Abstract
BackgroundAfter 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.ResultsA 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.ConclusionsBased 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0130-5) contains supplementary material, which is available to authorized users.
Highlights
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
A collection of 217 selected varieties was generated in order to analyse the population structure of rice grown under long photoperiod conditions
The collection was composed of modern and old cultivars as well as some landraces to cover a wider genetic diversity (Additional file 1: Table S1, Additional file 2: Figure S1). In this compilation (26 countries, 52.5 % arising from Europe; Additional file 1: Table S1), the core collection was composed of cultivars considered as japonica type from different geographical origins and cultivated in temperate climates in northern latitudes
Summary
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. Full list of author information is available at the end of the article diverse climates (Gross and Zhao 2014) As a consequence, it was generated an extensive and vast array of genetic diversity that in principle can be predominantly structured in two main subgroups (Childs 2004), including the indica and japonica varietal groups. It was generated an extensive and vast array of genetic diversity that in principle can be predominantly structured in two main subgroups (Childs 2004), including the indica and japonica varietal groups These genetic groups are characterized by adaptations to specific climates, according to the agro-ecological conditions where they were cultivated.
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