New gene-derived simple sequence repeat markers for common bean (Phaseolus vulgaris L.)

Mol Ecol Resour. 2012 Jul;12(4):661-8. doi: 10.1111/j.1755-0998.2012.03136.x. Epub 2012 Apr 28.


Common bean is an important and diverse crop legume with several wild relatives that are all part of the Phaseoleae tribe of tropical crop legumes. Sequence databases have been a good source of sequences to mine for simple sequence repeats (SSRs). The objective of this research was to evaluate 14 sequence collections from common bean for SSRs and to evaluate the diversity of the polymorphic microsatellites derived from these collections. SSRs were found in 10 of the GenBank sequence collections with an average of 11.3% of sequences containing microsatellite motifs. The most common motifs were based on tri- and dinucleotides. In a marker development programme, primers were designed for 125 microsatellites which were tested on a panel of 18 common bean genotypes. The markers were named as part of the bean microsatellite-database (BMd) series, and the average polymorphism information content was 0.404 for polymorphic markers and predicted well the genepool structure of common beans and the status of the wild and cultivated accessions that were included in the study. Therefore, the BMd series of microsatellites is useful for multiple studies of genetic relatedness and as anchor markers in future mapping of wide crosses in the species.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Plant / genetics
  • Databases, Nucleic Acid
  • Genetic Markers
  • Genetic Speciation
  • Genetic Variation
  • Genome, Plant
  • Genotype
  • Microsatellite Repeats*
  • Phaseolus / genetics*
  • Phylogeny
  • Sequence Analysis, DNA


  • DNA, Plant
  • Genetic Markers