the efficiency of designs for fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage设计的精细定位的效率使用数量性状连锁不平衡和联系.pdf

Genet. Sel. Evol. 36 (2004) 145–161 145 c INRA, EDP Sciences, 2004 DOI: 10.1051/gse:2003056 Original article The efficiency of designs for fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage ∗ Sang Hong L , Julius H.J. van der W School of Rural Science and Agriculture, University of New England, Armidale, NSW 2351, Australia (Received 19 March 2003; accepted 1 October 2003) 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 es- timate 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 × 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 po- sition 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 generat