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...
| Authors: | , , , , |
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| Format: | article |
| Status: | Published version |
| Publication Date: | 2021 |
| Country: | Argentina |
| Institution: | Instituto Nacional de Tecnología Agropecuaria |
| Repository: | INTA Digital (INTA) |
| Language: | English |
| OAI Identifier: | oai:localhost:20.500.12123/8987 |
| Online Access: | 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 |
| Access Level: | Open access |
| Keyword: | Durazno Prunus persica Marcadores Genéticos Genómica Fitomejoramiento Genética Peaches Genetic Markers Genomics Plant Breeding Genetics Secuenciación Sequencing |
| Summary: | 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. |
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