Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain
The 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...
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| Format: | article |
| Language: | Inglés |
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Public Library of Science (PLOS)
2023
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| Online Access: | https://hdl.handle.net/20.500.11939/8698 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286839 |
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| author | Sales, Ester García-Romeral, Julia Domingo, Concha |
| author_browse | Domingo, Concha García-Romeral, Julia Sales, Ester |
| author_facet | Sales, Ester García-Romeral, Julia Domingo, Concha |
| author_sort | Sales, Ester |
| collection | ReDivia |
| description | The 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. |
| format | article |
| id | ReDivia8698 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Public Library of Science (PLOS) |
| publisherStr | Public Library of Science (PLOS) |
| record_format | dspace |
| spelling | ReDivia86982025-04-25T14:49:19Z Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain Sales, Ester García-Romeral, Julia Domingo, Concha SNP markers Japonica rice F30 Plant genetics and breeding U10 Mathematical and statistical methods Q01 Food science and technology Bioinformatics Cultivated varieties Molecular markers Identification The 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. 2023-08-29T11:25:05Z 2023-08-29T11:25:05Z 2023 article publishedVersion Sales, 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. 1932-6203 (Online ISSN) https://hdl.handle.net/20.500.11939/8698 10.1371/journal.pone.0286839 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286839 en This 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). JGR was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades (https://www.ciencia.gob.es/) (fellowship number PRE2019-089034). info:eu-repo/grantAgreement/ERDF/PCV 2021-2027/52201/ES/Relanzando la agroalimentación valenciana para una producción y consumo sostenibles y seguros/AgroAlimVal Attribution-NonCommercial-NoDerivatives 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/ openAccess Public Library of Science (PLOS) electronico |
| spellingShingle | SNP markers Japonica rice F30 Plant genetics and breeding U10 Mathematical and statistical methods Q01 Food science and technology Bioinformatics Cultivated varieties Molecular markers Identification Sales, Ester García-Romeral, Julia Domingo, Concha Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain |
| title | Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain |
| title_full | Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain |
| title_fullStr | Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain |
| title_full_unstemmed | Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain |
| title_short | Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain |
| title_sort | bioinformatics approach for developing a minimum set of snp markers for identification of temperate japonica rice varieties cultivated in spain |
| topic | SNP markers Japonica rice F30 Plant genetics and breeding U10 Mathematical and statistical methods Q01 Food science and technology Bioinformatics Cultivated varieties Molecular markers Identification |
| url | https://hdl.handle.net/20.500.11939/8698 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286839 |
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