Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)

A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessi...

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Autores: Duval, Henri, Coindre, Eva, Ramos-Onsins, Sebastian E., Alexiou, Konstantinos, Rubio-Cabetas, Maria J., Martínez-García, Pedro J., Wirthensohn, Michelle, Dhingra, Amit, Samarina, Anna, Arús, Pere
Tipo de recurso: artículo
Fecha de publicación:2023
País:España
Institución:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)
Repositorio:IRTA Pubpro. Open Digital Archive
OAI Identifier:oai:repositori.irta.cat:20.500.12327/2108
Acceso en línea:http://hdl.handle.net/20.500.12327/2108
https://doi.org/10.3390/plants12020242
Access Level:acceso abierto
Palabra clave:633
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spelling Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)Duval, HenriCoindre, EvaRamos-Onsins, Sebastian E.Alexiou, KonstantinosRubio-Cabetas, Maria J.Martínez-García, Pedro J.Wirthensohn, MichelleDhingra, AmitSamarina, AnnaArús, Pere633A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.info:eu-repo/semantics/publishedVersionMDPIProducció VegetalGenòmica i Biotecnologia202320232023info:eu-repo/semantics/article12application/pdfhttp://hdl.handle.net/20.500.12327/2108https://doi.org/10.3390/plants12020242reponame:IRTA Pubpro. Open Digital Archiveinstname:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)InglésPlantshttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.irta.cat:20.500.12327/21082026-06-16T08:51:17Z
dc.title.none.fl_str_mv Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)
title Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)
spellingShingle Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)
Duval, Henri
633
title_short Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)
title_full Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)
title_fullStr Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)
title_full_unstemmed Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)
title_sort Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)
dc.creator.none.fl_str_mv Duval, Henri
Coindre, Eva
Ramos-Onsins, Sebastian E.
Alexiou, Konstantinos
Rubio-Cabetas, Maria J.
Martínez-García, Pedro J.
Wirthensohn, Michelle
Dhingra, Amit
Samarina, Anna
Arús, Pere
author Duval, Henri
author_facet Duval, Henri
Coindre, Eva
Ramos-Onsins, Sebastian E.
Alexiou, Konstantinos
Rubio-Cabetas, Maria J.
Martínez-García, Pedro J.
Wirthensohn, Michelle
Dhingra, Amit
Samarina, Anna
Arús, Pere
author_role author
author2 Coindre, Eva
Ramos-Onsins, Sebastian E.
Alexiou, Konstantinos
Rubio-Cabetas, Maria J.
Martínez-García, Pedro J.
Wirthensohn, Michelle
Dhingra, Amit
Samarina, Anna
Arús, Pere
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Producció Vegetal
Genòmica i Biotecnologia
dc.subject.none.fl_str_mv 633
topic 633
description A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12327/2108
https://doi.org/10.3390/plants12020242
url http://hdl.handle.net/20.500.12327/2108
https://doi.org/10.3390/plants12020242
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Plants
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 12
application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:IRTA Pubpro. Open Digital Archive
instname:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)
instname_str Institut de Recerca i Tecnologia Agroalimentàries (IRTA)
reponame_str IRTA Pubpro. Open Digital Archive
collection IRTA Pubpro. Open Digital Archive
repository.name.fl_str_mv
repository.mail.fl_str_mv
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