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.
Highlights
Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
We carried out a series of simulation studies to evaluate the performance of the proposed QPTDT approach, 100 replicates were simulated in each simulation scenario
When the quantitative trait locus (QTL) effect was small, the power of QPTDT with mixed family selection was over 10% higher than with full-sib family selection
Summary
Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. 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. A classical family-based association test, the transmission disequilibrium test (TDT), was first proposed by Spielman et al [2], for disease traits in studies of nuclear families with one affected offspring and two parents. Larger pedigrees include more information on population substructure than nuclear families, and a test using larger pedigrees can use all potentially informative data, including related nuclear families and discordant sibs On this basis, Martin et al [6], proposed the pedigree disequilibrium test (PDT) approach to deal with. Ding X D, et al Chin Sci Bull July (2012) Vol. No.21 general pedigrees, but, until now, it has only been applied to dichotomous traits
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