Please use this identifier to cite or link to this item:
https://hdl.handle.net/1959.11/752
Title: | Efficient designs for fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage | Contributor(s): | Lee, Sang Hong (author); Van Der Werf, JH (author) | Publication Date: | 2004 | Open Access: | Yes | DOI: | 10.1051/gse:2003056 | Handle Link: | https://hdl.handle.net/1959.11/752 | Abstract: | In a simulation study, different designs were compared for efficiency of fine-mapping of QTL. The variance component method for fine-mapping of QTL was used to estimate QTL position and variance components. The design of many families with small size gave a higher mapping resolution than a design with few families of large size. However, the difference is small in half sib designs. The proportion of replicates with the QTL positioned within 3 cM of the true position is 0.71 in the best design, and 0.68 in the worst design applied to 128 animals with a phenotypic record and a QTL explaining 25% of the phenotypic variance. The design of two half sib families each of size 64 was further investigated for a hypothetical population with effective size of 1000 simulated for 6000 generations with a marker density of 0.25 cM and with marker mutation rate 4 x 10-4 per generation.In mapping using bi-allelic markers, 42~55% of replicated simulations could position QTL within 0.75 cM of the true position whereas this was higher for multi allelic markers (48~76%). The accuracy was lowest (48%) when mutation age was 100 generations and increased to 68% and 76% for mutation ages of 200 and 500 generations, respectively, after which it was about 70% for mutation ages of 1000 generations and older. When effective size was linearly decreasing in the last 50 generations, the accuracy was decreased (56 to 70%). We show that half sib designs that have often been used for linkage mapping can have sufficient information for fine-mapping of QTL. It is suggested that the same design with the same animals for linkage mapping should be used for fine-mapping so gene mapping can be cost effective in livestock populations. | Publication Type: | Journal Article | Source of Publication: | Genetics Selection Evolution, 36(2), p. 145-161 | Publisher: | BioMed Central Ltd | Place of Publication: | United Kingdom | ISSN: | 1297-9686 0999-193X |
Fields of Research (FoR) 2008: | 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics) | Peer Reviewed: | Yes | HERDC Category Description: | C1 Refereed Article in a Scholarly Journal |
---|---|
Appears in Collections: | Journal Article |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
open/SOURCE02.pdf | Publisher version (open access) | 216.08 kB | Adobe PDF Download Adobe | View/Open |
Items in Research UNE are protected by copyright, with all rights reserved, unless otherwise indicated.