The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris
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2011
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Background: Over 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.
Results: From 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.
Conclusions: A 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.
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GARCIA, Robertha A. V.; RANGEL, Priscila N.; BRONDANI, Claudio; MARTINS, Wellington S.; MELO, Leonardo C.; CARNEIRO, Monalisa S.; BORBA, Tereza C. O.; BRONDANI, Rosana P. V. The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris. BMC Genetics, London, v. 12, n. 41, p. 1-14, 2011.