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 Sánchez, Juan, Sales, Esther, 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:Universidad de Sevilla (US)
Repositorio:idUS. Depósito de Investigación de la Universidad de Sevilla
OAI Identifier:oai:idus.us.es:11441/61079
Acceso en línea:http://hdl.handle.net/11441/61079
https://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 Regions Reig Valiente, Juan L. Viruel Sánchez, Juan Sales, Esther 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. SpringerOpen http://hdl.handle.net/11441/61079 https://doi.org/10.1186/s12284-016-0130-5
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
author Reig Valiente, Juan L.
author_facet Reig Valiente, Juan L.
Viruel Sánchez, Juan
Sales, Esther
Marqués, Luis
Terol, Javier
Gut, Marta
Derdak, Sophia
Talón, Manuel
Domingo, Concha
author_role author
author2 Viruel Sánchez, Juan
Sales, Esther
Marqués, Luis
Terol, Javier
Gut, Marta
Derdak, Sophia
Talón, Manuel
Domingo, Concha
author2_role author
author
author
author
author
author
author
author
topic SNPs
Oryza sativa
Infinium SNP genotyping array
topic_facet 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
format article
status_str publishedVersion
url http://hdl.handle.net/11441/61079
https://doi.org/10.1186/s12284-016-0130-5
eu_rights_str_mv openAccess
publisher SpringerOpen
institution Universidad de Sevilla (US)
collection idUS. Depósito de Investigación de la Universidad de Sevilla
reponame_str idUS. Depósito de Investigación de la Universidad de Sevilla
instname_str Universidad de Sevilla (US)
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publishDateSort 2016
author_browse Derdak, Sophia
Domingo, Concha
Gut, Marta
Marqués, Luis
Reig Valiente, Juan L.
Sales, Esther
Talón, Manuel
Terol, Javier
Viruel Sánchez, Juan
publisherStr SpringerOpen
score 6,924472

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