Functional Mapping Of Quantitative Trait Loci In A Full-sib Family In Forest Trees

Functional mapping of quantitative trait loci (QTL) has embedded the biological mechanisms and processes of dynamic traits in the statistical method of QTL mapping. Although the functional mapping statistical model for mapping QTL has been well developed in inbred lines, it has not been proposed in outbred species, e.g. a full-sib family, in which the number of alleles may vary over loci and the linkage phases are usually unknown between loci. Since forest trees have several unique biological characteristics and most of them are outbred species, we should not directly apply the functional mapping model for inbred species to them.The objective of this study is to develop a functional mapping statistical model for a full-sib family in forest trees. We suppose that the QTL genotype of one parent is heterozygous but the other is homozygous, and consider all pairwise combinations of marker segregation types and all possible linkage phases between mark loci in a diploid full-sib family into our model. A maximum likelihood approach based on a logistic-mixture model, implemented with EM algorithm, was developed to provide the estimates of QTL positions, QTL effects, and other model parameters responsible for growth trajectories.According to the results of a large number of simulations, we can infer that the estimation precision of the QTL effects and position is dependent on dimensions of measured variable, sample size and heritability. Even though when the dimension of measured variable, heritability and sample size are all smaller, the mean of the estimation of QTL location and each effective parameters approximates to the true value very closely and all the SMSEs of MLEs are also smaller, increased one of the factors (i.e. dimensions of measured variable, sample size and heritability) can decrease the SMSEs of MLEs of partial or all parameters obviously. All that indicate our model was robust for identifying the QTL position and estimating the parameters of QTL effects and residual (co)variance.We use an example of poplar to demonstrate the validation of our functional mapping method for mapping QTL affecting growth trajectories in practice. The high-density genetic linkage map has been constructed with a mix of marker systems. Functional mapping identified two QTL affecting MRL (maximal root length) on the linkage 3 and one QTL affecting TNR (total root number per cutting) on the linkage 8.We have developed Windows software, FsQtlFunMap 1.0, which was written in Visual C++ 6.0 to implement our functional mapping method for a full-sib family. FsQtlFunMap 1.0, which was used to map QTL in a full-sib family in forest trees, can do QTL statistical analysis and draw relevant figures. It has the remarkable advantage of speed for calculating.