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

Description

Implements the methodology proposed by Wu et al. (2002a), which uses the maximum likelihood approach to estimate linkage and linkage phases for a mixed set of different marker types containing various segregation patterns. Furthermore, implements the Hidden Markov Model- based approach for constructing multipoint maximum likelihood linkage maps (Wu et al. 2002b). 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), Oliveira et al. (2007) and Oliveira et al. (2008).

Arguments

Details

ll{ Package: onemap Type: Package Version: 1.0-0 Date: 2009-03-09 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.
rf.2ptsto perform two-point analyses between all pairs of markers.
marker.typeto check the segregation type of a marker.
make.seqto define a sequence of markers, which are the input of most mapping functions.
groupto assign markers to linkage groups.
compareto compare all possible orders of markers in a sequence.
try.seqto try a given marker in every position of a framework of mapped markers.
order.seqto automate the process of mapping a sequence of markers, combining compare and try.seq functions.
rippleto check a set of mapped markers, looking for (plausible) alternative orders.
mapto construct a map for a sequence in a given order.

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. Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B. (2008) qtl: Tools for analyzing QTL experiments R package version 1.09-43 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. Jiang, C. and Zeng, Z.-B. (1997). Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101: 47-58.

Kosambi, D. D. (1944) The estimation of map distance from recombination values. Annuaire of Eugenetics 12: 172-175. Lander, E. S. and Green, P. (1987). Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci. USA 84: 2363-2367.

Lander, E. S., Green, P., Abrahamson, J., Barlow, A., Daly, M. J., Lincoln, S. E. and Newburg, L. (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.

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.

Oliveira, E. J., Vieira, M. L. C., Garcia, A. A. F., Munhoz, C. F.,Margarido, G. R.A., Consoli, L., Matta, F. P., Moraes, M. C., Zucchi, M. I., and Fungaro,M. H. P. (2008) An Integrated Molecular Map of Yellow Passion Fruit Based on Simultaneous Maximum-likelihood Estimation of Linkage and Linkage Phases J. Amer. Soc. Hort. Sci. 133: 35-41. Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002a) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.

Wu, R., Ma, C.-X., Wu, S. S. and Zeng, Z.-B. (2002b). Linkage mapping of sex-specific differences. Genetical Research 79: 85-96