ArticleBMC proceedings2009
A strategy for QTL fine-mapping using a dense SNP map.
Article in BMC proceedings, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed, 3 citations in OpenAlex.
- Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping.BMC proceedings · 2009Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDense marker maps require efficient statistical methods for QTL fine mapping that work fast and efficiently with a large number of markers. In this study, the simulated dataset for the XIIth QTLMAS workshop was analyzed using a QTL fine mapping set of tools.
methodsThe QTL fine-mapping strategy was based on the use of statistical methods combining linkage and linkage disequilibrium analysis. Variance component based linkage analysis provided confidence intervals for the QTL. Within these regions, two additional analyses combining both linkage analysis and linkage disequilibrium information were applied. The first method estimated identity-by-descent probabilities among base haplotypes that were used to group them in different clusters. The second method constructed haplotype groups based on identity-by-state probabilities.
resultsTwo QTL explaining 9.4 and 3.3% of the genetic variance were found with high significance on chromosome 1 at positions 19.5 and 76.6 cM. On chromosome 2, two QTL were also detected at positions 26.0 and 53.2 explaining respectively 9.0 and 7.8 of total genetic variance. The QTL detected on chromosome 3 at position 11.9 cM (5% of variance) was less important. The QTL with the highest effect (37% of variance) was detected on chromosome 4 at position 3.1 cM and another QTL (13.6% of variance) was detected on chromosome 5 at position 93.9 cM.
conclusionThe proposed strategy for fine-mapping of QTL combining linkage and linkage disequilibrium analysis allowed detecting the most important QTL with an additive effect in a short period but it should be extended in the future in order to fine-map linked and epistatic QTL.
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Registered trials
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