Acquadro, Alberto

Knapp, Steven J

Lanteri, Sergio

Portis, Ezio

Scaglione, Davide

Tirone, Matteo

BMC Genomics

English

PubMed

Davide Scaglione

Alberto Acquadro

Ezio Portis

Matteo Tirone

Steven J Knapp

Sergio Lanteri

Springer - Publisher Connector

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

Abstract
          
            Background
            The 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.
          
          
            Results
            RAD 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.
          
          
            Conclusion
            The 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.
          </jats:sec

Crossref

Institutional Research Information System University of Turin

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L.

A: Biodiesel fuels from vegetable oils: Transesterification of Cynara cardunculus L. oils with ethanol. Energ Fuel

A: Identification and quantification of caffeoylquinic acids and flavonolds from artichoke (Cynara scolymus L.) heads, juice, and pomace by HPLC-DAD-ESI/MSn. J Agr Food Chem

A: SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res

al: A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. Plos One

Anti-hyperlipidemic Sesquiterpenes and new sesquiterpene glycosides from the leaves of artichoke (Cynara scolymus L.): Structure requirement and mode of action. Bioorg Med Chem Lett

Antioxidative and protective properties of extracts from leaves of the artichoke (Cynara scolymus L) against hydroperoxideinduced oxidative stress in cultured rat hepatocytes. Toxicol Appl Pharm

Biomass and grain oil yields in Cynara cardunculus L. genotypes grown in a Mediterranean environment. Field Crop Res

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics

C: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics

Cao L: The mining of citrus EST-SNP and its application in cultivar discrimination. Agricultural Sciences in China

Compositional differences within and between eukaryotic genomes.

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley.

D: Genetic map of artichoke × wild cardoon: toward a consensus map for Cynara cardunculus. Theor Appl Genet

E: A first linkage map of globe artichoke (Cynara cardunculus var. scolymus L.) based on AFLP, S-SAP, M-AFLP and microsatellite markers. Theor Appl Genet

E: RAPD variation within and among populations of globe artichoke cultivar ‘Spinoso sardo’. Plant Breeding

E: Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. Plos One

E: The isolation and mapping of a novel hydroxycinnamoyltransferase in the globe artichoke chlorogenic acid pathway.

EA: Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads. Plos One

Epigenetic regulation of transposable elements in plants. Annual Review of Plant Biology

Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell

et al: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature

et al: The genome of woodland strawberry (Fragaria vesca). Nat Genet

Inhibition of cholesterol biosynthesis in HepG2 cells by artichoke extracts is reinforced by glucosidase pretreatment. Phytother Res

JoinMap® 4: software for the calculation of genetic linkage maps in experimental populations.

Lanteri S: Construction of a reference linkage map for globe artichoke.

Lanteri S: Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus). Theor Appl Genet

Lanteri S: Construction of an SSR-based linkage map for Cynara cardunculus. 2009, 8th Plant Genomics European Meeting.

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism. PLoS One 2011, 6(4):e19315. Scaglione et al.

Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res

Massingham T: Genomic DNA k-mer spectra: models and modalities. Genome Biol

Mauromicale G: Cynara cardunculus L. genotypes as a crop for energy purposes in a Mediterranean environment. Biomass Bioenerg

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Mol Ecol Res

O: BatchPrimer3: A high throughput web application for PCR and sequencing primer design. Bmc Bioinformatics

Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database.

Population structure and genetic variation in autochthonous globe artichoke germplasm from Sicily Island. Plant Sci

Rapid and costeffective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res

Rotino GL: Identification of SNP and SSR markers in eggplant using RAD tag sequencing.

S: A cytometric exercise in plant DNA histograms, with 2C values for 70 species. Biol Cell

S: Identification and mapping of genes related to caffeoylquinic acid synthesis in Cynara cardunculus L. Plant Sci

Slabaugh EA: Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet

Steam gasification of Cynara cardunculus L.: influence of variables.

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature

The molecular basis for the lack of immunostimulatory activity of vertebrate DNA.

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res

WR: Maize Genome Sequencing by Methylation Filtration. Science

Zohary D: The wild ancestry of the cultivated artichoke. Genet Resour Crop Ev

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3269995

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

Abstract

Similar works

Full text

Available Versions

Springer - Publisher Connector

Crossref

Institutional Research Information System University of Turin