ArticlePlant methods2016
Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants.
Article in Plant methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
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- Genetic structure and conservation relevance in the narrowly distributed tree Catalpa huangxin revealed by RAD-Seq.Heredity · 2026Article
- Comparative analysis of multiple hybrid zones ofPlant diversity · 2025Article
- A novel method for effectively selecting fragments not associated with restriction sites for whole-genome genotyping.BMC biology · 2025Article
- Replacement of chromosome 3D with Thinopyrum chromosome 3St led to increased drought tolerance during the flowering stage in wheat.Plant cell reports · 2025Article
- Genetic diversity analysis and conservation strategy recommendations for ex situ conservation of Cupressus chengiana.BMC plant biology · 2025Article
- Genotyping-by-sequencing uncovers a Thinopyrum 4StS·1JTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genetic Diversity of the Collection of Far EasternPlants (Basel, Switzerland) · 2024Article
- Morpho-Phenological, Chemical, and Genetic Characterization of Italian Maize Landraces from the Lazio Region.Plants (Basel, Switzerland) · 2024Article
- Genetic Diversity Analysis and Prediction of Potential Suitable Areas for the Rare and Endangered Wild PlantPlants (Basel, Switzerland) · 2024Article
- Ancient allopatry and ecological divergence act together to promote plant diversity in mountainous regions: evidence from comparative phylogeography of two genera in the Sino-Himalayan region.BMC plant biology · 2023Article
- RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized.Scientific reports · 2023Article
- The identity ofPlant diversity · 2023Article
- Recombinant inbred lines and next-generation sequencing enable rapid identification of candidate genes involved in morphological and agronomic traits in foxtail millet.Scientific reports · 2022Article
- Natural hybridization among three Rhododendron species (Ericaceae) revealed by morphological and genomic evidence.BMC plant biology · 2021Article
- Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos.Systematic biology · 2021Article
- Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?Molecular genetics and genomics : MGG · 2021Article
- Divergent lineages in a semi-arid mallee species,Ecology and evolution · 2021Article
- Development of novel microsatellite markers using RAD sequencing technology for diversity assessment of rambutan (Heliyon · 2020Article
- ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean 'da serbo' type long shelf-life germplasm.Horticulture research · 2020Article
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10 authors.
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Abstract
backgroundThe double digest restriction-site associated DNA sequencing technology (ddRAD-seq) is a reduced representation sequencing technology by sampling genome-wide enzyme loci developed on the basis of next-generation sequencing. ddRAD-seq has been widely applied to SNP marker development and genotyping on animals, especially on marine animals as the original ddRAD protocol is mainly built and trained based on animal data. However, wide application of ddRAD-seq technology in plant species has not been achieved so far. Here, we aim to develop an optimized ddRAD library preparation protocol be accessible to most angiosperm plant species without much startup pre-experiment and costs.
resultsWe first tested several combinations of enzymes by in silico analysis of 23 plant species covering 17 families of angiosperm and 1 family of bryophyta and found AvaII + MspI enzyme pair produced consistently higher number of fragments in a broad range of plant species. Then we removed two purifying and one quantifying steps of the original protocol, replaced expensive consumables and apparatuses by conventional experimental apparatuses. Besides, we shortened P1 adapter from 37 to 25 bp and designed a new barcode-adapter system containing 20 pairs of barcodes of varying length. This is an optimized ddRAD strategy for angiosperm plants that is economical, time-saving and requires little technical expertise or investment in laboratory equipment. We refer to this simplified protocol as MiddRAD and we demonstrated the utility and flexibility of our approach by resolving phylogenetic relationships of two genera of woody bamboos (Dendrocalamus and Phyllostachys). Overall our results provide empirical evidence for using this method on different model and non-model plants to produce consistent data.
conclusionsAs MiddRAD adopts an enzyme pair that works for a broad range of angiosperm plants, simplifies library constructing procedure and requires less DNA input, it will greatly facilitate designing a ddRAD project. Our optimization of this method may make ddRAD be widely used in fields of plant population genetics, phylogenetics, phylogeography and molecular breeding.
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