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...

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Autores: Reig-Valiente, Juan L., Viruel, Juan, Sales, Ester, Marqués, Luis, Terol, Javier, Gut, Marta, Derdak, Sophia, Talón, Manuel, Domingo, Concha
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/68897
Acceso en línea:http://hdl.handle.net/10230/68897
http://dx.doi.org/10.1186/s12284-016-0130-5
Access Level:acceso abierto
Palabra clave:SNPs
Oryza sativa
Infinium SNP genotyping array
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spelling Genetic diversity and population structure of rice varieties cultivated in temperate regionsReig-Valiente, Juan L.Viruel, JuanSales, EsterMarqués, LuisTerol, JavierGut, MartaDerdak, SophiaTalón, ManuelDomingo, ConchaSNPsOryza sativaInfinium SNP genotyping arrayBackground. 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 Open202420242016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/68897http://dx.doi.org/10.1186/s12284-016-0130-5reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésRice. 2016;9:58This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/688972026-06-12T07:21:37Z
dc.title.none.fl_str_mv 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
spellingShingle Genetic diversity and population structure of rice varieties cultivated in temperate regions
Reig-Valiente, Juan L.
SNPs
Oryza sativa
Infinium SNP genotyping array
title_short 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_sort Genetic diversity and population structure of rice varieties cultivated in temperate regions
dc.creator.none.fl_str_mv Reig-Valiente, Juan L.
Viruel, Juan
Sales, Ester
Marqués, Luis
Terol, Javier
Gut, Marta
Derdak, Sophia
Talón, Manuel
Domingo, Concha
author Reig-Valiente, Juan L.
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
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
dc.subject.none.fl_str_mv SNPs
Oryza sativa
Infinium SNP genotyping array
topic SNPs
Oryza sativa
Infinium SNP genotyping array
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.
publishDate 2016
dc.date.none.fl_str_mv 2016
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/68897
http://dx.doi.org/10.1186/s12284-016-0130-5
url http://hdl.handle.net/10230/68897
http://dx.doi.org/10.1186/s12284-016-0130-5
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Rice. 2016;9:58
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
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application/pdf
dc.publisher.none.fl_str_mv Springer Open
publisher.none.fl_str_mv Springer Open
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instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
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