Genetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools that reliably access genes with orthology to the genomes of well-characterized reference species. Here we report an efficient platform for designing cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM designer is enhanced by graphical displays of query results, which we describe as “circular viewer” and “search-within-results” functions. CSGM platform provides a virtual PCR representation, called eHT-PCR, that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations. CSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding.

In recent years, genomic resources and information have accumulated at an ever increasing pace, in many plant species, through whole genome sequencing, large scale analysis of transcriptomes, DNA markers and functional studies of individual genes. Well-characterized species within key plant taxa, co-called "model systems", have played a pivotal role in nucleating the accumulation of genomic information and databases, thereby providing the basis for comparative genomic studies. In addition, recent advances to "Next Generation" sequencing technologies have propelled a new wave of genomics, enabling rapid, low cost analysis of numerous genomes, and the accumulation of genetic diversity data for large numbers of accessions within individual species. The resulting wealth of genomic information provides an opportunity to discern evolutionary processes that have impacted genome structure and the function of genes, using the tools of comparative analysis. Comparative genomics provides a platform to translate information from model species to crops, and to relate knowledge of genome function among crop species. Ultimately, the resulting knowledge will accelerate the development of more efficient breeding strategies through the identification of trait-associated orthologous genes and next generation functional gene-based markers.