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. and Omholt, S. (2006) Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males. Heredity, 97 1: 19-26. doi:10.1038/sj.hdy.6800827


Author Hayes, B. J.
Gjuvsland, A.
Omholt, S.
Title Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males
Journal name Heredity   Check publisher's open access policy
ISSN 0018-067X
1365-2540
Publication date 2006-07-03
Sub-type Article (original research)
DOI 10.1038/sj.hdy.6800827
Open Access Status Not yet assessed
Volume 97
Issue 1
Start page 19
End page 26
Total pages 8
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Language eng
Abstract 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.
Keyword Commercial salmon populations
Linkage disequilibrium mapping
QTL
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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