilibrium linkage analysis (LDLA) to detect QTL in the commercial population using simulation. When 15 half-sib sire families (each sire mated to 30 dams, each dam with 10 progeny) were sampled from the population for genotyping, we were able to detect a QTL explaining 10% of the phenotypic variance in 85% of replicates and position this QTL within 3 cM of the true position in 70% of replicates. When recombination was absent in males, a feature of the salmon genome, power to detect QTL increased; however, the accuracy of positioning the QTL was decreased. By increasing the number of sire families sampled from the population to be genotyped to 30, we were able to increase both the proportion of QTL detected and correctly positioned (even with no recombination in males). QTL with much smaller effect could also be detected. The results suggest that even with the existing recording structure in commercial salmon breeding programmes, there is considerable power to detect and accurately position QTL using LDLA. |
format |
Article in Journal/Newspaper |
author |
Hayes, B. J. Gjuvsland, A. Omholt, S. |
author_facet |
Hayes, B. J. Gjuvsland, A. Omholt, S. |
author_sort |
Hayes, B. J. |
title |
Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males |
title_short |
Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males |
title_full |
Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males |
title_fullStr |
Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males |
title_full_unstemmed |
Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males |
title_sort |
power of qtl mapping experiments in commercial atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males |
publisher |
Nature Publishing Group |
publishDate |
2006 |
url |
https://espace.library.uq.edu.au/view/UQ:398749 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
doi:10.1038/sj.hdy.6800827 issn:0018-067X issn:1365-2540 orcid:0000-0002-5606-3970 |
op_doi |
https://doi.org/10.1038/sj.hdy.6800827 |
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Heredity |
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97 |
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1 |
container_start_page |
19 |
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26 |
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1766362379105337344 |