With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F1 population. However, based on such genetic maps, quantitative trait loci (QTL) mapping cannot be directly conducted with traditional statistical methods or tools because the linkage phase and segregation pattern of molecular markers are not always fixed as in inbred lines. We implemented the traditional composite interval mapping (CIM) method to multivariate trait data in forest trees and developed the corresponding software, mvqtlcim. Our method not only incorporated the various segregations and linkage phases of molecular markers, but also applied Takeuchi’s information criterion (TIC) to discriminate the QTL segregation type among several possible alternatives. QTL mapping was performed in a hybrid F1 population of Populus deltoides and P. simonii, and 12 QTLs were detected for tree height over 6 time points. The software package allowed many options for parameters as well as parallel computing for permutation tests. The features of the software were demonstrated with the real data analysis and a large number of Monte Carlo simulations. We provided a powerful tool for QTL mapping of multiple or longitudinal traits in an outbred F1 population, in which the traditional software for QTL mapping cannot be used. This tool will facilitate studying of QTL mapping and thus will accelerate molecular breeding programs especially in forest trees. The tool package is freely available from https://github.com/tongchf /mvqtlcim.

MOTIVATION: Functional mapping that embeds the developmental mechanisms of complex traits shows great power to study the dynamic pattern of genetic effects triggered by individual quantitative trait loci (QTLs). A full-sib family, produced by crossing two heterozygous parents, is characteristic of uncertainties about cross-type at a locus and linkage phase between different loci. Integrating functional mapping into a full-sib family requires a model selection procedure capable of addressing these uncertainties. 3FunMap, written in VC++ 6.0, provides a flexible and extensible platform to perform full-sib functional mapping of dynamic traits. Functions in the package encompass linkage phase determination, marker map construction and the pattern identification of QTL segregation, dynamic tests of QTL effects, permutation tests and numerical simulation. We demonstrate the features of 3FunMap through real data analysis and computer simulation. AVAILABILITY: http://statgen.psu.edu/software.