Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa)
Identifieur interne : 002F08 ( Main/Exploration ); précédent : 002F07; suivant : 002F09Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa)
Auteurs : José F. Sánchez-Sevilla [Espagne] ; Aniko Horvath [France] ; Miguel A. Botella [Espagne] ; Amèlia Gaston [France] ; Kevin Folta [États-Unis] ; Andrzej Kilian [Australie] ; Beatrice Denoyes [France] ; Iraida Amaya [Espagne, États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
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Abstract
Cultivated strawberry (
Url:
DOI: 10.1371/journal.pone.0144960
PubMed: 26675207
PubMed Central: 4682937
Affiliations:
- Australie, Espagne, France, États-Unis
- Andalousie, Aquitaine, Nouvelle-Aquitaine
- Bordeaux, Malaga
- Université de Bordeaux, Université de Malaga
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (<italic>Fragaria × ananassa</italic>)</title><author><name sortKey="Sanchez Sevilla, Jose F" sort="Sanchez Sevilla, Jose F" uniqKey="Sanchez Sevilla J" first="José F." last="Sánchez-Sevilla">José F. Sánchez-Sevilla</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga, Spain</addr-line></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga</wicri:regionArea><wicri:noRegion>Málaga</wicri:noRegion></affiliation></author><author><name sortKey="Horvath, Aniko" sort="Horvath, Aniko" uniqKey="Horvath A" first="Aniko" last="Horvath">Aniko Horvath</name><affiliation wicri:level="4"><nlm:aff id="aff002"><addr-line>INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon</wicri:regionArea><wicri:noRegion>33140, Villenave d’Ornon</wicri:noRegion><orgName type="university">Université de Bordeaux</orgName><placeName><settlement type="city">Bordeaux</settlement><region type="region" nuts="2">Nouvelle-Aquitaine</region><region type="old region" nuts="2">Aquitaine</region></placeName></affiliation></author><author><name sortKey="Botella, Miguel A" sort="Botella, Miguel A" uniqKey="Botella M" first="Miguel A." last="Botella">Miguel A. Botella</name><affiliation wicri:level="4"><nlm:aff id="aff003"><addr-line>Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC),
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× ananassa</italic>)</title><author><name sortKey="Sanchez Sevilla, Jose F" sort="Sanchez Sevilla, Jose F" uniqKey="Sanchez Sevilla J" first="José F." last="Sánchez-Sevilla">José F. Sánchez-Sevilla</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga, Spain</addr-line></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga</wicri:regionArea><wicri:noRegion>Málaga</wicri:noRegion></affiliation></author><author><name sortKey="Horvath, Aniko" sort="Horvath, Aniko" uniqKey="Horvath A" first="Aniko" last="Horvath">Aniko Horvath</name><affiliation wicri:level="4"><nlm:aff id="aff002"><addr-line>INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon</wicri:regionArea><wicri:noRegion>33140, Villenave d’Ornon</wicri:noRegion><orgName type="university">Université de Bordeaux</orgName><placeName><settlement type="city">Bordeaux</settlement><region type="region" nuts="2">Nouvelle-Aquitaine</region><region type="old region" nuts="2">Aquitaine</region></placeName></affiliation></author><author><name sortKey="Botella, Miguel A" sort="Botella, Miguel A" uniqKey="Botella M" first="Miguel A." last="Botella">Miguel A. Botella</name><affiliation wicri:level="4"><nlm:aff id="aff003"><addr-line>Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC),
Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, 29071, Málaga, Spain</addr-line></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC),
Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, 29071, Málaga</wicri:regionArea><orgName type="university">Université de Malaga</orgName><placeName><settlement type="city">Malaga</settlement><region nuts="2" type="region">Andalousie</region></placeName></affiliation></author><author><name sortKey="Gaston, Amelia" sort="Gaston, Amelia" uniqKey="Gaston A" first="Amèlia" last="Gaston">Amèlia Gaston</name><affiliation wicri:level="4"><nlm:aff id="aff002"><addr-line>INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon</wicri:regionArea><wicri:noRegion>33140, Villenave d’Ornon</wicri:noRegion><orgName type="university">Université de Bordeaux</orgName><placeName><settlement type="city">Bordeaux</settlement><region type="region" nuts="2">Nouvelle-Aquitaine</region><region type="old region" nuts="2">Aquitaine</region></placeName></affiliation></author><author><name sortKey="Folta, Kevin" sort="Folta, Kevin" uniqKey="Folta K" first="Kevin" last="Folta">Kevin Folta</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>University of Florida, Horticultural Sciences Department, Gainesville, Florida, 32611, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of Florida, Horticultural Sciences Department, Gainesville, Florida, 32611</wicri:regionArea><wicri:noRegion>32611</wicri:noRegion></affiliation></author><author><name sortKey="Kilian, Andrzej" sort="Kilian, Andrzej" uniqKey="Kilian A" first="Andrzej" last="Kilian">Andrzej Kilian</name><affiliation wicri:level="1"><nlm:aff id="aff005"><addr-line>Diversity Arrays Technology Pty Ltd, Building 3, University of Canberra, Bruce, ACT 2617, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Diversity Arrays Technology Pty Ltd, Building 3, University of Canberra, Bruce, ACT 2617</wicri:regionArea><wicri:noRegion>ACT 2617</wicri:noRegion></affiliation></author><author><name sortKey="Denoyes, Beatrice" sort="Denoyes, Beatrice" uniqKey="Denoyes B" first="Beatrice" last="Denoyes">Beatrice Denoyes</name><affiliation wicri:level="4"><nlm:aff id="aff002"><addr-line>INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon</wicri:regionArea><wicri:noRegion>33140, Villenave d’Ornon</wicri:noRegion><orgName type="university">Université de Bordeaux</orgName><placeName><settlement type="city">Bordeaux</settlement><region type="region" nuts="2">Nouvelle-Aquitaine</region><region type="old region" nuts="2">Aquitaine</region></placeName></affiliation></author><author><name sortKey="Amaya, Iraida" sort="Amaya, Iraida" uniqKey="Amaya I" first="Iraida" last="Amaya">Iraida Amaya</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga, Spain</addr-line></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga</wicri:regionArea><wicri:noRegion>Málaga</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>University of Florida, Horticultural Sciences Department, Gainesville, Florida, 32611, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of Florida, Horticultural Sciences Department, Gainesville, Florida, 32611</wicri:regionArea><wicri:noRegion>32611</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Mapping</term><term>Cluster Analysis</term><term>Diploidy</term><term>Fragaria (genetics)</term><term>Genetic Linkage</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Genomics (methods)</term><term>High-Throughput Nucleotide Sequencing</term><term>Oligonucleotide Array Sequence Analysis</term><term>Polymorphism, Single Nucleotide</term><term>Polyploidy</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de regroupements</term><term>Cartographie chromosomique</term><term>Diploïdie</term><term>Fragaria (génétique)</term><term>Génome végétal</term><term>Génomique ()</term><term>Liaison génétique</term><term>Polymorphisme de nucléotide simple</term><term>Polyploïdie</term><term>Séquençage nucléotidique à haut débit</term><term>Séquençage par oligonucléotides en batterie</term><term>Variation génétique</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fragaria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Fragaria</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Cluster Analysis</term><term>Diploidy</term><term>Genetic Linkage</term><term>Genetic Variation</term><term>Genome, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Oligonucleotide Array Sequence Analysis</term><term>Polymorphism, Single Nucleotide</term><term>Polyploidy</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Cartographie chromosomique</term><term>Diploïdie</term><term>Génome végétal</term><term>Génomique</term><term>Liaison génétique</term><term>Polymorphisme de nucléotide simple</term><term>Polyploïdie</term><term>Séquençage nucléotidique à haut débit</term><term>Séquençage par oligonucléotides en batterie</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Cultivated strawberry (<italic>Fragaria × ananassa</italic>) is a genetically complex allo-octoploid crop with 28 pairs of chromosomes (2n = 8x = 56) for which a genome sequence is not yet available. The diploid <italic>Fragaria vesca</italic> is considered the donor species of one of the octoploid sub-genomes and its available genome sequence can be used as a reference for genomic studies. A wide number of strawberry cultivars are stored in <italic>ex situ</italic> germplasm collections world-wide but a number of previous studies have addressed the genetic diversity present within a limited number of these collections. Here, we report the development and application of two platforms based on the implementation of Diversity Array Technology (DArT) markers for high-throughput genotyping in strawberry. The first DArT microarray was used to evaluate the genetic diversity of 62 strawberry cultivars that represent a wide range of variation based on phenotype, geographical and temporal origin and pedigrees. A total of 603 DArT markers were used to evaluate the diversity and structure of the population and their cluster analyses revealed that these markers were highly efficient in classifying the accessions in groups based on historical, geographical and pedigree-based cues. The second DArTseq platform took benefit of the complexity reduction method optimized for strawberry and the development of next generation sequencing technologies. The strawberry DArTseq was used to generate a total of 9,386 SNP markers in the previously developed ‘232’ × ‘1392’ mapping population, of which, 4,242 high quality markers were further selected to saturate this map after several filtering steps. The high-throughput platforms here developed for genotyping strawberry will facilitate genome-wide characterizations of large accessions sets and complement other available options.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jaccoud, D" uniqKey="Jaccoud D">D Jaccoud</name></author><author><name sortKey="Peng, K" uniqKey="Peng K">K Peng</name></author><author><name sortKey="Feinstein, D" uniqKey="Feinstein D">D Feinstein</name></author><author><name sortKey="Kilian, A" uniqKey="Kilian A">A Kilian</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wenzl, P" uniqKey="Wenzl P">P Wenzl</name></author><author><name sortKey="Carling, J" uniqKey="Carling J">J Carling</name></author><author><name sortKey="Kudrna, D" uniqKey="Kudrna D">D Kudrna</name></author><author><name sortKey="Jaccoud, D" uniqKey="Jaccoud D">D Jaccoud</name></author><author><name sortKey="Huttner, E" uniqKey="Huttner E">E 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Sánchez-Sevilla</name></noRegion><name sortKey="Amaya, Iraida" sort="Amaya, Iraida" uniqKey="Amaya I" first="Iraida" last="Amaya">Iraida Amaya</name><name sortKey="Botella, Miguel A" sort="Botella, Miguel A" uniqKey="Botella M" first="Miguel A." last="Botella">Miguel A. Botella</name></country><country name="France"><region name="Nouvelle-Aquitaine"><name sortKey="Horvath, Aniko" sort="Horvath, Aniko" uniqKey="Horvath A" first="Aniko" last="Horvath">Aniko Horvath</name></region><name sortKey="Denoyes, Beatrice" sort="Denoyes, Beatrice" uniqKey="Denoyes B" first="Beatrice" last="Denoyes">Beatrice Denoyes</name><name sortKey="Gaston, Amelia" sort="Gaston, Amelia" uniqKey="Gaston A" first="Amèlia" last="Gaston">Amèlia Gaston</name></country><country name="États-Unis"><noRegion><name sortKey="Folta, Kevin" sort="Folta, Kevin" uniqKey="Folta K" first="Kevin" last="Folta">Kevin Folta</name></noRegion><name sortKey="Amaya, Iraida" sort="Amaya, Iraida" uniqKey="Amaya I" first="Iraida" last="Amaya">Iraida Amaya</name></country><country name="Australie"><noRegion><name sortKey="Kilian, Andrzej" sort="Kilian, Andrzej" uniqKey="Kilian A" first="Andrzej" last="Kilian">Andrzej Kilian</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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