ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2016
Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
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- Near-complete genome assembly of tomato (Plant biotechnology (Tokyo, Japan) · 2024Article
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- Analyzing genetic diversity in luffa and developing a Fusarium wilt-susceptible linked SNP marker through a single plant genome-wide association (sp-GWAS) study.BMC plant biology · 2024Article
- Self-incompatibility phenotypes of SRK mutants can be predicted with high accuracy.bioRxiv : the preprint server for biology · 2024Article
- Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers.PloS one · 2024Article
- A self-compatible pear mutant derived from γ-irradiated pollen carries an 11-Mb duplication in chromosome 17.Frontiers in plant science · 2024Article
- From green to red: Urban heat stress drives leaf color evolution.Science advances · 2023Article
- Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
14 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Double-digest restriction site-associated DNA sequencing (ddRAD-Seq) enables high-throughput genome-wide genotyping with next-generation sequencing technology. Consequently, this method has become popular in plant genetics and breeding. Although computational in silico prediction of restriction sites from the genome sequence is recognized as an effective approach for choosing the restriction enzymes to be used, few reports have evaluated the in silico predictions in actual experimental data. In this study, we designed and demonstrated a workflow for in silico and empirical ddRAD-Seq analysis in tomato, as follows: (i)in silico prediction of optimum restriction enzymes from the reference genome, (ii) verification of the prediction by actual ddRAD-Seq data of four restriction enzyme combinations, (iii) establishment of a computational data processing pipeline for high-confidence single nucleotide polymorphism (SNP) calling, and (iv) validation of SNP accuracy by construction of genetic linkage maps. The quality of SNPs based on de novo assembly reference of the ddRAD-Seq reads was comparable with that of SNPs obtained using the published reference genome of tomato. Comparisons of SNP calls in diverse tomato lines revealed that SNP density in the genome influenced the detectability of SNPs by ddRAD-Seq. In silico prediction prior to actual analysis contributed to optimization of the experimental conditions for ddRAD-Seq, e.g. choices of enzymes and plant materials. Following optimization, this ddRAD-Seq pipeline could help accelerate genetics, genomics, and molecular breeding in both model and non-model plants, including crops.
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