An 11 cM region with 6 to 38 segregating SNPs and a central QTL was simulated. After 100 generations of mating with effective population sizes (Ne) of 50, 100 or 200, marker genotypes and phenotypes were generated on 200, 500 or 1000 individuals with effects of the biallelic QTL set to explain 2 or 5% of phenotypic variance. Phenotypes were regressed on genotypes or haplotypes for 1, 2, or 4 linked markers. Power increased with sample size, marker density and QTL effect, decreased with Ne, and was similar between methods. Sample size had a greater effect on power than density. For significant replicates, precision of position increased with sample size, density, and QTL effect, but was little affected by Ne. Single marker regression had similar or better precision than other models. Thus, with adequate sample size, QTL can be detected and mapped by regression on SNP genotypes without recovering haplotypes.

H. H Zhao, Jack CM Dekkers, Rohan L Fernando

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 21.20, 2006
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