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...
| Authors: | ; ; ; ; ; ; ; ; |
|---|---|
| Format: | Article |
| Status: | Published version |
| Publication date: | 2016 |
| Country: | España |
| Institution: | Universitat Pompeu Fabra |
| Repository: | Repositorio Digital de la UPF |
| OAI Identifier: | oai:repositori.upf.edu:10230/68897 |
| Online Access: | http://hdl.handle.net/10230/68897 http://dx.doi.org/10.1186/s12284-016-0130-5 |
| Access Level: | Open access |
| Keyword: | SNPs Oryza sativa Infinium SNP genotyping array |
| _version_ | 1878741740318359552 |
|---|---|
| author | Reig-Valiente, Juan L. |
| author2 | Viruel, Juan Sales, Ester Marqués, Luis Terol, Javier Gut, Marta Derdak, Sophia Talón, Manuel Domingo, Concha |
| author2_role | author author author author author author author author |
| 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_role | author |
| collection | Repositorio Digital de la UPF |
| 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. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | ES_ea934ceaef65d7c8c02ccb5ef76cd73f |
| institution | Universitat Pompeu Fabra |
| instname_str | Universitat Pompeu Fabra |
| network_acronym_str | ES |
| network_name_str | España |
| oai_identifier_str | oai:repositori.upf.edu:10230/68897 |
| publishDate | 2016 |
| publishDateSort | 2016 |
| publisher | Springer Open |
| publisherStr | Springer Open |
| reponame_str | Repositorio Digital de la UPF |
| spelling | 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 Oryza sativa Infinium SNP genotyping array 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. Springer Open http://hdl.handle.net/10230/68897 http://dx.doi.org/10.1186/s12284-016-0130-5 |
| spellingShingle | Genetic diversity and population structure of rice varieties cultivated in temperate regions Reig-Valiente, Juan L. SNPs Oryza sativa Infinium SNP genotyping array |
| status_str | publishedVersion |
| 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 Oryza sativa Infinium SNP genotyping array |
| topic_facet | SNPs Oryza sativa Infinium SNP genotyping array |
| url | http://hdl.handle.net/10230/68897 http://dx.doi.org/10.1186/s12284-016-0130-5 |