Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions
Background After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a...
| Autores principales: | , , , , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2020
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| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.11939/6290 https://link.springer.com/article/10.1186/s12284-016-0130-5 |
| _version_ | 1855492054007676928 |
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| author | Reig-Valiente, Juan L. Viruel, Juan Sales, Ester Marqués, Luis Terol, Javier Gut, Marta Derdak, Sophia Talón, Manuel Domingo, Concha |
| author_browse | Derdak, Sophia Domingo, Concha Gut, Marta Marqués, Luis Reig-Valiente, Juan L. Sales, Ester Talón, Manuel Terol, Javier Viruel, Juan |
| author_facet | Reig-Valiente, Juan L. Viruel, Juan Sales, Ester Marqués, Luis Terol, Javier Gut, Marta Derdak, Sophia Talón, Manuel Domingo, Concha |
| author_sort | Reig-Valiente, Juan L. |
| collection | ReDivia |
| description | Background
After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits. Comprehensive maps of genome variability and population structure would facilitate genome-wide association studies of complex traits, functional gene investigations and the selection of appropriate donors for breeding purposes.
Results
A collection of 217 rice varieties mainly cultivated in temperate regions was generated. The collection encompasses modern elite and old cultivars, as well as traditional landraces covering a wide genetic diversity available for rice breeders. Whole Genome Sequencing was performed on 14 cultivars representative of the collection and the genomic profiles of all cultivars were constructed using a panel of 2697 SNPs with wide coverage throughout the rice genome, obtained from the sequencing data. The population structure and genetic relationship analyses showed a strong substructure in the temperate rice population, predominantly based on grain type and the origin of the cultivars. Dendrogram also agrees population structure results.
Conclusions
Based on SNP markers, we have elucidated the genetic relationship and the degree of genetic diversity among a collection of 217 temperate rice varieties possessing an enormous variety of agromorphological and physiological characters. Taken together, the data indicated the occurrence of relatively high gene flow and elevated rates of admixture between cultivars grown in remote regions, probably favoured by local breeding activities. The results of this study significantly expand the current genetic resources available for temperate varieties of rice, providing a valuable tool for future association mapping studies. |
| format | Artículo |
| id | ReDivia6290 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | ReDivia62902025-04-25T14:46:46Z Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions Reig-Valiente, Juan L. Viruel, Juan Sales, Ester Marqués, Luis Terol, Javier Gut, Marta Derdak, Sophia Talón, Manuel Domingo, Concha SNPs Infinium SNP genotyping array F30 Plant genetics and breeding Oryza sativa Background After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits. Comprehensive maps of genome variability and population structure would facilitate genome-wide association studies of complex traits, functional gene investigations and the selection of appropriate donors for breeding purposes. Results A collection of 217 rice varieties mainly cultivated in temperate regions was generated. The collection encompasses modern elite and old cultivars, as well as traditional landraces covering a wide genetic diversity available for rice breeders. Whole Genome Sequencing was performed on 14 cultivars representative of the collection and the genomic profiles of all cultivars were constructed using a panel of 2697 SNPs with wide coverage throughout the rice genome, obtained from the sequencing data. The population structure and genetic relationship analyses showed a strong substructure in the temperate rice population, predominantly based on grain type and the origin of the cultivars. Dendrogram also agrees population structure results. Conclusions Based on SNP markers, we have elucidated the genetic relationship and the degree of genetic diversity among a collection of 217 temperate rice varieties possessing an enormous variety of agromorphological and physiological characters. Taken together, the data indicated the occurrence of relatively high gene flow and elevated rates of admixture between cultivars grown in remote regions, probably favoured by local breeding activities. The results of this study significantly expand the current genetic resources available for temperate varieties of rice, providing a valuable tool for future association mapping studies. 2020-01-08T09:42:13Z 2020-01-08T09:42:13Z 2016 article publishedVersion Reig-Valiente, J. L., Viruel, J., Sales, E., Marqués, L., Terol, J., Gut, M., ... & Domingo, C. (2016). Genetic diversity and population structure of rice varieties cultivated in temperate regions. Rice, 9(1), 58. 1939-8425 http://hdl.handle.net/20.500.11939/6290 10.1186/s12284-016-0130-5 https://link.springer.com/article/10.1186/s12284-016-0130-5 en Atribución-NoComercial-SinDerivadas 3.0 España http://creativecommons.org/licenses/by-nc-nd/3.0/es/ Springer electronico |
| spellingShingle | SNPs Infinium SNP genotyping array F30 Plant genetics and breeding Oryza sativa Reig-Valiente, Juan L. Viruel, Juan Sales, Ester Marqués, Luis Terol, Javier Gut, Marta Derdak, Sophia Talón, Manuel Domingo, Concha Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions |
| title | Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions |
| title_full | Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions |
| title_fullStr | Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions |
| title_full_unstemmed | Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions |
| title_short | Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions |
| title_sort | genetic diversity and population structure of rice varieties cultivated in temperate regions |
| topic | SNPs Infinium SNP genotyping array F30 Plant genetics and breeding Oryza sativa |
| url | http://hdl.handle.net/20.500.11939/6290 https://link.springer.com/article/10.1186/s12284-016-0130-5 |
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