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dc.contributor.authorSales, Ester
dc.contributor.authorGarcía-Romeral, Julia
dc.contributor.authorDomingo, Concha 
dc.date.accessioned2023-08-29T11:25:05Z
dc.date.available2023-08-29T11:25:05Z
dc.date.issued2023es
dc.identifier.citationales, E., García-Romeral, J. & Domingo, C. (2023) Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain. PLoS ONE, 18(6), e0286839.es
dc.identifier.issn1932-6203 (Online ISSN)
dc.identifier.urihttps://hdl.handle.net/20.500.11939/8698
dc.description.abstractThe use of molecular markers for plant variety identification and protection is increasing. For this purpose, SNP markers have provided a reliable and stable tool for plant genotyping. The availability of small and low-cost SNP panels to accelerate the identification of the cultivated rice varieties should be beneficial for breeders, seed certification entities and rice industry. With the intention of providing of such a facility, we first developed a simple and easy-handle bioinformatics tool based on the widely used and freely available software R to generate small sets of SNPs that can discriminate varieties, by selecting markers from a larger genotyping dataset. By applying this algorithm to data from a previously genotyped collection of temperate japonica varieties from different countries, we identified a minimal set of 31 SNPs markers to distinguish 210 varieties. In addition, we used this algorithm to discriminate the 43 most cultivated in Spain rice varieties with minimal sets of 8 SNPs. We then developed and tested 22 Kompetitive Allele-Specific PCR (KASP) assays for the markers included in these panels, and obtained reliable genotype patterns for rice varieties identification. The complete 22 markers panel and the rice genotypes data could offer a useful and low-cost tool for rice breeders and industry to identify varieties and therefore to guarantee the quality of rice. The provided R-based algorithm can be applied to other genomic resources to develop core sets of discriminating markers.es
dc.language.isoenes
dc.publisherPublic Library of Science (PLOS)es
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internacional*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subjectSNP markerses
dc.subjectJaponica ricees
dc.titleBioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spaines
dc.typearticlees
dc.authorAddressdomingo_concar@gva.eses
dc.entidadIVIACentro de Genómicaes
dc.identifier.doi10.1371/journal.pone.0286839es
dc.identifier.urlhttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286839es
dc.journal.issueNumber6es
dc.journal.titlePlosOnees
dc.journal.volumeNumber18es
dc.page.finale0286839es
dc.page.initiale0286839es
dc.relation.projectIDThis work was supported by the project IVIA-GVA 52201 from Instituto Valenciano de Investigaciones Agrarias (co-financed by the European Union through the ERDF Program 2021-2027 Comunitat Valenciana).es
dc.relation.projectIDJGR was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades (https://www.ciencia.gob.es/) (fellowship number PRE2019-089034).es
dc.relation.projectIDinfo:eu-repo/grantAgreement/ERDF/PCV 2021-2027/52201/ES/Relanzando la agroalimentación valenciana para una producción y consumo sostenibles y seguros/AgroAlimVales
dc.rights.accessRightsopenAccesses
dc.source.typeelectronicoes
dc.subject.agrisF30 Plant genetics and breedinges
dc.subject.agrisU10 Mathematical and statistical methodses
dc.subject.agrisQ01 Food science and technologyes
dc.subject.agrovocBioinformatics es
dc.subject.agrovocCultivated varieties es
dc.subject.agrovocMolecular markers es
dc.subject.agrovocIdentification es
dc.type.hasVersionpublishedVersiones


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Attribution-NonCommercial-NoDerivatives 4.0 Internacional
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