title: CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.
abstract: BACKGROUND
  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, a situation that is well documented for a number of agronomic traits. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools (e.g., oligonucleotide primers) that reliably access genes with orthology to the genomes of well-characterized reference species.
  
  
  RESULTS
  Here we report an efficient platform for the design of 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 is enhanced by graphical displays of query results, which we describe as "circular viewer" and "search-within-results" functions. CSGM provides a virtual PCR representation (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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Medical Bioscience, Dong-A University, Saha-Gu Nakdong-Daero 550 beongil 37, Busan, 604-714 Republic of Korea.
authors.forename: Jin-Hyun
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Medical Bioscience, Dong-A University, Saha-Gu Nakdong-Daero 550 beongil 37, Busan, 604-714 Republic of Korea.
authors.forename: Chaeyoung
authors.initials: C
authors.lastname: Lee
authors.affiliation: Department of Computer Science, Dong-A University, Saha-Gu Nakdong-Daero 550 beongil 37, Busan, 604-714 Republic of Korea.
authors.forename: Daejin
authors.initials: D
authors.lastname: Hyung
authors.affiliation: Department of Genetic Engineering, Dong-A University, Saha-Gu Nakdong-Daero 550 beongil 37, Busan, 604-714 Republic of Korea.
authors.forename: Ye-Jin
authors.initials: YJ
authors.lastname: Jo
authors.affiliation: Department of Applied Bioscience, Dong-A University, Saha-Gu Nakdong-Daero 550 beongil 37, Busan, 604-714 Republic of Korea.
authors.forename: Joo-Seok
authors.initials: JS
authors.lastname: Park
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA 95616 USA.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Cook
authors.affiliation: Department of Genetic Engineering, Dong-A University, Saha-Gu Nakdong-Daero 550 beongil 37, Busan, 604-714 Republic of Korea.
authors.forename: Hong-Kyu
authors.initials: HK
authors.lastname: Choi
keywords: Circular viewer; Genic marker; Legumes; Marker design; eHT-PCR