ddRADseq‑mediated detection of genetic variants in sugarcane

Autores
Molina, Catalina; Aguirre, Natalia Cristina; Vera, Pablo Alfredo; Filippi, Carla Valeria; Puebla, Andrea Fabiana; Marcucci Poltri, Susana Noemi; Paniego, Norma Beatriz; Acevedo, Alberto
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Sugarcane (Saccharum sp.), a world-wide known feedstock for sugar production, bioethanol, and energy, has an extremely complex genome, being highly polyploid and aneuploid. A double-digestion restriction site-associated DNA sequencing protocol (ddRADseq) was tested in four commercial sugarcane hybrids and one high-fbre biotype for the detec tion of single nucleotide polymorphisms (SNPs). In this work we tested two Illumina sequencing platforms, read size (70 vs. 150 bp), diferent sequencing coverage per individual (medium and high coverage), and single-reads versus paired-end reads. We also explored diferent variant calling strategies (with and without reference genome) and fltering schemes [com bining two minor allele frequencies (MAFs) with three depth of coverage thresholds]. For the discovery of a large number of novel SNPs in sugarcane, we recommend longer size and paired-end reads, medium sequencing coverage per individual and Illumina platform NovaSeq6000 for a cost-efective approach, and flter parameters of lower MAF and higher depth coverages thresholds. Although the de novo analysis retrieved more SNPs, the reference-based method allows downstream characterization of variants. For the two best performing matrices, the number of SNPs per chromosome correlated positively with chromosome length, demonstrating the presence of variants throughout the genome. Multivariate comparisons, with both matrices, showed closer relationships among commercial hybrids than with the high-fbre biotype. Functional analysis of the SNPs demonstrated that more than half of them landed within regulatory regions, whereas the other half afected cod ing, intergenic and intronic regions. Allelic distances values were lower than 0.07 when analysing two replicated genotypes, confrming the protocol robustness.
Fil: Molina, Catalina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Vera, Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Acevedo, Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina
Fuente
Plant Molecular Biology (Published: 11 November 2022)
Materia
Single Nucleotide Polymorphism
Hybrids
Sugar Cane
Polimorfismo de un Solo Nucleótido
Saccharum
Híbridos
Caña de Azúcar
Genotyping by Sequencing
Polyploid Genome
Sequencing
Genotipado por Secuenciación
Genoma Poliploide
Secuenciación
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/13460
Acceder
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oai_identifier_str oai:localhost:20.500.12123/13460
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network_name_str INTA Digital (INTA)
spelling ddRADseq‑mediated detection of genetic variants in sugarcaneMolina, CatalinaAguirre, Natalia CristinaVera, Pablo AlfredoFilippi, Carla ValeriaPuebla, Andrea FabianaMarcucci Poltri, Susana NoemiPaniego, Norma BeatrizAcevedo, AlbertoSingle Nucleotide PolymorphismHybridsSugar CanePolimorfismo de un Solo NucleótidoSaccharumHíbridosCaña de AzúcarGenotyping by SequencingPolyploid GenomeSequencingGenotipado por SecuenciaciónGenoma PoliploideSecuenciaciónSugarcane (Saccharum sp.), a world-wide known feedstock for sugar production, bioethanol, and energy, has an extremely complex genome, being highly polyploid and aneuploid. A double-digestion restriction site-associated DNA sequencing protocol (ddRADseq) was tested in four commercial sugarcane hybrids and one high-fbre biotype for the detec tion of single nucleotide polymorphisms (SNPs). In this work we tested two Illumina sequencing platforms, read size (70 vs. 150 bp), diferent sequencing coverage per individual (medium and high coverage), and single-reads versus paired-end reads. We also explored diferent variant calling strategies (with and without reference genome) and fltering schemes [com bining two minor allele frequencies (MAFs) with three depth of coverage thresholds]. For the discovery of a large number of novel SNPs in sugarcane, we recommend longer size and paired-end reads, medium sequencing coverage per individual and Illumina platform NovaSeq6000 for a cost-efective approach, and flter parameters of lower MAF and higher depth coverages thresholds. Although the de novo analysis retrieved more SNPs, the reference-based method allows downstream characterization of variants. For the two best performing matrices, the number of SNPs per chromosome correlated positively with chromosome length, demonstrating the presence of variants throughout the genome. Multivariate comparisons, with both matrices, showed closer relationships among commercial hybrids than with the high-fbre biotype. Functional analysis of the SNPs demonstrated that more than half of them landed within regulatory regions, whereas the other half afected cod ing, intergenic and intronic regions. Allelic distances values were lower than 0.07 when analysing two replicated genotypes, confrming the protocol robustness.Fil: Molina, Catalina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vera, Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Acevedo, Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; ArgentinaSpringer2022-11-28T11:17:30Z2022-11-28T11:17:30Z2022-11-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/13460https://link.springer.com/article/10.1007/s11103-022-01322-42223-7747https://doi.org/10.1007/s11103-022-01322-4Plant Molecular Biology (Published: 11 November 2022)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/2019-PE-E6-I114-001/2019-PE-E6-I114-001/AR./Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.info:eu-repograntAgreement/INTA/2019-PE-E6-I516-001/2019-PE-E6-I516-001/AR./Mejoramiento genético y desarrollo de ideotipos de cultivos industriales (CI) caña, maní, yerba, mandioca, stevia, quinua y te para sistemas productivos resilientesinfo:eu-repo/semantics/restrictedAccess2025-10-16T09:30:59Zoai:localhost:20.500.12123/13460instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-16 09:31:00.448INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv ddRADseq‑mediated detection of genetic variants in sugarcane
title ddRADseq‑mediated detection of genetic variants in sugarcane
spellingShingle ddRADseq‑mediated detection of genetic variants in sugarcane
Molina, Catalina
Single Nucleotide Polymorphism
Hybrids
Sugar Cane
Polimorfismo de un Solo Nucleótido
Saccharum
Híbridos
Caña de Azúcar
Genotyping by Sequencing
Polyploid Genome
Sequencing
Genotipado por Secuenciación
Genoma Poliploide
Secuenciación
title_short ddRADseq‑mediated detection of genetic variants in sugarcane
title_full ddRADseq‑mediated detection of genetic variants in sugarcane
title_fullStr ddRADseq‑mediated detection of genetic variants in sugarcane
title_full_unstemmed ddRADseq‑mediated detection of genetic variants in sugarcane
title_sort ddRADseq‑mediated detection of genetic variants in sugarcane
dc.creator.none.fl_str_mv Molina, Catalina
Aguirre, Natalia Cristina
Vera, Pablo Alfredo
Filippi, Carla Valeria
Puebla, Andrea Fabiana
Marcucci Poltri, Susana Noemi
Paniego, Norma Beatriz
Acevedo, Alberto
author Molina, Catalina
author_facet Molina, Catalina
Aguirre, Natalia Cristina
Vera, Pablo Alfredo
Filippi, Carla Valeria
Puebla, Andrea Fabiana
Marcucci Poltri, Susana Noemi
Paniego, Norma Beatriz
Acevedo, Alberto
author_role author
author2 Aguirre, Natalia Cristina
Vera, Pablo Alfredo
Filippi, Carla Valeria
Puebla, Andrea Fabiana
Marcucci Poltri, Susana Noemi
Paniego, Norma Beatriz
Acevedo, Alberto
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Single Nucleotide Polymorphism
Hybrids
Sugar Cane
Polimorfismo de un Solo Nucleótido
Saccharum
Híbridos
Caña de Azúcar
Genotyping by Sequencing
Polyploid Genome
Sequencing
Genotipado por Secuenciación
Genoma Poliploide
Secuenciación
topic Single Nucleotide Polymorphism
Hybrids
Sugar Cane
Polimorfismo de un Solo Nucleótido
Saccharum
Híbridos
Caña de Azúcar
Genotyping by Sequencing
Polyploid Genome
Sequencing
Genotipado por Secuenciación
Genoma Poliploide
Secuenciación
dc.description.none.fl_txt_mv Sugarcane (Saccharum sp.), a world-wide known feedstock for sugar production, bioethanol, and energy, has an extremely complex genome, being highly polyploid and aneuploid. A double-digestion restriction site-associated DNA sequencing protocol (ddRADseq) was tested in four commercial sugarcane hybrids and one high-fbre biotype for the detec tion of single nucleotide polymorphisms (SNPs). In this work we tested two Illumina sequencing platforms, read size (70 vs. 150 bp), diferent sequencing coverage per individual (medium and high coverage), and single-reads versus paired-end reads. We also explored diferent variant calling strategies (with and without reference genome) and fltering schemes [com bining two minor allele frequencies (MAFs) with three depth of coverage thresholds]. For the discovery of a large number of novel SNPs in sugarcane, we recommend longer size and paired-end reads, medium sequencing coverage per individual and Illumina platform NovaSeq6000 for a cost-efective approach, and flter parameters of lower MAF and higher depth coverages thresholds. Although the de novo analysis retrieved more SNPs, the reference-based method allows downstream characterization of variants. For the two best performing matrices, the number of SNPs per chromosome correlated positively with chromosome length, demonstrating the presence of variants throughout the genome. Multivariate comparisons, with both matrices, showed closer relationships among commercial hybrids than with the high-fbre biotype. Functional analysis of the SNPs demonstrated that more than half of them landed within regulatory regions, whereas the other half afected cod ing, intergenic and intronic regions. Allelic distances values were lower than 0.07 when analysing two replicated genotypes, confrming the protocol robustness.
Fil: Molina, Catalina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Vera, Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Acevedo, Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina
description Sugarcane (Saccharum sp.), a world-wide known feedstock for sugar production, bioethanol, and energy, has an extremely complex genome, being highly polyploid and aneuploid. A double-digestion restriction site-associated DNA sequencing protocol (ddRADseq) was tested in four commercial sugarcane hybrids and one high-fbre biotype for the detec tion of single nucleotide polymorphisms (SNPs). In this work we tested two Illumina sequencing platforms, read size (70 vs. 150 bp), diferent sequencing coverage per individual (medium and high coverage), and single-reads versus paired-end reads. We also explored diferent variant calling strategies (with and without reference genome) and fltering schemes [com bining two minor allele frequencies (MAFs) with three depth of coverage thresholds]. For the discovery of a large number of novel SNPs in sugarcane, we recommend longer size and paired-end reads, medium sequencing coverage per individual and Illumina platform NovaSeq6000 for a cost-efective approach, and flter parameters of lower MAF and higher depth coverages thresholds. Although the de novo analysis retrieved more SNPs, the reference-based method allows downstream characterization of variants. For the two best performing matrices, the number of SNPs per chromosome correlated positively with chromosome length, demonstrating the presence of variants throughout the genome. Multivariate comparisons, with both matrices, showed closer relationships among commercial hybrids than with the high-fbre biotype. Functional analysis of the SNPs demonstrated that more than half of them landed within regulatory regions, whereas the other half afected cod ing, intergenic and intronic regions. Allelic distances values were lower than 0.07 when analysing two replicated genotypes, confrming the protocol robustness.
publishDate 2022
dc.date.none.fl_str_mv 2022-11-28T11:17:30Z
2022-11-28T11:17:30Z
2022-11-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/13460
https://link.springer.com/article/10.1007/s11103-022-01322-4
2223-7747
https://doi.org/10.1007/s11103-022-01322-4
url http://hdl.handle.net/20.500.12123/13460
https://link.springer.com/article/10.1007/s11103-022-01322-4
https://doi.org/10.1007/s11103-022-01322-4
identifier_str_mv 2223-7747
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/2019-PE-E6-I114-001/2019-PE-E6-I114-001/AR./Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.
info:eu-repograntAgreement/INTA/2019-PE-E6-I516-001/2019-PE-E6-I516-001/AR./Mejoramiento genético y desarrollo de ideotipos de cultivos industriales (CI) caña, maní, yerba, mandioca, stevia, quinua y te para sistemas productivos resilientes
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv Plant Molecular Biology (Published: 11 November 2022)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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