ArticleBMC genomics2012
RAD tag sequencing as a source of SNP markers in Cynara cardunculus L.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Genetic diversity study and molecular marker development for economic traits in Korean pine based on RAD-Seq.Frontiers in plant science · 2026Article
- Marginal Lands to Grow Novel Bio-Based Crops: A Plant Breeding Perspective.Frontiers in plant science · 2020Review
- A Multi-Level Strategy Based on Metabolic and Molecular Genetic Approaches for the Characterization of DifferentMolecules (Basel, Switzerland) · 2018Article
- A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting.Ecology and evolution · 2018Article
- Article
- An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals.Royal Society open science · 2018Article
- Genotyping-by-sequencing highlights patterns of genetic structure and domestication in artichoke and cardoon.PloS one · 2018Article
- Article
- Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation.Scientific reports · 2017Article
- Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application.Plant biotechnology journal · 2017Review
- Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing.PloS one · 2017Article
- Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis.The ISME journal · 2016Article
- Article
- The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny.Scientific reports · 2016Article
- Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life.Genome biology and evolution · 2015Article
- Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Identification of sex-linked SNP markers using RAD sequencing suggests ZW/ZZ sex determination in Pistacia vera L.BMC genomics · 2015Article
- Thousands of RAD-seq Loci Fully Resolve the Phylogeny of the Highly Disjunct Arctic-Alpine Genus Diapensia (Diapensiaceae).PloS one · 2015Article
- Assessing patterns of hybridization between North Atlantic eels using diagnostic single-nucleotide polymorphisms.Heredity · 2014Article
- Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map.BMC genomics · 2014Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe globe artichoke (Cynara cardunculus L. var. scolymus) genome is relatively poorly explored, especially compared to those of the other major Asteraceae crops sunflower and lettuce. No SNP markers are in the public domain. We have combined the recently developed restriction-site associated DNA (RAD) approach with the Illumina DNA sequencing platform to effect the rapid and mass discovery of SNP markers for C. cardunculus.
resultsRAD tags were sequenced from the genomic DNA of three C. cardunculus mapping population parents, generating 9.7 million reads, corresponding to ~1 Gbp of sequence. An assembly based on paired ends produced ~6.0 Mbp of genomic sequence, separated into ~19,000 contigs (mean length 312 bp), of which ~21% were fragments of putative coding sequence. The shared sequences allowed for the discovery of ~34,000 SNPs and nearly 800 indels, equivalent to a SNP frequency of 5.6 per 1,000 nt, and an indel frequency of 0.2 per 1,000 nt. A sample of heterozygous SNP loci was mapped by CAPS assays and this exercise provided validation of our mining criteria. The repetitive fraction of the genome had a high representation of retrotransposon sequence, followed by simple repeats, AT-low complexity regions and mobile DNA elements. The genomic k-mers distribution and CpG rate of C. cardunculus, compared with data derived from three whole genome-sequenced dicots species, provided a further evidence of the random representation of the C. cardunculus genome generated by RAD sampling.
conclusionThe RAD tag sequencing approach is a cost-effective and rapid method to develop SNP markers in a highly heterozygous species. Our approach permitted to generate a large and robust SNP datasets by the adoption of optimized filtering criteria.
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