1. MapSynteny: Software to create images of synteny 1 Sugarbeet and Bean Research Unit, Agricultural Research Service, United States Department of Agriculture, East Lansing, Michigan, United States of America. 2 Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, K.U. Leuven, Heverlee, Belgium. MapSynteny is a macro in MS Excel® able to create images to show the relationship between genetic maps and large sequences (scaffolds, chromosomes, BACs, etc.). Based on tab-delimited BLAST results and some formulas, a suitable image of syntenic relationships or physical mapping can be obtained. This simple and versatile software can produce four types of outputs based on traditional linkage map figures (Figure 1). Fernandez AC 1, Galeano CH 2, Cichy KA 1, Blair MW. Introduction Galeano CH, Fernandez AC, Franco N, Cichy K, McClean P, Vanderleyden J. Blair MW. Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean. PLoS ONE 2011 Dec 8. Galeano CH, Fernandez AC, Gómez M, Blair MW. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.). BMC Genomics. 2009 Dec 23;10:629. Lorieux M. 2011. http://mapdisto.free.fr/http://mapdisto.free.fr/ References Scaffolds are large DNA sequences produced by the next generation sequence assembling processes. The Map Synteny program can be used to graph linkage map and DNA sequence relationships at the chromosome level (Figure 2). Applications Synteny between species Macro-assembly of scaffolds Figure 2. Example in P. vulgaris of scaffold/ linkage map relationship Methods The software is written in Visual script of Microsoft Excel 2010®. The program uses BLAST result dataset in tab-delimited format (BLAST Version 2.2.24). This dataset is the comparison between the markers sequences (defined in the program as: spB) and the genome sequences of the comparison species (defined in the program as: spC). The linkage map (spB) could be imported using the flat file obtained from MapDisto (Lorieux 2011) Download This software and a tutorial is available at http://www.automatizacionysistemas.com/download.html The application of this program is shown in recent publication by Galeano et al. (2009 and 2011). Figure 1. Types of visualization. A) Large macro-synteny blocks. B) Small macro-synteny blocks. C) Marker labeled small synteny blocks. D) Micro-synteny relationship between Phaseolus vulgaris and Glycine max. B CA D Many important crop plants have few genomic resources. Those species are referred to as orphan crops. Often related species are rich sources of genomic information. MapSynteny is a useful tool to take advantage of this information. The visualization with blocks is useful for macro-synteny analysis. Large blocks allow visualization of poorly saturated maps (Figure 1a). Small blocks can be used for a highly saturated map (Figure 1b). Marker labels can also be added (Figure 1c). The forth type is useful for micro-synteny analyses and extrapolations (inSilico mapping) (Figure 1d).