title: Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions.
abstract: 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.
authors.affiliation: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada - Náquera Km 4.5), 46113, Moncada, Spain.
authors.forename: Juan L
authors.initials: JL
authors.lastname: Reig-Valiente
authors.affiliation: Dpto. Biología Vegetal y Ecología, SGI Herbario - Universidad de Sevilla, Edif. Celestino Mutis, Av. Reina Mercedes s/n, 41012, Sevilla, Spain.|Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), Aix Marseille Université, Chemin de la Batterie des Lions, 13007, Marseille, France.
authors.forename: Juan
authors.initials: J
authors.lastname: Viruel
authors.affiliation: Dpto. Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior, Universidad de Zaragoza, Ctra. Cuarte s/n, 22071, Huesca, Spain.
authors.forename: Ester
authors.initials: E
authors.lastname: Sales
authors.affiliation: Cooperativa de Productores de Semillas de Arroz, Avenida del Mar 1, 46410, Sueca, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Marqués
authors.affiliation: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada - Náquera Km 4.5), 46113, Moncada, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Terol
authors.affiliation: Centre Nacional d'Anàlisi Genòmica - Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.affiliation: Centre Nacional d'Anàlisi Genòmica - Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 4, 08028, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Sophia
authors.initials: S
authors.lastname: Derdak
authors.affiliation: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada - Náquera Km 4.5), 46113, Moncada, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Talón
authors.affiliation: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada - Náquera Km 4.5), 46113, Moncada, Spain. domingo_concar@gva.es.
authors.forename: Concha
authors.identifier: http://orcid.org/0000-0002-7204-7591
authors.initials: C
authors.lastname: Domingo
keywords: Infinium SNP genotyping array; Oryza sativa; SNPs