onemap-package: Software for constructing genetic maps in outcrossing species

Description

Implements the methodology proposed by Wu et al. (2002), which uses the maximum likelihood approach to estimate linkage and linkage phases for a mixed set of different marker types containing various segregation patterns. The software was developed to construct genetic maps using full-sib families derived from two outbred parent plants, such as done for example by Garcia et al. (2006) and Oliveira et al. (2007).

Arguments

Details

ll{ Package: onemap Type: Package Version: 0.1-0 Date: 2007-09-25 License: GNU GENERAL PUBLIC LICENSE (Version 2 or higher) } Usage of onemap is completely described in a tutorial distributed with the package. You can look for it in directory /doc of the package distribution.

The most important functions are:

read.outcrossfor data importing.
est.rf.2ptsto perform two-point analyses between all pairs of markers.
modify.rf.2ptsto update two-point analyses with different criteria.
arbitr.rf.2ptsto arbitrarily (ad hoc) define the most probable linkage phase between two markers.
mrktypeto check the segregation type of a marker.
groupto assign markers to linkage groups.
extract.grouptoextracta linkage group for further analysis.
remove.markerto drop a marker from a linkage group.
mapto estimate the genetic map (marker order and distances) for a given linkage group.
make.mapto arbitrarily define a genetic map.
est.rf.3ptsto refine a genetic map using three-point analyses for a triplet of markers.

References

Basten, C. J., Weir, B. S. and Zeng, Z.-B. (2005) QTL Cartographer Version 1.17: A Reference Manual and Tutorial for QTL Mapping. Doerge, R. W. (1996) Constructing genetic maps by rapid chain delineation. Journal of Quantitative Trait Loci 2: 121-132. Garcia, A. A. F., Kido, E. A., Meza, A. N., Souza, H. M. B., Pinto, L. R., Pastina, M. M., Leite, C. S., Silva, J. A. G., Ulian, E. C., Figueira, A. V. O. and Souza, A. P. (2006) Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases. Theoretical and Applied Genetics 112: 298-314. Haldane, J. B. S. (1919) The combination of linkage values and the calculation of distance between the loci of linked factors. Journal of Genetics 8: 299-309. Kosambi, D. D. (1944) The estimation of map distance from recombination values. Annuaire of Eugenetics 12: 172-175. Lincoln, S. E., Daly, M. J. and Lander, E. S. (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical Research Technical Report. Margarido, G. R. A., Souza, A.P. and Garcia, A. A. F. (2007) OneMap: software for genetic mapping in outcrossing species. Hereditas 144: 78-79. Oliveira, K. M., Pinto, L. R., Marconi, T. G., Margarido, G. R. A., Pastina, M. M., Teixeira, L. H. M., Figueira, A. V. O., Ulian, E. C., Garcia, A. A. F. and Souza, A. P. (2007) Functional genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross. Molecular Breeding 20: 189-208. Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.