RAD tag sequencing as a source of SNP markers in Cynara cardunculus L
Identifieur interne : 000915 ( Ncbi/Merge ); précédent : 000914; suivant : 000916RAD tag sequencing as a source of SNP markers in Cynara cardunculus L
Auteurs : Davide Scaglione [Italie] ; Alberto Acquadro [Italie] ; Ezio Portis [Italie] ; Matteo Tirone [Italie] ; Steven J. Knapp ; Sergio Lanteri [Italie]Source :
- BMC Genomics [ 1471-2164 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Genetic Markers.
- chemical , metabolism : DNA Restriction Enzymes.
- genetics : Cynara.
- Contig Mapping, Gene Frequency, Genetic Linkage, Heterozygote, Polymorphism, Single Nucleotide, Sequence Analysis, DNA.
Abstract
The globe artichoke (
RAD tags were sequenced from the genomic DNA of three
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.
Url:
DOI: 10.1186/1471-2164-13-3
PubMed: 22214349
PubMed Central: 3269995
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PMC:3269995Le document en format XML
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Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Portis, Ezio" sort="Portis, Ezio" uniqKey="Portis E" first="Ezio" last="Portis">Ezio Portis</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Tirone, Matteo" sort="Tirone, Matteo" uniqKey="Tirone M" first="Matteo" last="Tirone">Matteo Tirone</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Knapp, Steven J" sort="Knapp, Steven J" uniqKey="Knapp S" first="Steven J" last="Knapp">Steven J. Knapp</name><affiliation><nlm:aff id="I2">Institute for Plant Breeding, Genetics, and Genomics, University of Georgia, 111 Riverbend Rd., 30602 Athens, Georgia USA</nlm:aff><wicri:noCountry code="subfield">Georgia USA</wicri:noCountry></affiliation></author><author><name sortKey="Lanteri, Sergio" sort="Lanteri, Sergio" uniqKey="Lanteri S" first="Sergio" last="Lanteri">Sergio Lanteri</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Contig Mapping</term><term>Cynara (genetics)</term><term>DNA Restriction Enzymes (metabolism)</term><term>Gene Frequency</term><term>Genetic Linkage</term><term>Genetic Markers (genetics)</term><term>Heterozygote</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Cartographie de contigs</term><term>Cynara (génétique)</term><term>DNA restriction enzymes (métabolisme)</term><term>Fréquence d'allèle</term><term>Hétérozygote</term><term>Liaison génétique</term><term>Marqueurs génétiques (génétique)</term><term>Polymorphisme de nucléotide simple</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA Restriction Enzymes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cynara</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Cynara</term><term>Marqueurs génétiques</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>DNA restriction enzymes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Contig Mapping</term><term>Gene Frequency</term><term>Genetic Linkage</term><term>Heterozygote</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Cartographie de contigs</term><term>Fréquence d'allèle</term><term>Hétérozygote</term><term>Liaison génétique</term><term>Polymorphisme de nucléotide simple</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The globe artichoke (<italic>Cynara cardunculus </italic>L. var. <italic>scolymus</italic>) genome is relatively poorly explored, especially compared to those of the other major <italic>Asteraceae </italic>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 <italic>C. cardunculus</italic>.</p></sec><sec><title>Results</title><p>RAD tags were sequenced from the genomic DNA of three <italic>C. cardunculus </italic>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 <italic>C. cardunculus</italic>, compared with data derived from three whole genome-sequenced dicots species, provided a further evidence of the random representation of the <italic>C. cardunculus </italic>genome generated by RAD sampling.</p></sec><sec><title>Conclusion</title><p>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.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Marie, D" uniqKey="Marie D">D Marie</name></author><author><name sortKey="Brown, S" uniqKey="Brown S">S Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rottenberg, A" uniqKey="Rottenberg A">A Rottenberg</name></author><author><name sortKey="Zohary, D" uniqKey="Zohary D">D Zohary</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shimoda, H" uniqKey="Shimoda H">H Shimoda</name></author><author><name sortKey="Ninomiya, K" uniqKey="Ninomiya K">K Ninomiya</name></author><author><name sortKey="Nishida, N" uniqKey="Nishida N">N Nishida</name></author><author><name sortKey="Yoshino, T" uniqKey="Yoshino T">T Yoshino</name></author><author><name sortKey="Morikawa, T" uniqKey="Morikawa T">T Morikawa</name></author><author><name sortKey="Matsuda, H" uniqKey="Matsuda H">H Matsuda</name></author><author><name sortKey="Yoshikawa, M" uniqKey="Yoshikawa M">M Yoshikawa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gebhardt, R" uniqKey="Gebhardt R">R Gebhardt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gebhardt, R" uniqKey="Gebhardt R">R Gebhardt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schutz, K" uniqKey="Schutz K">K Schutz</name></author><author><name sortKey="Kammerer, D" uniqKey="Kammerer D">D Kammerer</name></author><author><name sortKey="Carle, R" uniqKey="Carle R">R Carle</name></author><author><name sortKey="Schieber, A" uniqKey="Schieber A">A Schieber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ierna, A" uniqKey="Ierna A">A Ierna</name></author><author><name sortKey="Mauromicale, G" uniqKey="Mauromicale G">G Mauromicale</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Raccuia, S" uniqKey="Raccuia S">S Raccuia</name></author><author><name sortKey="Melilli, M" uniqKey="Melilli M">M Melilli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Encinar, J" uniqKey="Encinar J">J Encinar</name></author><author><name sortKey="Gonzalez, J" uniqKey="Gonzalez J">J Gonzalez</name></author><author><name sortKey="Rodriguez, J" uniqKey="Rodriguez J">J Rodriguez</name></author><author><name sortKey="Tejedor, A" uniqKey="Tejedor A">A Tejedor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Encinar, J" uniqKey="Encinar J">J Encinar</name></author><author><name sortKey="Gonzalez, J" uniqKey="Gonzalez J">J Gonzalez</name></author><author><name sortKey="Gonzalez, J" uniqKey="Gonzalez J">J Gonzalez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lanteri, S" uniqKey="Lanteri S">S Lanteri</name></author><author><name sortKey="Acquadro, A" uniqKey="Acquadro A">A Acquadro</name></author><author><name sortKey="Comino, C" uniqKey="Comino C">C Comino</name></author><author><name sortKey="Mauro, R" uniqKey="Mauro R">R Mauro</name></author><author><name sortKey="Mauromicale, G" uniqKey="Mauromicale G">G Mauromicale</name></author><author><name sortKey="Portis, E" uniqKey="Portis E">E Portis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Portis, E" uniqKey="Portis E">E Portis</name></author><author><name sortKey="Mauromicale, G" uniqKey="Mauromicale G">G Mauromicale</name></author><author><name sortKey="Mauro, R" uniqKey="Mauro R">R Mauro</name></author><author><name sortKey="Acquadro, A" uniqKey="Acquadro A">A Acquadro</name></author><author><name sortKey="Scaglione, D" uniqKey="Scaglione D">D Scaglione</name></author><author><name sortKey="Lanteri, S" uniqKey="Lanteri S">S 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wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Portis, Ezio" sort="Portis, Ezio" uniqKey="Portis E" first="Ezio" last="Portis">Ezio Portis</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Tirone, Matteo" sort="Tirone, Matteo" uniqKey="Tirone M" first="Matteo" last="Tirone">Matteo Tirone</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Knapp, Steven J" sort="Knapp, Steven J" uniqKey="Knapp S" first="Steven J" last="Knapp">Steven J. Knapp</name><affiliation><nlm:aff id="I2">Institute for Plant Breeding, Genetics, and Genomics, University of Georgia, 111 Riverbend Rd., 30602 Athens, Georgia USA</nlm:aff><wicri:noCountry code="subfield">Georgia USA</wicri:noCountry></affiliation></author><author><name sortKey="Lanteri, Sergio" sort="Lanteri, Sergio" uniqKey="Lanteri S" first="Sergio" last="Lanteri">Sergio Lanteri</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22214349</idno><idno type="pmc">3269995</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269995</idno><idno type="RBID">PMC:3269995</idno><idno type="doi">10.1186/1471-2164-13-3</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000A97</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A97</idno><idno type="wicri:Area/Pmc/Curation">000A97</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000A97</idno><idno type="wicri:Area/Pmc/Checkpoint">001288</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001288</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">RAD tag sequencing as a source of SNP markers in <italic>Cynara cardunculus </italic>L</title><author><name sortKey="Scaglione, Davide" sort="Scaglione, Davide" uniqKey="Scaglione D" first="Davide" last="Scaglione">Davide Scaglione</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Portis, Ezio" sort="Portis, Ezio" uniqKey="Portis E" first="Ezio" last="Portis">Ezio Portis</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Tirone, Matteo" sort="Tirone, Matteo" uniqKey="Tirone M" first="Matteo" last="Tirone">Matteo Tirone</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Knapp, Steven J" sort="Knapp, Steven J" uniqKey="Knapp S" first="Steven J" last="Knapp">Steven J. Knapp</name><affiliation><nlm:aff id="I2">Institute for Plant Breeding, Genetics, and Genomics, University of Georgia, 111 Riverbend Rd., 30602 Athens, Georgia USA</nlm:aff><wicri:noCountry code="subfield">Georgia USA</wicri:noCountry></affiliation></author><author><name sortKey="Lanteri, Sergio" sort="Lanteri, Sergio" uniqKey="Lanteri S" first="Sergio" last="Lanteri">Sergio Lanteri</name><affiliation wicri:level="1"><nlm:aff id="I1">Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The globe artichoke (<italic>Cynara cardunculus </italic>L. var. <italic>scolymus</italic>) genome is relatively poorly explored, especially compared to those of the other major <italic>Asteraceae </italic>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 <italic>C. cardunculus</italic>.</p></sec><sec><title>Results</title><p>RAD tags were sequenced from the genomic DNA of three <italic>C. cardunculus </italic>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 <italic>C. cardunculus</italic>, compared with data derived from three whole genome-sequenced dicots species, provided a further evidence of the random representation of the <italic>C. cardunculus </italic>genome generated by RAD sampling.</p></sec><sec><title>Conclusion</title><p>The RAD tag sequencing approach is a cost-effective and rapid method to develop SNP markers in a highly heterozygous species. 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Plant Genetics and Breeding, University of Torino, via L. da Vinci44, 10095 Grugliasco (Torino), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name></author><author><name sortKey="Portis, Ezio" sort="Portis, Ezio" uniqKey="Portis E" first="Ezio" last="Portis">Ezio Portis</name></author><author><name sortKey="Tirone, Matteo" sort="Tirone, Matteo" uniqKey="Tirone M" first="Matteo" last="Tirone">Matteo Tirone</name></author><author><name sortKey="Knapp, Steven J" sort="Knapp, Steven J" uniqKey="Knapp S" first="Steven J" last="Knapp">Steven J. Knapp</name></author><author><name sortKey="Lanteri, Sergio" sort="Lanteri, Sergio" uniqKey="Lanteri S" first="Sergio" last="Lanteri">Sergio Lanteri</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22214349</idno><idno type="pmid">22214349</idno><idno type="doi">10.1186/1471-2164-13-3</idno><idno type="wicri:Area/PubMed/Corpus">001E21</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001E21</idno><idno type="wicri:Area/PubMed/Curation">001E21</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001E21</idno><idno type="wicri:Area/PubMed/Checkpoint">001C45</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001C45</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">RAD tag sequencing as a source of SNP markers in Cynara cardunculus L.</title><author><name sortKey="Scaglione, Davide" sort="Scaglione, Davide" uniqKey="Scaglione D" first="Davide" last="Scaglione">Davide Scaglione</name><affiliation wicri:level="1"><nlm:affiliation>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci44, 10095 Grugliasco (Torino), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci44, 10095 Grugliasco (Torino)</wicri:regionArea><wicri:noRegion>10095 Grugliasco (Torino)</wicri:noRegion></affiliation></author><author><name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name></author><author><name sortKey="Portis, Ezio" sort="Portis, Ezio" uniqKey="Portis E" first="Ezio" last="Portis">Ezio Portis</name></author><author><name sortKey="Tirone, Matteo" sort="Tirone, Matteo" uniqKey="Tirone M" first="Matteo" last="Tirone">Matteo Tirone</name></author><author><name sortKey="Knapp, Steven J" sort="Knapp, Steven J" uniqKey="Knapp S" first="Steven J" last="Knapp">Steven J. Knapp</name></author><author><name sortKey="Lanteri, Sergio" sort="Lanteri, Sergio" uniqKey="Lanteri S" first="Sergio" last="Lanteri">Sergio Lanteri</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Contig Mapping</term><term>Cynara (genetics)</term><term>DNA Restriction Enzymes (metabolism)</term><term>Gene Frequency</term><term>Genetic Linkage</term><term>Genetic Markers (genetics)</term><term>Heterozygote</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Cartographie de contigs</term><term>Cynara (génétique)</term><term>DNA restriction enzymes (métabolisme)</term><term>Fréquence d'allèle</term><term>Hétérozygote</term><term>Liaison génétique</term><term>Marqueurs génétiques (génétique)</term><term>Polymorphisme de nucléotide simple</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA Restriction Enzymes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cynara</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Cynara</term><term>Marqueurs génétiques</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>DNA restriction enzymes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Contig Mapping</term><term>Gene Frequency</term><term>Genetic Linkage</term><term>Heterozygote</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Cartographie de contigs</term><term>Fréquence d'allèle</term><term>Hétérozygote</term><term>Liaison génétique</term><term>Polymorphisme de nucléotide simple</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI></pubmed></double></record>Pour manipuler ce document sous Unix (Dilib)
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