ArticleScientific reports2021
Fine-tuning the performance of ddRAD-seq in the peach genome.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 16 citations in OpenAlex.
- Multi-Season Genome-Wide Association Study Reveals Loci and Candidate Genes for Fruit Quality and Maturity Traits in Peach.Plants (Basel, Switzerland) · 2026Article
- A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach.Plant methods · 2025Article
- Comparative analysis of RAD-seq methods for SNP discovery and genetic diversity assessment in oil seed crop safflower.Scientific reports · 2025Article
- Genetic Diversity Analysis and Prediction of Potential Suitable Areas for the Rare and Endangered Wild PlantPlants (Basel, Switzerland) · 2024Article
- Linkage mapping of root shape traits in two carrot populations.G3 (Bethesda, Md.) · 2024Article
- Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers.PloS one · 2024Article
- Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection inFrontiers in genetics · 2024Article
- Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach.Frontiers in plant science · 2022Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.