Development, characterization, and comparative analysis of polymorphism at common bean SSR loci isolated from genic and genomic sources

Abstract

Microsatellites or SSRs (single sequence repeats) have been used to construct and integrate genetic maps in crop species, including Phaseolus vulgaris. In the present study, 3 cDNA libraries generated by the Bean EST project (http://lgm.esalq.usp.br/BEST/), comprising a unigene collection of 3126 sequences and a genomic microsatellite-enriched library, were analyzed for the presence of SSRs. A total of 219 expressed sequence tags (ESTs) were found to carry 240 SSRs (named EST-SSR), whereas 714 genomic sequences contained 471 SSRs (named genomic-SSR). A subset of 80 SSRs, 40 EST-SSRs, and 40 genomic-SSRs were evaluated for molecular polymorphism in 23 genotypes of cultivated beans from the Mesoamerican and Andean genetic pools, including Brazilian cultivars and 2 related species. Of the common bean genotypes, 31 EST-SSR loci were polymorphic, yielding 2-12 alleles as compared with 26 polymorphic genomic-SSRs, accounting for 2-7 alleles. Cluster analysis from data using both genic and genomic-SSR revealed a clear separation between Andean and Mesoamerican beans. The usefulness of these loci for distinguishing bean genotypes and genetic mapping is discussed.

Genetic diversity in local and commercial dry bean (Phaseolus vulgaris) accessions based on microsatellite markers

“…Cabral et al locus varied from 2 to 4, with a mean of 2.23; primer SSR BM141 gave the largest number of alleles. Similar numbers of alleles per locus were found for beans by Campos et al (2007), Hanai et al (2007) and Cardoso (2009).…”

Development and Application of Molecular Markers to Breed Common Bean (Phaseolus vulgaris L.) for Resistance to Common Bacterial Blight (CBB) — Current Status and Future Directions

“…The core map is composed of some 550 markers, including RFLP, RAPD, SCAR, allozyme, and seed protein markers; when considering markers from the other, correlated maps, at least 1000 markers have been mapped which would average one marker per 1-2 cM (Freyre et al, 1998;Gepts, 1999;Kelly et al, 2003, Miklas et al, 2006. Another development in the genetic mapping of the bean genome includes the development of simple sequence repeat (SSR) or microsatellite markers (Yu et al, 1999(Yu et al, , 2000bBlair et al, 2003;Melotto et al, 2005;Hanai et al, 2007). The first preliminary study of the existence of microsatellite markers in the bean genome was conducted by Yu et al (1999Yu et al ( , 2000b, who were able to map 15 of the SSR markers onto the core linkage map.…”

“…Therefore these studies bring to a total of 115 microsatellite loci on the common bean genetic map, and provides coverage for every chromosome in the genome with from five to 20 SSR markers each (Blair et al, 2003). Two hundreds forty-three SSR sequences were identified from 5,255 bean expressed sequence tag (EST) sequences (Melotto et al, 2005) and 471 SSRs were found from 714 genomic sequences in a microsatellite-enriched genomic library (Hanai et al, 2007). These SSR markers will be invaluable for fine mapping the bean genome and tagging genes of economic interest.…”

Development and application of microsatellites in plant breeding

“…Given the high polymorphism level of microsatellites when compared to other markers, many worldwide researchers have preferred using these markers on the study of common bean population structure, genetic divergence and genetic mapping (Díaz and Blair 2006, Hanai et al 2007, Campos et al 2011.…”