Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae
Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and r...
| Main Authors: | , , , , , |
|---|---|
| Format: | Artículo |
| Language: | Inglés |
| Published: |
2018
|
| Subjects: | |
| Online Access: | https://link.springer.com/article/10.1007/s00438-018-1442-5 http://hdl.handle.net/20.500.12123/2466 https://doi.org/10.1007/s00438-018-1442-5 |
| _version_ | 1855483061214380032 |
|---|---|
| author | Barboza Rojas, Karina Beretta, Hebe Vanesa Kozub, Perla C. Salinas Palmieri, Maria Cecilia Galmarini, Claudio Romulo Cavagnaro, Pablo |
| author_browse | Barboza Rojas, Karina Beretta, Hebe Vanesa Cavagnaro, Pablo Galmarini, Claudio Romulo Kozub, Perla C. Salinas Palmieri, Maria Cecilia |
| author_facet | Barboza Rojas, Karina Beretta, Hebe Vanesa Kozub, Perla C. Salinas Palmieri, Maria Cecilia Galmarini, Claudio Romulo Cavagnaro, Pablo |
| author_sort | Barboza Rojas, Karina |
| collection | INTA Digital |
| description | Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related Allium (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized—along with 112 previously developed SSRs—at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the Allium species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of Allium species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across Allium species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2–5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of Allium transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other Allium. |
| format | Artículo |
| id | INTA2466 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| record_format | dspace |
| spelling | INTA24662018-11-27T17:45:08Z Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae Barboza Rojas, Karina Beretta, Hebe Vanesa Kozub, Perla C. Salinas Palmieri, Maria Cecilia Galmarini, Claudio Romulo Cavagnaro, Pablo Ajo Microsatélites Variación Genética Alliaceae Marcadores Genéticos Garlic Microsatellites Genetic Variation Genetic Markers Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related Allium (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized—along with 112 previously developed SSRs—at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the Allium species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of Allium species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across Allium species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2–5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of Allium transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other Allium. EEA La Consulta Fil: Barboza Rojas, Karina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina Fil: Beretta, Hebe Vanesa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina Fil: Kozub, Perla C. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina Fil: Salinas Palmieri, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina Fil: Galmarini, Claudio Romulo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina Fil: Cavagnaro, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria La Consulta; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina 2018-05-23T14:48:09Z 2018-05-23T14:48:09Z 2018-04 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion https://link.springer.com/article/10.1007/s00438-018-1442-5 http://hdl.handle.net/20.500.12123/2466 1617-4615 1617-4623 https://doi.org/10.1007/s00438-018-1442-5 eng info:eu-repo/semantics/restrictedAccess application/pdf Molecular Genetics and Genomics 293 (5) : 1091–1106 (October 2018) |
| spellingShingle | Ajo Microsatélites Variación Genética Alliaceae Marcadores Genéticos Garlic Microsatellites Genetic Variation Genetic Markers Barboza Rojas, Karina Beretta, Hebe Vanesa Kozub, Perla C. Salinas Palmieri, Maria Cecilia Galmarini, Claudio Romulo Cavagnaro, Pablo Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae |
| title | Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae |
| title_full | Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae |
| title_fullStr | Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae |
| title_full_unstemmed | Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae |
| title_short | Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae |
| title_sort | microsatellite analysis and marker development in garlic distribution in est sequence genetic diversity analysis and marker transferability across alliaceae |
| topic | Ajo Microsatélites Variación Genética Alliaceae Marcadores Genéticos Garlic Microsatellites Genetic Variation Genetic Markers |
| url | https://link.springer.com/article/10.1007/s00438-018-1442-5 http://hdl.handle.net/20.500.12123/2466 https://doi.org/10.1007/s00438-018-1442-5 |
| work_keys_str_mv | AT barbozarojaskarina microsatelliteanalysisandmarkerdevelopmentingarlicdistributioninestsequencegeneticdiversityanalysisandmarkertransferabilityacrossalliaceae AT berettahebevanesa microsatelliteanalysisandmarkerdevelopmentingarlicdistributioninestsequencegeneticdiversityanalysisandmarkertransferabilityacrossalliaceae AT kozubperlac microsatelliteanalysisandmarkerdevelopmentingarlicdistributioninestsequencegeneticdiversityanalysisandmarkertransferabilityacrossalliaceae AT salinaspalmierimariacecilia microsatelliteanalysisandmarkerdevelopmentingarlicdistributioninestsequencegeneticdiversityanalysisandmarkertransferabilityacrossalliaceae AT galmariniclaudioromulo microsatelliteanalysisandmarkerdevelopmentingarlicdistributioninestsequencegeneticdiversityanalysisandmarkertransferabilityacrossalliaceae AT cavagnaropablo microsatelliteanalysisandmarkerdevelopmentingarlicdistributioninestsequencegeneticdiversityanalysisandmarkertransferabilityacrossalliaceae |