OneMap: software for genetic mapping in outcrossing species

Abstract

OneMap is an environment for constructing linkage maps of outcrossing plant species, using full-sib families derived from two outbred parents. The analyses are performed using a novel methodology based on the maximum likelihood approach for simultaneous estimation of linkage and linkage phases (WU et al. 2002), which has been successfully applied to sugarcane (GARCIA et al. 2006). It is implemented as a set of functions for the freely distributed software R, and handles pairwise marker analysis, marker ordering and map refinement. The software is freely available at

Evaluation of algorithms used to order markers on genetic maps

“…The codes to run all algorithms and criteria presented on this paper are being incorporated in the OneMap software (Margarido et al, 2007) and will be made available in a near future. Details can be obtained with the corresponding author.…”

“…Several algorithms to obtain approximate solutions for ordering markers have been proposed, including simulated annealing (Thompson, 1984;Weeks and Lange, 1987), stepwise likelihood (Lathrop et al, 1984), branch and bound (Lathrop et al, 1985), try and ripple , seriation (SER) (Buetow and Chakravarti, 1987), rapid chain delineation (RCD) (Doerge, 1996), genetic and evolutionary algorithm (Mester et al, 2003), recombination counting and ordering (RECORD) (Van Os et al, 2005) and unidirectional growth (UG) (Tan and Fu, 2006). Some of them have been implemented into friendly user softwares, such as Linkage (Lathrop et al, 1984), MAPMAKER/EXP , JoinMap (Stam, 1993), Emap from the program suite QTL Cartographer (Basten et al, 2003) and OneMap (Margarido et al, 2007). Moreover, there are several criteria to evaluate and compare the orders, such as, sum of adjacent recombination fractions (SARF, Falk, 1989), product of adjacent recombination fractions (PARF, Wilson, 1988), sum of adjacent LOD scores (SALOD, Weeks and Lange, 1987), SALOD-equivalent number of fully informative meiosis (SALEQ, Edwards, 1971;Olson and Boehnke, 1990), SALOD-polymorphism information content (SALPIC, Botstein et al, 1980;Olson and Boehnke, 1990), likelihood through hidden Markov chains (LHMC, , least squares (Weeks and Lange, 1987) and weighted least squares (Stam, 1993).…”

A model for quantitative trait loci mapping, linkage phase, and segregation pattern estimation for a full-sib progeny

“…Although two-point analysis could be used, multipoint methods are strongly recommended because they allow the inclusion of all individuals, including the ones with missing markers, and also because of the partial information provided by nonfully informative markers on the genetic map (Jiang and Zeng 1997;Wu et al 2002b). For this reason, in the present work, conditional probabilities for QTL genotypes were obtained using OneMap software, which implements a multipoint approach using hidden Markov models (Margarido et al 2007(Margarido et al , 2011.…”

“…The conditional probabilities p uvj were calculated at every 1 cM along each chromosome using the multipoint approach implemented in the OneMap software (Margarido et al 2007(Margarido et al , 2011. Subsequently, composite interval mapping was performed, using the new model.…”

“…Ling (2000), Wu et al (2002b), and Tong et al (2010) proposed methods based on multipoint maximum likelihood using hidden Markov models (HMM). HMMs have been incorporated into software, such as OneMap (Margarido et al 2007(Margarido et al , 2011. The main advantage of these methods is the ability to obtain linkage maps with higher saturation and good representation of the genetic polymorphism generated by the cross, because markers with all segregation patterns can be used in the statistical analysis.…”