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Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species

Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several r...

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Autores principales: Gouda, Arnaud Comlan, Warburton, Marilyn L., Djedatin, Gustave L., Kpeki, Sèdjro Bienvenu, Wambugu, Peterson W., Gnikoua, Karlin, Ndjiondjop, Marie Noelle
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8452751/
https://www.ncbi.nlm.nih.gov/pubmed/34545105
http://dx.doi.org/10.1038/s41598-021-97689-3
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author Gouda, Arnaud Comlan
Warburton, Marilyn L.
Djedatin, Gustave L.
Kpeki, Sèdjro Bienvenu
Wambugu, Peterson W.
Gnikoua, Karlin
Ndjiondjop, Marie Noelle
author_facet Gouda, Arnaud Comlan
Warburton, Marilyn L.
Djedatin, Gustave L.
Kpeki, Sèdjro Bienvenu
Wambugu, Peterson W.
Gnikoua, Karlin
Ndjiondjop, Marie Noelle
author_sort Gouda, Arnaud Comlan
collection PubMed
description Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology (“DArTseq”). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies’ diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymorphic, and distinguished the five species/subspecies tested. Based on these validation test results, we recommend a panel of 36 SNP markers that clearly delineate O. barthii, O. glaberrima, O. longistaminata, O. sativa spp. indica and japonica. The KASP assays provide a flexible, rapid turnaround and cost-effective tool to facilitate germplasm curation and management of these four Oryza AA genome species across multiple genebanks.
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spelling pubmed-84527512021-09-22 Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species Gouda, Arnaud Comlan Warburton, Marilyn L. Djedatin, Gustave L. Kpeki, Sèdjro Bienvenu Wambugu, Peterson W. Gnikoua, Karlin Ndjiondjop, Marie Noelle Sci Rep Article Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology (“DArTseq”). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies’ diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymorphic, and distinguished the five species/subspecies tested. Based on these validation test results, we recommend a panel of 36 SNP markers that clearly delineate O. barthii, O. glaberrima, O. longistaminata, O. sativa spp. indica and japonica. The KASP assays provide a flexible, rapid turnaround and cost-effective tool to facilitate germplasm curation and management of these four Oryza AA genome species across multiple genebanks. Nature Publishing Group UK 2021-09-20 /pmc/articles/PMC8452751/ /pubmed/34545105 http://dx.doi.org/10.1038/s41598-021-97689-3 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Gouda, Arnaud Comlan
Warburton, Marilyn L.
Djedatin, Gustave L.
Kpeki, Sèdjro Bienvenu
Wambugu, Peterson W.
Gnikoua, Karlin
Ndjiondjop, Marie Noelle
Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species
title Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species
title_full Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species
title_fullStr Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species
title_full_unstemmed Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species
title_short Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species
title_sort development and validation of diagnostic snp markers for quality control genotyping in a collection of four rice (oryza) species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8452751/
https://www.ncbi.nlm.nih.gov/pubmed/34545105
http://dx.doi.org/10.1038/s41598-021-97689-3
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