Fine-mapping quantitative trait loci with a medium density marker panel: efficiency of population structures and comparison of linkage disequilibrium linkage analysis models
2012
Roldan, Dana, D. | Gilbert, Hélène | Henshall, J.M. | Legarra, Andres | Elsen, Jean Michel, J. M. | Station d'Amélioration Génétique des Animaux (SAGA) ; Institut National de la Recherche Agronomique (INRA) | Instituto Nacional de Tecnología Agropecuaria (INTA) | Laboratoire de Génétique Cellulaire (LGC) ; Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT) | Livestock Industries
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Mostrar más [+] Menos [-]Inglés. Recently, a Haley–Knott-type regression method using combined linkage disequilibrium and linkage analyses (LDLA) was proposed to map quantitative trait loci (QTLs). Chromosome of 5 and 25 cM with 0.25 and 0.05 cM, respectively, between markers were simulated. The differences between the LDLA approaches with regard to QTL position accuracy were very limited, with a significantly better mean square error (MSE) with the LDLA regression (LDLA_reg) in sparse map cases ; the contrary was observed, but not significantly, in dense map situations. The computing time required for the LDLA variance components (LDLA_vc) model was much higher than the LDLA_reg model. The precision of QTL position estimation was compared for four numbers of half-sib families, four different family sizes and two experimental designs (half-sibs, and full- and half-sibs). Regarding the number of families, MSE values were lowest for 15 or 50 half-sib families, differences not being significant. We observed that the greater the number of progenies per sire, the more accurate the QTL position. However, for a fixed population size, reducing the number of families (e.g. using a small number of large full-sibfamilies) could lead to less accuracy of estimated QTL position.
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