Manual of 3FunMap 1.0

3FunMap is a windows software that can be used to construct genetic linkage maps and perform functional QTL mapping with molecular markers generated in a full-sib family. For linkage analysis, the software utilizes seven segregation types of markers to estimate the recombination and simultaneously predict the linkage phase between any two markers. After two-point linkage analysis, markers are classified into linkage groups according to the threshold of recombination fraction or LOD score. It takes heuristic search method for ordering large number of markers of a linkage group by incorporating a local ordering method. Multi-locus linkage phases for the optimal order of each linkage group are predicted based on three-point linkage analysis. For functional QTL mapping, the algorithm is based on interval mapping method, and the growth trajectory is described by Legendre polynomial. The QTL segregation patterns are considered to be sorted into three types, full cross (segregating 1:1:1:1), F2 cross (segregating 1:2:1), and test cross (segregating 1:1). The model selection criteria of AIC and BIC are applied not only to determine the order of Legendre polynomial, but also to discriminate the QTL segregation pattern. A maximum likelihood approach implemented with EM algorithm provides the estimates of QTL positions and model parameters responsible for growth trajectories. 3FunMap uses the free software, gnuplot, to plot likelihood ratio (LR) profiles along the whole genome and the Legendre polynomial curves for each QTL genotype. In practical QTL mapping, the threshold of LR for each QTL model can be obtained through permutations.