The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris

Abstract

BackgroundOver recent years, a growing effort has been made to develop microsatellite markers for the genomic analysis of the common bean (Phaseolus vulgaris) to broaden the knowledge of the molecular genetic basis of this species. The availability of large sets of expressed sequence tags (ESTs) in public databases has given rise to an expedient approach for the identification of SSRs (Simple Sequence Repeats), specifically EST-derived SSRs. In the present work, a battery of new microsatellite markers was obtained from a search of the Phaseolus vulgaris EST database. The diversity, degree of transferability and polymorphism of these markers were tested.ResultsFrom 9,583 valid ESTs, 4,764 had microsatellite motifs, from which 377 were used to design primers, and 302 (80.11%) showed good amplification quality. To analyze transferability, a group of 167 SSRs were tested, and the results showed that they were 82% transferable across at least one species. The highest amplification rates were observed between the species from the Phaseolus (63.7%), Vigna (25.9%), Glycine (19.8%), Medicago (10.2%), Dipterix (6%) and Arachis (1.8%) genera. The average PIC (Polymorphism Information Content) varied from 0.53 for genomic SSRs to 0.47 for EST-SSRs, and the average number of alleles per locus was 4 and 3, respectively. Among the 315 newly tested SSRs in the BJ (BAT93 X Jalo EEP558) population, 24% (76) were polymorphic. The integration of these segregant loci into a framework map composed of 123 previously obtained SSR markers yielded a total of 199 segregant loci, of which 182 (91.5%) were mapped to 14 linkage groups, resulting in a map length of 1,157 cM.ConclusionsA total of 302 newly developed EST-SSR markers, showing good amplification quality, are available for the genetic analysis of Phaseolus vulgaris. These markers showed satisfactory rates of transferability, especially between species that have great economic and genomic values. Their diversity was comparable to genomic SSRs, and they were incorporated in the common bean reference genetic map, which constitutes an important contribution to and advance in Phaseolus vulgaris genomic research.

Discrimination of common bean cultivars using multiplexed microsatellite markers

“…Distinct molecular profiles for the 50 cultivars analyzed could be generated using 11 of the loci included in the analysis. The genetic diversity estimates obtained for five of these markers are consistent with the published literature (Blair et al, 2006;Buso et al, 2006;Garcia et al, 2011), validating these markers in terms of genetic content and supporting the recommendation to include these loci in an international genotyping system for common bean. The results for the remaining 19 loci, which were highly informative and demonstrated the analytical robustness of the present study, were consistent with previous reports (Garcia et al, 2011) and should also be considered for inclusion in the international genotyping set.…”

“…Several collections of SSR markers are publicly available for molecularly characterized plant species, including common bean (Garcia et al, 2011). SSR-based molecular genotyping has rapidly evolved, and methods for the simultaneous amplification of multiple loci coupled to semi-automated detection systems have been developed (Masi et al, 2003;Borba et al, 2009;Cardoso et al, 2013).…”

Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.)

“…The most frequent N A detected per marker were three (32.56%) and four (34.88%). This is consistent with the highly conserved nature of the primer sequences flanking the SSR region, which is higher than that previously reported in some plant species such as Phaseolus vulgaris (Garcia et al, 2011). H O and H E ranged from 0.0 to 0.983 (mean 0.458) and 0.096 to 0.774 (mean 0.536), respectively.…”

Molecular characterization of high performance inbred lines of Brazilian common beans

“…Over the years, the goal has been to develop universal and robust genetic identification systems to analyze genetic relationships individual identification, population structure, and genetic diversity. The nine multiplex systems used in the present study consisted of 36 microsatellite markers exhibiting no evidence of linkage and were widely distributed across 11 chromosomes in the bean genome according to genetic map information (Grisi et al, 2007;Garcia et al, 2011). The number of marker sets per system ranged from 3 to 6, with an average of 4 markers per panel.…”