onemap-package: Software for constructing genetic maps

Description

In its earlier version, the software implemented 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, to building genetic maps in outcrossing species. After, it was modified to also using a Hidden Markov Model approach for constructing multipoint maximum likelihood linkage maps (Wu et al. 2002b). It was then applied in several studies, such as Garcia et al. (2006), Oliveira et al. (2007) and Oliveira et al. (2008). Nowadays, the latest versions (2.0-0) was fully modified to also handle with backcrosses, F_2 and recombinant inbred lines (RIL) populations, allowing fully integration with software for QTL mapping, such as R/qtl and QTL Cartographer. OneMap can read and export files to this packages, and also from the widely used software MAPMAKER.

Arguments

Details

ll{ Package: onemap Type: Package Version: 2.0-0 Date: 2011-01-04 License: GNU GENERAL PUBLIC LICENSE (Version 3) } 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.
read.mapmakerfor importing data from a MAPMAKER raw file.
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.
ripple.seqto 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

Buetow KH, Chakravarti A (1987). Multipoint gene mapping using seriation. I. General methods. Am J Hum Genet 41: 180-188. 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.

Mollinari, M., Margarido, G. R. A., Vencovsky, R. and Garcia, A. A. F. (2009) Evaluation of algorithms used to order markers on genetic maps. Heredity 103: 494-502 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.

Tan, Y., Fu, Y. (2006). A novel method for estimating linkage maps. Genetics 173: 2383-2390.

Van Os H, Stam P, Visser RGF, Van Eck HJ (2005). RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112: 30-40. 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