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

Garcia RA, Rangel PN, Brondani C, Martins WS, Melo LC, Carneiro MS, Borba TC, Brondani RP - BMC Genet. (2011)

Bottom Line: 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 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Embrapa Arroz e Feijão, Rodovia GO-462, km 12 Zona Rural, CEP 75375-000, Santo Antônio de Goiás, GO, Brazil.

ABSTRACT

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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Common bean linkage map based on 182 SSR markers. The mapped markers include genomic and EST-derived SSR loci segregating in the BAT93 × Jalo EEP558 population. Distances are indicated in cM Kosambi. Microsatellites were mapped with a minimum LOD of 3.0. Markers that showed segregation distortions are starred (*; p < 0.05) and labeled with (B) or (J), indicating the predominance of alleles from BAT93 or Jalo EEP558, respectively.
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Figure 1: Common bean linkage map based on 182 SSR markers. The mapped markers include genomic and EST-derived SSR loci segregating in the BAT93 × Jalo EEP558 population. Distances are indicated in cM Kosambi. Microsatellites were mapped with a minimum LOD of 3.0. Markers that showed segregation distortions are starred (*; p < 0.05) and labeled with (B) or (J), indicating the predominance of alleles from BAT93 or Jalo EEP558, respectively.

Mentions: The integration of the SSRs into the BJ linkage map resulted in a dataset of 199 polymorphic markers, from which 117 were genomic SSRs and 82 were EST-SSRs. A total of 182 (91.5%) markers could be mapped at an LOD score ≥3.0 (θ = 0.30) and were distributed into 14 linkage groups. These groups represent the 11 chromosomes of the common bean and the three extra small chromosome segments (Figure 1). The extra chromosomes (1A, 7A and 11B) had three markers each and are unlinked segments mapped to the tip of chromosomes 1 and 7 and the end of chromosome 11. Chromosome assignments were performed according to [31]. Marker distribution along the chromosomes ranged from 3 (chromosomes 1A, 7A and 11B) to 26 (chromosome 2), and chromosome sizes varied from 12.33 cM (chromosome 1A) to 176.72 cM (chromosome 2) with an average size of 88.82 ± 44.07 cM. The total map distance was estimated at 1,156.2 cM with an average marker distance of 6.65 ± 1.64 cM, and the maximum distance between two markers was 26.0 cM (PVEST159 and AJ416391 on the end of chromosome 3). The distribution of the EST-SSRs appeared to be relatively random and dispersed throughout the Phaseolus genome. Among the 72 polymorphic EST-SSRs, 65 were assigned to 12 chromosomes with the number of markers ranging from 3 (chromosomes 11A, 11B, 5, 3, 8 and 9) to 11 (chromosome 2).


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

Garcia RA, Rangel PN, Brondani C, Martins WS, Melo LC, Carneiro MS, Borba TC, Brondani RP - BMC Genet. (2011)

Common bean linkage map based on 182 SSR markers. The mapped markers include genomic and EST-derived SSR loci segregating in the BAT93 × Jalo EEP558 population. Distances are indicated in cM Kosambi. Microsatellites were mapped with a minimum LOD of 3.0. Markers that showed segregation distortions are starred (*; p < 0.05) and labeled with (B) or (J), indicating the predominance of alleles from BAT93 or Jalo EEP558, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3102039&req=5

Figure 1: Common bean linkage map based on 182 SSR markers. The mapped markers include genomic and EST-derived SSR loci segregating in the BAT93 × Jalo EEP558 population. Distances are indicated in cM Kosambi. Microsatellites were mapped with a minimum LOD of 3.0. Markers that showed segregation distortions are starred (*; p < 0.05) and labeled with (B) or (J), indicating the predominance of alleles from BAT93 or Jalo EEP558, respectively.
Mentions: The integration of the SSRs into the BJ linkage map resulted in a dataset of 199 polymorphic markers, from which 117 were genomic SSRs and 82 were EST-SSRs. A total of 182 (91.5%) markers could be mapped at an LOD score ≥3.0 (θ = 0.30) and were distributed into 14 linkage groups. These groups represent the 11 chromosomes of the common bean and the three extra small chromosome segments (Figure 1). The extra chromosomes (1A, 7A and 11B) had three markers each and are unlinked segments mapped to the tip of chromosomes 1 and 7 and the end of chromosome 11. Chromosome assignments were performed according to [31]. Marker distribution along the chromosomes ranged from 3 (chromosomes 1A, 7A and 11B) to 26 (chromosome 2), and chromosome sizes varied from 12.33 cM (chromosome 1A) to 176.72 cM (chromosome 2) with an average size of 88.82 ± 44.07 cM. The total map distance was estimated at 1,156.2 cM with an average marker distance of 6.65 ± 1.64 cM, and the maximum distance between two markers was 26.0 cM (PVEST159 and AJ416391 on the end of chromosome 3). The distribution of the EST-SSRs appeared to be relatively random and dispersed throughout the Phaseolus genome. Among the 72 polymorphic EST-SSRs, 65 were assigned to 12 chromosomes with the number of markers ranging from 3 (chromosomes 11A, 11B, 5, 3, 8 and 9) to 11 (chromosome 2).

Bottom Line: 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 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Embrapa Arroz e Feijão, Rodovia GO-462, km 12 Zona Rural, CEP 75375-000, Santo Antônio de Goiás, GO, Brazil.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus