Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data
Gene banks have been established to conserve the genetic diversity of crop species. Large germplasm collections lead to management problems (space, maintenance costs, etc.), especially in collections involving species with recalcitrant seeds that must be maintained as growing plants. Core collection...
| Autores principales: | , , , |
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| Formato: | article |
| Lenguaje: | Inglés |
| Publicado: |
2018
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| Acceso en línea: | http://hdl.handle.net/20.500.11939/6045 |
| _version_ | 1855032357252235264 |
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| author | García-Lor, Andrés Luro, Francois Ollitrault, Patrick Navarro, Luis |
| author_browse | García-Lor, Andrés Luro, Francois Navarro, Luis Ollitrault, Patrick |
| author_facet | García-Lor, Andrés Luro, Francois Ollitrault, Patrick Navarro, Luis |
| author_sort | García-Lor, Andrés |
| collection | ReDivia |
| description | Gene banks have been established to conserve the genetic diversity of crop species. Large germplasm collections lead to management problems (space, maintenance costs, etc.), especially in collections involving species with recalcitrant seeds that must be maintained as growing plants. Core collections (CCs) are thus developed to reduce the size of large germplasm collections while keeping the maximum variability. This also facilitates fine phenotypic evaluation. In this study, several software packages (DARwin, PowerMarker and MSTRAT) and methods (Max length subtree, M strategy, simulated annealing and MinSD) were compared to define a mandarin (Citrus reticulata) CC. One hundred and sixty-seven accessions were sampled from two germplasm collections, which were genotyped with 50 SSR, 24 InDel and 68 single nucleotide polymorphism markers. All the CC obtained were tested for the maintenance of the genetic variability parameters (Ho and He) of the initial collection, the level of linkage disequilibrium (LD) and the phenotypic diversity retention. The Max length subtree function from DARWin seemed to be the most appropriate method for establishing a CC in C. reticulata. It maintained 96.82% of the allelic richness and 17.96% of the size of the initial collection with only 30 accessions. Besides it did not increase the LD (r(2) value) of the initial collection and retained the vast majority of the phenotypic variability. However, a CC with 70 accessions would be more helpful for genetic association studies. |
| format | article |
| id | ReDivia6045 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| record_format | dspace |
| spelling | ReDivia60452025-04-25T14:46:01Z Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data García-Lor, Andrés Luro, Francois Ollitrault, Patrick Navarro, Luis Gene banks have been established to conserve the genetic diversity of crop species. Large germplasm collections lead to management problems (space, maintenance costs, etc.), especially in collections involving species with recalcitrant seeds that must be maintained as growing plants. Core collections (CCs) are thus developed to reduce the size of large germplasm collections while keeping the maximum variability. This also facilitates fine phenotypic evaluation. In this study, several software packages (DARwin, PowerMarker and MSTRAT) and methods (Max length subtree, M strategy, simulated annealing and MinSD) were compared to define a mandarin (Citrus reticulata) CC. One hundred and sixty-seven accessions were sampled from two germplasm collections, which were genotyped with 50 SSR, 24 InDel and 68 single nucleotide polymorphism markers. All the CC obtained were tested for the maintenance of the genetic variability parameters (Ho and He) of the initial collection, the level of linkage disequilibrium (LD) and the phenotypic diversity retention. The Max length subtree function from DARWin seemed to be the most appropriate method for establishing a CC in C. reticulata. It maintained 96.82% of the allelic richness and 17.96% of the size of the initial collection with only 30 accessions. Besides it did not increase the LD (r(2) value) of the initial collection and retained the vast majority of the phenotypic variability. However, a CC with 70 accessions would be more helpful for genetic association studies. 2018-05-09T16:30:58Z 2018-05-09T16:30:58Z 2017 article Garcia-Lor, A., Luro, F., Ollitrault, P., Navarro, L. (2017). Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data. Annals of Applied Biology, 171(3), 327-339. 0003-4746 http://hdl.handle.net/20.500.11939/6045 10.1111/aab.12376 en Atribución-NoComercial-SinDerivadas 3.0 España http://creativecommons.org/licenses/by-nc-nd/3.0/es/ electronico |
| spellingShingle | García-Lor, Andrés Luro, Francois Ollitrault, Patrick Navarro, Luis Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data |
| title | Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data |
| title_full | Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data |
| title_fullStr | Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data |
| title_full_unstemmed | Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data |
| title_short | Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data |
| title_sort | comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data |
| url | http://hdl.handle.net/20.500.11939/6045 |
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