ddRADseq‑mediated detection of genetic variants in sugarcane
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 hybri...
| Autores principales: | , , , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2022
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| Materias: | |
| Acceso en línea: | 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 |
| _version_ | 1855485172739211264 |
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| author | Molina, Catalina Aguirre, Natalia Cristina Vera, Pablo Alfredo Filippi, Carla Valeria Puebla, Andrea Fabiana Marcucci Poltri, Susana Noemi Paniego, Norma Beatriz Acevedo, Alberto |
| author_browse | Acevedo, Alberto Aguirre, Natalia Cristina Filippi, Carla Valeria Marcucci Poltri, Susana Noemi Molina, Catalina Paniego, Norma Beatriz Puebla, Andrea Fabiana Vera, Pablo Alfredo |
| 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_sort | Molina, Catalina |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA13460 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | INTA134602022-11-28T11:26:17Z ddRADseq‑mediated detection of genetic variants in sugarcane Molina, Catalina Aguirre, Natalia Cristina Vera, Pablo Alfredo Filippi, Carla Valeria Puebla, Andrea Fabiana Marcucci Poltri, Susana Noemi Paniego, Norma Beatriz Acevedo, Alberto 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 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 2022-11-28T11:17:30Z 2022-11-28T11:17:30Z 2022-11-11 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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 info:eu-repo/semantics/restrictedAccess application/pdf Springer Plant Molecular Biology (Published: 11 November 2022) |
| spellingShingle | 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 Molina, Catalina Aguirre, Natalia Cristina Vera, Pablo Alfredo Filippi, Carla Valeria Puebla, Andrea Fabiana Marcucci Poltri, Susana Noemi Paniego, Norma Beatriz Acevedo, Alberto ddRADseq‑mediated detection of genetic variants in sugarcane |
| title | 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_short | ddRADseq‑mediated detection of genetic variants in sugarcane |
| title_sort | ddradseq mediated detection of genetic variants in sugarcane |
| 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 |
| 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 |
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