Abstract
General pedigrees are very common in farm animals, and the recent availability of large panels of SNPs in domestic species has given new momentum to the search for the mutations underlying variation in quantitative traits. In this paper, we proposed a new transmission disequilibrium test approach, called the pedigree transmission disequilibrium test, which deals with general pedigrees and quantitative traits in farm animals. Compared with the existing pedigree disequilibrium test (PDT) and general linear model-based method QTDT, our approach performed better with higher power and lower type I error, especially in scenarios where the quantitative trait locus (QTL) effect was small. We also investigated the application of our approach in selective genotyping design. Our simulation studies indicated that it was plausible to implement a selective genotyping strategy in the proposed pedigree transmission disequilibrium test. We found that our approach performed equally well or better when only some proportion of the individuals in the two tails were genotyped compared with its performance when all the individuals in the pedigree were genotyped.
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