Fine-tuning the performance of ddRAD-seq in the peach genome
The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI...
| Autores principales: | , , , , |
|---|---|
| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
Springer Nature
2021
|
| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12123/8987 https://www.nature.com/articles/s41598-021-85815-0 https://doi.org/10.1038/s41598-021-85815-0 |
| _version_ | 1855484304436494336 |
|---|---|
| author | Aballay, Maximiliano Martín Aguirre, Natalia Cristina Filippi, Carla Valeria Valentini, Gabriel Hugo Sanchez, Gerardo |
| author_browse | Aballay, Maximiliano Martín Aguirre, Natalia Cristina Filippi, Carla Valeria Sanchez, Gerardo Valentini, Gabriel Hugo |
| author_facet | Aballay, Maximiliano Martín Aguirre, Natalia Cristina Filippi, Carla Valeria Valentini, Gabriel Hugo Sanchez, Gerardo |
| author_sort | Aballay, Maximiliano Martín |
| collection | INTA Digital |
| description | The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach. |
| format | Artículo |
| id | INTA8987 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Springer Nature |
| publisherStr | Springer Nature |
| record_format | dspace |
| spelling | INTA89872021-03-29T11:35:09Z Fine-tuning the performance of ddRAD-seq in the peach genome Aballay, Maximiliano Martín Aguirre, Natalia Cristina Filippi, Carla Valeria Valentini, Gabriel Hugo Sanchez, Gerardo Durazno Prunus persica Marcadores Genéticos Genómica Fitomejoramiento Genética Peaches Genetic Markers Genomics Plant Breeding Genetics Secuenciación Sequencing The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach. EEA San Pedro Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina. Fil: Aballay, Maximiliano Martín. Consejo Nacional de Investigaciones Científica y Técnicas; Argentina Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Fil: Aguirre, Natalia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina. Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Filippi, Carla Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina Fil: Sánchez, Gerardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina 2021-03-29T11:19:42Z 2021-03-29T11:19:42Z 2021-03 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/8987 https://www.nature.com/articles/s41598-021-85815-0 2045-2322 https://doi.org/10.1038/s41598-021-85815-0 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf Springer Nature Scientific reports 11 : 6298 (2021) |
| spellingShingle | Durazno Prunus persica Marcadores Genéticos Genómica Fitomejoramiento Genética Peaches Genetic Markers Genomics Plant Breeding Genetics Secuenciación Sequencing Aballay, Maximiliano Martín Aguirre, Natalia Cristina Filippi, Carla Valeria Valentini, Gabriel Hugo Sanchez, Gerardo Fine-tuning the performance of ddRAD-seq in the peach genome |
| title | Fine-tuning the performance of ddRAD-seq in the peach genome |
| title_full | Fine-tuning the performance of ddRAD-seq in the peach genome |
| title_fullStr | Fine-tuning the performance of ddRAD-seq in the peach genome |
| title_full_unstemmed | Fine-tuning the performance of ddRAD-seq in the peach genome |
| title_short | Fine-tuning the performance of ddRAD-seq in the peach genome |
| title_sort | fine tuning the performance of ddrad seq in the peach genome |
| topic | Durazno Prunus persica Marcadores Genéticos Genómica Fitomejoramiento Genética Peaches Genetic Markers Genomics Plant Breeding Genetics Secuenciación Sequencing |
| url | http://hdl.handle.net/20.500.12123/8987 https://www.nature.com/articles/s41598-021-85815-0 https://doi.org/10.1038/s41598-021-85815-0 |
| work_keys_str_mv | AT aballaymaximilianomartin finetuningtheperformanceofddradseqinthepeachgenome AT aguirrenataliacristina finetuningtheperformanceofddradseqinthepeachgenome AT filippicarlavaleria finetuningtheperformanceofddradseqinthepeachgenome AT valentinigabrielhugo finetuningtheperformanceofddradseqinthepeachgenome AT sanchezgerardo finetuningtheperformanceofddradseqinthepeachgenome |