Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping
Background Common bean (Phaseolus vulgaris) is an important grain legume and there has been a recent resurgence in interest in its relative, tepary bean (P. acutifolius), owing to this species’ ability to better withstand abiotic stresses. Genomic resources are scarce for this minor crop species an...
| Autores principales: | , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2016
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/72712 |
| _version_ | 1855516211548258304 |
|---|---|
| author | Gujaria-Verma, Neha Ramsay, Larissa Sharpe, Andrew G. Sanderson, Lacey-Anne Debouck, Daniel G. Tar’an, Bunyamin Bett, Kirstin E. |
| author_browse | Bett, Kirstin E. Debouck, Daniel G. Gujaria-Verma, Neha Ramsay, Larissa Sanderson, Lacey-Anne Sharpe, Andrew G. Tar’an, Bunyamin |
| author_facet | Gujaria-Verma, Neha Ramsay, Larissa Sharpe, Andrew G. Sanderson, Lacey-Anne Debouck, Daniel G. Tar’an, Bunyamin Bett, Kirstin E. |
| author_sort | Gujaria-Verma, Neha |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background
Common bean (Phaseolus vulgaris) is an important grain legume and there has been a recent resurgence in interest in its relative, tepary bean (P. acutifolius), owing to this species’ ability to better withstand abiotic stresses. Genomic resources are scarce for this minor crop species and a better knowledge of the genome-level relationship between these two species would facilitate improvement in both. High-throughput genotyping has facilitated large-scale single nucleotide polymorphism (SNP) identification leading to the development of molecular markers with associated sequence information that can be used to place them in the context of a full genome assembly.
Results
Transcript-based SNPs were identified from six common bean and two tepary bean accessions and a subset were used to generate a 768-SNP Illumina GoldenGate assay for each species. The tepary bean assay was used to assess diversity in wild and cultivated tepary bean and to generate the first gene-based map of the tepary bean genome. Genotypic analyses of the diversity panel showed a clear separation between domesticated and cultivated tepary beans, two distinct groups within the domesticated types, and P. parvifolius was confirmed to be distinct. The genetic map of tepary bean was compared to the common bean genome assembly to demonstrate high levels of collinearity between the two species with differences limited to a few intra-chromosomal rearrangements.
Conclusions
The development of the first set of genomic resources specifically for tepary bean has allowed for greater insight into the structure of this species and its relationship to its agriculturally more prominent relative, common bean. These resources will be helpful in the development of efficient breeding strategies for both species and will facilitate the introgression of agriculturally important traits from one crop into the other. |
| format | Journal Article |
| id | CGSpace72712 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace727122025-03-13T09:43:59Z Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping Gujaria-Verma, Neha Ramsay, Larissa Sharpe, Andrew G. Sanderson, Lacey-Anne Debouck, Daniel G. Tar’an, Bunyamin Bett, Kirstin E. phaseolus vulgaris genetic markers polymorphism genomes genetic resources plant breeding marcadores genéticos recursos genéticos polimorfismo genomas fitomejoramiento genetics biotechnology Background Common bean (Phaseolus vulgaris) is an important grain legume and there has been a recent resurgence in interest in its relative, tepary bean (P. acutifolius), owing to this species’ ability to better withstand abiotic stresses. Genomic resources are scarce for this minor crop species and a better knowledge of the genome-level relationship between these two species would facilitate improvement in both. High-throughput genotyping has facilitated large-scale single nucleotide polymorphism (SNP) identification leading to the development of molecular markers with associated sequence information that can be used to place them in the context of a full genome assembly. Results Transcript-based SNPs were identified from six common bean and two tepary bean accessions and a subset were used to generate a 768-SNP Illumina GoldenGate assay for each species. The tepary bean assay was used to assess diversity in wild and cultivated tepary bean and to generate the first gene-based map of the tepary bean genome. Genotypic analyses of the diversity panel showed a clear separation between domesticated and cultivated tepary beans, two distinct groups within the domesticated types, and P. parvifolius was confirmed to be distinct. The genetic map of tepary bean was compared to the common bean genome assembly to demonstrate high levels of collinearity between the two species with differences limited to a few intra-chromosomal rearrangements. Conclusions The development of the first set of genomic resources specifically for tepary bean has allowed for greater insight into the structure of this species and its relationship to its agriculturally more prominent relative, common bean. These resources will be helpful in the development of efficient breeding strategies for both species and will facilitate the introgression of agriculturally important traits from one crop into the other. 2016-12 2016-03-22T20:55:18Z 2016-03-22T20:55:18Z Journal Article https://hdl.handle.net/10568/72712 en Open Access Springer Gujaria-Verma, Neha; Ramsay, Larissa; Sharpe, Andrew G.; Sanderson, Lacey-Anne; Debouck, Daniel G.; Tar’an, Bunyamin; Bett, Kirstin E. 2016. Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping. BMC Genomics 17 (239): 1-16. |
| spellingShingle | phaseolus vulgaris genetic markers polymorphism genomes genetic resources plant breeding marcadores genéticos recursos genéticos polimorfismo genomas fitomejoramiento genetics biotechnology Gujaria-Verma, Neha Ramsay, Larissa Sharpe, Andrew G. Sanderson, Lacey-Anne Debouck, Daniel G. Tar’an, Bunyamin Bett, Kirstin E. Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping |
| title | Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping |
| title_full | Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping |
| title_fullStr | Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping |
| title_full_unstemmed | Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping |
| title_short | Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping |
| title_sort | gene based snp discovery in tepary bean phaseolus acutifolius and common bean p vulgaris for diversity analysis and comparative mapping |
| topic | phaseolus vulgaris genetic markers polymorphism genomes genetic resources plant breeding marcadores genéticos recursos genéticos polimorfismo genomas fitomejoramiento genetics biotechnology |
| url | https://hdl.handle.net/10568/72712 |
| work_keys_str_mv | AT gujariavermaneha genebasedsnpdiscoveryinteparybeanphaseolusacutifoliusandcommonbeanpvulgarisfordiversityanalysisandcomparativemapping AT ramsaylarissa genebasedsnpdiscoveryinteparybeanphaseolusacutifoliusandcommonbeanpvulgarisfordiversityanalysisandcomparativemapping AT sharpeandrewg genebasedsnpdiscoveryinteparybeanphaseolusacutifoliusandcommonbeanpvulgarisfordiversityanalysisandcomparativemapping AT sandersonlaceyanne genebasedsnpdiscoveryinteparybeanphaseolusacutifoliusandcommonbeanpvulgarisfordiversityanalysisandcomparativemapping AT debouckdanielg genebasedsnpdiscoveryinteparybeanphaseolusacutifoliusandcommonbeanpvulgarisfordiversityanalysisandcomparativemapping AT taranbunyamin genebasedsnpdiscoveryinteparybeanphaseolusacutifoliusandcommonbeanpvulgarisfordiversityanalysisandcomparativemapping AT bettkirstine genebasedsnpdiscoveryinteparybeanphaseolusacutifoliusandcommonbeanpvulgarisfordiversityanalysisandcomparativemapping |