resumen
Abstract
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
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dc.contributor.author | Molina, Catalina | |
dc.contributor.author | Aguirre, Natalia Cristina | |
dc.contributor.author | Vera, Pablo Alfredo | |
dc.contributor.author | Filippi, Carla Valeria | |
dc.contributor.author | Puebla, Andrea Fabiana | |
dc.contributor.author | Marcucci Poltri, Susana Noemi | |
dc.contributor.author | Paniego, Norma Beatriz | |
dc.contributor.author | Acevedo, Alberto | |
dc.date.accessioned | 2022-11-28T11:17:30Z | |
dc.date.available | 2022-11-28T11:17:30Z | |
dc.date.issued | 2022-11-11 | |
dc.identifier.issn | 2223-7747 | |
dc.identifier.other | https://doi.org/10.1007/s11103-022-01322-4 | |
dc.identifier.uri | http://hdl.handle.net/20.500.12123/13460 | |
dc.identifier.uri | https://link.springer.com/article/10.1007/s11103-022-01322-4 | |
dc.description.abstract | 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. | eng |
dc.format | application/pdf | es_AR |
dc.language.iso | eng | es_AR |
dc.publisher | Springer | es_AR |
dc.relation | 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. | |
dc.relation | 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 | info:eu-repo/semantics/restrictedAccess | es_AR |
dc.source | Plant Molecular Biology (Published: 11 November 2022) | es_AR |
dc.subject | Single Nucleotide Polymorphism | eng |
dc.subject | Polimorfismo de un Solo Nucleótido | es_AR |
dc.subject | Saccharum | es_AR |
dc.subject | Hybrids | eng |
dc.subject | Híbridos | es_AR |
dc.subject | Sugar Cane | eng |
dc.subject | Caña de Azúcar | es_AR |
dc.subject.other | Genotyping by Sequencing | eng |
dc.subject.other | Genotipado por Secuenciación | es_AR |
dc.subject.other | Polyploid Genome | eng |
dc.subject.other | Genoma Poliploide | es_AR |
dc.subject.other | Sequencing | eng |
dc.subject.other | Secuenciación | es_AR |
dc.title | ddRADseq‑mediated detection of genetic variants in sugarcane | es_AR |
dc.type | info:ar-repo/semantics/artículo | es_AR |
dc.type | info:eu-repo/semantics/article | es_AR |
dc.type | info:eu-repo/semantics/publishedVersion | es_AR |
dc.description.fil | Fil: Molina, Catalina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina | es_AR |
dc.description.fil | Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina | es_AR |
dc.description.fil | Fil: Vera, Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina | es_AR |
dc.description.fil | Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina | es_AR |
dc.description.fil | Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina | es_AR |
dc.description.fil | Fil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina | es_AR |
dc.description.fil | Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina | es_AR |
dc.description.fil | Fil: Acevedo, Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina | es_AR |
dc.subtype | cientifico |
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