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Synteny mapping between common bean and soybean reveals extensive blocks of shared loci

Phillip E McClean12*, Sujan Mamidi1, Melody McConnell1, Shireen Chikara1 and Rian Lee12

Author Affiliations

1 Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58105, USA

2 Department of Plant Sciences, Loftsgard Hall, North Dakota State University, Fargo, ND 58105, USA

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BMC Genomics 2010, 11:184  doi:10.1186/1471-2164-11-184

Published: 18 March 2010



Understanding syntentic relationship between two species is critical to assessing the potential for comparative genomic analysis. Common bean (Phaseolus vulgaris L.) and soybean (Glycine max L.), the two most important members of the Phaseoleae legumes, appear to have a diploid and polyploidy recent past, respectively. Determining the syntentic relationship between these two species will allow researchers to leverage not only genomic resources but also genetic data for important agronomic traits to improve both of these species.


Genetically-positioned transcript loci of common bean were mapped relative to the recent soybean 1.01 pseudochromosome assembly. In nearly every case, each common bean locus mapped to two loci in soybean, a result consistent with the duplicate polyploidy history of soybean. Blocks of synteny averaging 32 cM in common bean and 4.9 Mb in soybean were observed for all 11 common bean linkage groups, and these blocks mapped to all 20 soybean pseudochromosomes. The median physical-to-genetic distance ratio in common bean (based on soybean physical distances) was ~120 kb/cM. ~15,000 common bean sequences (primarily EST contigs and EST singletons) were electronically positioned onto the common bean map using the shared syntentic blocks as references points.


The collected evidence from this mapping strongly supports the duplicate history of soybean. It further provides evidence that the soybean genome was fractionated and reassembled at some point following the duplication event. These well mapped syntentic relationships between common bean and soybean will enable researchers to target specific genomic regions to discover genes or loci that affect phenotypic expression in both species.