Fine-tuning the performance of ddRAD-seq in the peach genome

Abstract 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 w...

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Autores principales:	Maximiliano Martín Aballay, Natalia Cristina Aguirre, Carla Valeria Filippi, Gabriel Hugo Valentini, Gerardo Sánchez
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9b9fffad4b354097bc41f04e40cae49e
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spelling	oai:doaj.org-article:9b9fffad4b354097bc41f04e40cae49e2021-12-02T13:17:42ZFine-tuning the performance of ddRAD-seq in the peach genome10.1038/s41598-021-85815-02045-2322https://doaj.org/article/9b9fffad4b354097bc41f04e40cae49e2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85815-0https://doaj.org/toc/2045-2322Abstract 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.Maximiliano Martín AballayNatalia Cristina AguirreCarla Valeria FilippiGabriel Hugo ValentiniGerardo SánchezNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maximiliano Martín Aballay Natalia Cristina Aguirre Carla Valeria Filippi Gabriel Hugo Valentini Gerardo Sánchez Fine-tuning the performance of ddRAD-seq in the peach genome
description	Abstract 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	article
author	Maximiliano Martín Aballay Natalia Cristina Aguirre Carla Valeria Filippi Gabriel Hugo Valentini Gerardo Sánchez
author_facet	Maximiliano Martín Aballay Natalia Cristina Aguirre Carla Valeria Filippi Gabriel Hugo Valentini Gerardo Sánchez
author_sort	Maximiliano Martín Aballay
title	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_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_sort	fine-tuning the performance of ddrad-seq in the peach genome
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9b9fffad4b354097bc41f04e40cae49e
work_keys_str_mv	AT maximilianomartinaballay finetuningtheperformanceofddradseqinthepeachgenome AT nataliacristinaaguirre finetuningtheperformanceofddradseqinthepeachgenome AT carlavaleriafilippi finetuningtheperformanceofddradseqinthepeachgenome AT gabrielhugovalentini finetuningtheperformanceofddradseqinthepeachgenome AT gerardosanchez finetuningtheperformanceofddradseqinthepeachgenome
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Fine-tuning the performance of ddRAD-seq in the peach genome

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