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Precision of estimated QTL positions in granddaughter designs using combined haplotype sharing TDT and linkage analysis |
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| Authors: | Davood Kolbehdari Gerald B Jansen Ian McMillan LR Schaeffer |
| Institution: | aCenter for Genetic Improvement of Livestock, Department of Animal and Poultry, Science, University of Guelph, Guelph, Ontario, Canada N1G 2W1 bDepartment of Animal Science, Abureihan Higher Education Complex, University of Tehran, Iran c87 Terraview CR., Guelph, Ontario, Canada N1G 5E9 dDekoppel Consulting, Guelph, Ontario, Canada N1G 2Y8 |
| Abstract: | The aim of this study was to develop the linear haplotype sharing transmission disequilibrium test (LHS-TDT) method and combine this method with the simple regression method to estimate the precision of QTL positions in granddaughter designs. This precision was determined by Monte Carlo simulation in granddaughter designs. A single bi-allelic QTL at the midpoint of a linkage group and 26 markers with 1 cM intervals and with two alleles each were simulated. Three linear models, (i.e. the simple regression model, the linear haplotype sharing TDT method and the combination of these two models) were compared. The mean of absolute differences (A) between the estimated and true QTL position of each method was considered for six different scenarios consisting of combinations of a number of markers and the most frequent haplotypes. The mean of A, using the simple regression method, was 4.38 centimorgan (cM). The means of A using the LHS-TDT method were less than the simple regression method in all scenarios and ranged from 1.86 to 3.82 cM depending on the scenario. The mean of A using the combined method was more than the LHS-TDT method and less than the simple regression method. The means of A using the combined method ranged from 2.32 to 4.36 cM. Therefore, for populations similar to those population simulated in this study, the LHS-TDT was better than the simple regression method and the combined method for precision of estimated QTL position in granddaughter designs. |
| Keywords: | Quantitative trait loci (QTL) Haplotype sharing transmission disequilibrium test (HS-TDT) Granddaughter designs |
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