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.
Highlights
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
SSR amplification A total of 9,583 valid expressed sequence tags (ESTs) corresponding to 3,281 contigs and 6,302 singletons were screened for the presence of useful SSRs
Our results show that more than half (57.9%) of the EST-SSRs sequences were associated with sequences of putative genes in the GenBank, demonstrating the potential of these markers to be used for the genomic exploitation of the common bean
Summary
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. Important progress has been made on the genome sequencing of the legumes, including soybean (Glycine max), barrel medic (Medicago truncatula), and birdsfoot trefoil (Lotus japonicus), all of which are considered model organisms due to their biological functions, reduced genome sizes and economic importance [6]. Among these species, the soybean genome was the largest sequenced using a shotgun approach, and the assembled sequences were integrated in a genetic and physical map, allowing the investigation of the genome composition, duplication, organization and transcriptional factors [7]. Phylogenetic relationships within the legume family [8] are reflected in relatively high similarity, or synteny, at the genome level among the temperate climate legumes, including Medicago sp. and pea [9], or between the tropical climate legumes, such as the common bean and soybean [10]
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