Single nucleotide polymorphisms in common bean : Their discovery and genotyping using a multiplex detection system
Single nucleotide polymorphism (SNP) markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean (Phaseolus vulgaris L.) by comparing sequences from coding and noncoding regions obtained from the GenBank and genomic DNA a...
| Main Authors: | , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Wiley
2008
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/44103 |
| _version_ | 1855536264924626944 |
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| author | Gaitán Solís, Eliana Choi, I.Y. Quigley, C Cregan, P.B. Tohme, Joseph M. |
| author_browse | Choi, I.Y. Cregan, P.B. Gaitán Solís, Eliana Quigley, C Tohme, Joseph M. |
| author_facet | Gaitán Solís, Eliana Choi, I.Y. Quigley, C Cregan, P.B. Tohme, Joseph M. |
| author_sort | Gaitán Solís, Eliana |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Single nucleotide polymorphism (SNP) markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean (Phaseolus vulgaris L.) by comparing sequences from coding and noncoding regions obtained from the GenBank and genomic DNA and to compare sequencing results with those obtained using single base extension (SBE) assays on the Luminex-100 system for use in high-throughput germplasm evaluation. We assessed the frequency of SNPs in 47 fragments of common bean DNA, using SBE as the evaluation methodology. We conducted a sequence analysis of 10 genotypes of cultivated and wild beans belonging to the Mesoamerican and Andean genetic pools of P. vulgaris. For the 10 genotypes evaluated, a total of 20,964 bp of sequence were analyzed in each genotype and compared, resulting in the discovery of 239 SNPs and 133 InDels, giving an average SNP frequency of one per 88 bp and an InDel frequency of one per 157 bp. This is the equivalent of a nucleotide diversity (?) of 6.27 × 10?3. Comparisons with the SNP genotypes previously obtained by direct sequencing showed that the SBE assays on the Luminex-100 were accurate, with 2.5% being miscalled and 1% showing no signal. These results indicate that the Luminex-100 provides a high-throughput system that can be used to analyze SNPs in large samples of genotypes both for purposes of assessing diversity and also for mapping studies. |
| format | Journal Article |
| id | CGSpace44103 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2008 |
| publishDateRange | 2008 |
| publishDateSort | 2008 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace441032024-05-01T08:19:05Z Single nucleotide polymorphisms in common bean : Their discovery and genotyping using a multiplex detection system Gaitán Solís, Eliana Choi, I.Y. Quigley, C Cregan, P.B. Tohme, Joseph M. phaseolus vulgaris polymorphism germplam genotypes genetic markers kidney beans polimorfismo germoplasma genotipos marcadores genéticos Single nucleotide polymorphism (SNP) markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean (Phaseolus vulgaris L.) by comparing sequences from coding and noncoding regions obtained from the GenBank and genomic DNA and to compare sequencing results with those obtained using single base extension (SBE) assays on the Luminex-100 system for use in high-throughput germplasm evaluation. We assessed the frequency of SNPs in 47 fragments of common bean DNA, using SBE as the evaluation methodology. We conducted a sequence analysis of 10 genotypes of cultivated and wild beans belonging to the Mesoamerican and Andean genetic pools of P. vulgaris. For the 10 genotypes evaluated, a total of 20,964 bp of sequence were analyzed in each genotype and compared, resulting in the discovery of 239 SNPs and 133 InDels, giving an average SNP frequency of one per 88 bp and an InDel frequency of one per 157 bp. This is the equivalent of a nucleotide diversity (?) of 6.27 × 10?3. Comparisons with the SNP genotypes previously obtained by direct sequencing showed that the SBE assays on the Luminex-100 were accurate, with 2.5% being miscalled and 1% showing no signal. These results indicate that the Luminex-100 provides a high-throughput system that can be used to analyze SNPs in large samples of genotypes both for purposes of assessing diversity and also for mapping studies. 2008-11 2014-10-02T08:33:15Z 2014-10-02T08:33:15Z Journal Article https://hdl.handle.net/10568/44103 en Open Access Wiley |
| spellingShingle | phaseolus vulgaris polymorphism germplam genotypes genetic markers kidney beans polimorfismo germoplasma genotipos marcadores genéticos Gaitán Solís, Eliana Choi, I.Y. Quigley, C Cregan, P.B. Tohme, Joseph M. Single nucleotide polymorphisms in common bean : Their discovery and genotyping using a multiplex detection system |
| title | Single nucleotide polymorphisms in common bean : Their discovery and genotyping using a multiplex detection system |
| title_full | Single nucleotide polymorphisms in common bean : Their discovery and genotyping using a multiplex detection system |
| title_fullStr | Single nucleotide polymorphisms in common bean : Their discovery and genotyping using a multiplex detection system |
| title_full_unstemmed | Single nucleotide polymorphisms in common bean : Their discovery and genotyping using a multiplex detection system |
| title_short | Single nucleotide polymorphisms in common bean : Their discovery and genotyping using a multiplex detection system |
| title_sort | single nucleotide polymorphisms in common bean their discovery and genotyping using a multiplex detection system |
| topic | phaseolus vulgaris polymorphism germplam genotypes genetic markers kidney beans polimorfismo germoplasma genotipos marcadores genéticos |
| url | https://hdl.handle.net/10568/44103 |
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