Structure of genetic diversity among common bean (Phaseolus vulgaris L.) varieties of Mesoamerican and Andean origins using new developed microsatellite markers

Abstract

A common bean genomic library was constructed using the 'IAC-UNA' variety enriched for (CT) and (GT) for microsatellite motifs. From 1,209 sequenced clones, 714 showed microsatellites distributed over 471 simple and 243 compound motifs. GA/CT and GT/CA were the most frequent motifs found among these sequences. A total of 123 microsatellites has been characterized. Out of these, 87 were polymorphic (73.7%), 33 monomorphic (26.8%), and 3 (2.4%) did not amplify at all. In a sample of 20 common bean materials selected from the Agronomic Institute Germplasm Bank, the number of alleles per locus varied 2-9, with an average of 2.82. The polymorphic information content (PIC) of each marker varied from 0.05 to 0.83, with a 0.45 average value. Cluster and principal coordinate analysis of the microsatellite data were consistent with the original assignment of the germplasm accessions into the Andean and Mesoamerican gene pools of common bean. Low polymorphism levels detected could be associated with the domestication process. These microsatellites could be a valuable resource for the bean community because of their use as new markers for genetic studies.

Nucleotide diversity based on phaseolin and iron reductase genes in common bean accessions of different geographical origins

“…The cluster patterns obtained in our study revealed the formation of two well-defined clusters in the ␣-Phs data sequence that are in accordance with the variation at SSR loci (Hanai et al 2007;Benchimol et al 2007) in the sizes of bean seed (Singh 2001), and they are also consistent with the hierarchical organization into two P. vulgaris gene pools. In regard to the PvFRO1 gene and aside from the Andean cluster, the Mesoamerican beans, landraces, and the Brazilian cultivars grouped together, but three Mesoamerican accessions ('Puebla 152', 'Tu', and 'IAC-UNA') and one Brazilian cultivar ('BRS Pontal'), which share common genetic backgrounds, grouped close to the Andean cluster.…”

“…The bean sample we used was similar to the one in Hanai et al (2007) and included some of the accessions evaluated by Benchimol et al (2007); this particular analysis was performed using a different set of SSR loci to evaluate diversity, and revealed a distinct grouping pattern within each cluster.…”

Comparative analysis of diversity based on morpho-agronomic traits and microsatellite markers in common bean

“…There should be integrated use of advanced functional genomics and traditional breeding approaches. More newly developed SSRs should be utilized for large scale common bean germplasm evaluation Benchimol et al 2007;Blair et al 2006). To look into real ''perfect'' marker-trait associations markers like EST (expressed sequence tag)-SSRs which score only the expressed region of the genome should also be used (Ramirez et al 2005).…”

“…Among molecular markers, microsatellites are one of the most popular genetic markers due to their characteristic features like high polymorphism, abundant informativeness, convenience of assay by PCR, and distribution throughout the genome (Gupta and Varshney 2000). In common bean also, microsatellites have been successfully used for genetic diversity analysis (Metais et al 2002;Blair et al 2006;Benchimol et al 2007;Campos et al 2007). …”

Genetic progress resulting from forty-three years of breeding of the carioca common bean in Brazil

“…Common bean (Phaseolus vulgaris L.) is one of the most important food legumes globally in terms of socioeconomic and nutritional importance (Benchimol et al, 2007). The carioca bean type was developed in Brazil in 1970.…”