title: Fine-mapping quantitative trait loci with a medium density marker panel: efficiency of population structures and comparison of linkage disequilibrium linkage analysis models.
abstract: 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-sib families) could lead to less accuracy of estimated QTL position.
authors.affiliation: Instituto de Genética CICVyA-INTA Castelar, cc 1712, Buenos Aires, Argentina. droldan@cnia.inta.gov.ar
authors.forename: Dana L
authors.initials: DL
authors.lastname: Roldan
authors.forename: Hélène
authors.initials: H
authors.lastname: Gilbert
authors.forename: John M
authors.initials: JM
authors.lastname: Henshall
authors.forename: Andrés
authors.initials: A
authors.lastname: Legarra
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Elsen
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D005190:Family; D008040:Genetic Linkage; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D011156:Population Density; D040641:Quantitative Trait Loci / Q000235:genetics*