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

Abstract 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...

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Autores principales:	Arnaud Comlan Gouda, Marilyn L. Warburton, Gustave L. Djedatin, Sèdjro Bienvenu Kpeki, Peterson W. Wambugu, Karlin Gnikoua, Marie Noelle Ndjiondjop
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fe77ee57861441da9c7519cf97234f7d
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spelling	oai:doaj.org-article:fe77ee57861441da9c7519cf97234f7d2021-12-02T15:14:55ZDevelopment and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species10.1038/s41598-021-97689-32045-2322https://doaj.org/article/fe77ee57861441da9c7519cf97234f7d2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97689-3https://doaj.org/toc/2045-2322Abstract 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.Arnaud Comlan GoudaMarilyn L. WarburtonGustave L. DjedatinSèdjro Bienvenu KpekiPeterson W. WambuguKarlin GnikouaMarie Noelle NdjiondjopNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Arnaud Comlan Gouda Marilyn L. Warburton Gustave L. Djedatin Sèdjro Bienvenu Kpeki Peterson W. Wambugu Karlin Gnikoua Marie Noelle Ndjiondjop Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species
description	Abstract 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.
format	article
author	Arnaud Comlan Gouda Marilyn L. Warburton Gustave L. Djedatin Sèdjro Bienvenu Kpeki Peterson W. Wambugu Karlin Gnikoua Marie Noelle Ndjiondjop
author_facet	Arnaud Comlan Gouda Marilyn L. Warburton Gustave L. Djedatin Sèdjro Bienvenu Kpeki Peterson W. Wambugu Karlin Gnikoua Marie Noelle Ndjiondjop
author_sort	Arnaud Comlan Gouda
title	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_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_sort	development and validation of diagnostic snp markers for quality control genotyping in a collection of four rice (oryza) species
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fe77ee57861441da9c7519cf97234f7d
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Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species

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