New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array.
Identifieur interne : 000031 ( Main/Exploration ); précédent : 000030; suivant : 000032New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array.
Auteurs : P. Faivre-Rampant [France] ; G. Zaina [Italie] ; V. Jorge [France] ; S. Giacomello [Italie] ; V. Segura [France] ; S. Scalabrin [Italie] ; V. Guérin [France] ; E. De Paoli [Italie] ; C. Aluome [France] ; M. Viger [Royaume-Uni] ; F. Cattonaro [Italie] ; A. Payne [Royaume-Uni] ; P. Paulstephenraj [France] ; M C Le Paslier [France] ; A. Berard [France] ; M R Allwright [Royaume-Uni] ; M. Villar [France] ; G. Taylor [Royaume-Uni] ; C. Bastien [France] ; M. Morgante [Italie]Source :
- Molecular ecology resources [ 1755-0998 ] ; 2016.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (MeSH), Analyse sur microréseau (méthodes), Europe (MeSH), Génome végétal (MeSH), Génétique des populations (méthodes), Polymorphisme de nucléotide simple (MeSH), Populus (classification), Populus (génétique), Séquençage nucléotidique à haut débit (MeSH), Techniques de génotypage (méthodes), Variation génétique (MeSH).
- MESH :
English descriptors
- KwdEn :
- Europe (MeSH), Genetic Variation (MeSH), Genetics, Population (methods), Genome, Plant (MeSH), Genotyping Techniques (methods), High-Throughput Nucleotide Sequencing (MeSH), Microarray Analysis (methods), Polymorphism, Single Nucleotide (MeSH), Populus (classification), Populus (genetics), Sequence Analysis, DNA (MeSH).
- MESH :
- geographic : Europe.
- classification : Populus.
- genetics : Populus.
- methods : Genetics, Population, Genotyping Techniques, Microarray Analysis.
- Genetic Variation, Genome, Plant, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Sequence Analysis, DNA.
Abstract
Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.
DOI: 10.1111/1755-0998.12513
PubMed: 26929265
Affiliations:
- France, Italie, Royaume-Uni
- Centre-Val de Loire, Région Centre, Île-de-France
- Orléans, Évry (Essonne)
Links toward previous steps (curation, corpus...)
Le document en format XML
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Guérin</name><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="De Paoli, E" sort="De Paoli, E" uniqKey="De Paoli E" first="E" last="De Paoli">E. De Paoli</name><affiliation wicri:level="1"><nlm:affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Aluome, C" sort="Aluome, C" uniqKey="Aluome C" first="C" last="Aluome">C. Aluome</name><affiliation wicri:level="3"><nlm:affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Viger, M" sort="Viger, M" uniqKey="Viger M" first="M" last="Viger">M. Viger</name><affiliation wicri:level="1"><nlm:affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton</wicri:regionArea><wicri:noRegion>Southampton</wicri:noRegion></affiliation></author><author><name sortKey="Cattonaro, F" sort="Cattonaro, F" uniqKey="Cattonaro F" first="F" last="Cattonaro">F. Cattonaro</name><affiliation wicri:level="1"><nlm:affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Payne, A" sort="Payne, A" uniqKey="Payne A" first="A" last="Payne">A. Payne</name><affiliation wicri:level="1"><nlm:affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton</wicri:regionArea><wicri:noRegion>Southampton</wicri:noRegion></affiliation></author><author><name sortKey="Paulstephenraj, P" sort="Paulstephenraj, P" uniqKey="Paulstephenraj P" first="P" last="Paulstephenraj">P. Paulstephenraj</name><affiliation wicri:level="3"><nlm:affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Le Paslier, M C" sort="Le Paslier, M C" uniqKey="Le Paslier M" first="M C" last="Le Paslier">M C Le Paslier</name><affiliation wicri:level="3"><nlm:affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Berard, A" sort="Berard, A" uniqKey="Berard A" first="A" last="Berard">A. Berard</name><affiliation wicri:level="3"><nlm:affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Allwright, M R" sort="Allwright, M R" uniqKey="Allwright M" first="M R" last="Allwright">M R Allwright</name><affiliation wicri:level="1"><nlm:affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton</wicri:regionArea><wicri:noRegion>Southampton</wicri:noRegion></affiliation></author><author><name sortKey="Villar, M" sort="Villar, M" uniqKey="Villar M" first="M" last="Villar">M. Villar</name><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Taylor, G" sort="Taylor, G" uniqKey="Taylor G" first="G" last="Taylor">G. Taylor</name><affiliation wicri:level="1"><nlm:affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton</wicri:regionArea><wicri:noRegion>Southampton</wicri:noRegion></affiliation></author><author><name sortKey="Bastien, C" sort="Bastien, C" uniqKey="Bastien C" first="C" last="Bastien">C. Bastien</name><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Morgante, M" sort="Morgante, M" uniqKey="Morgante M" first="M" last="Morgante">M. Morgante</name><affiliation wicri:level="1"><nlm:affiliation>DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>DI4A, University of Udine, via delle Scienze 206, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:26929265</idno><idno type="pmid">26929265</idno><idno type="doi">10.1111/1755-0998.12513</idno><idno type="wicri:Area/Main/Corpus">000030</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000030</idno><idno type="wicri:Area/Main/Curation">000030</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000030</idno><idno type="wicri:Area/Main/Exploration">000030</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array.</title><author><name sortKey="Faivre Rampant, P" sort="Faivre Rampant, P" uniqKey="Faivre Rampant P" first="P" last="Faivre-Rampant">P. Faivre-Rampant</name><affiliation wicri:level="3"><nlm:affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Zaina, G" sort="Zaina, G" uniqKey="Zaina G" first="G" last="Zaina">G. Zaina</name><affiliation wicri:level="1"><nlm:affiliation>DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>DI4A, University of Udine, via delle Scienze 206, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Jorge, V" sort="Jorge, V" uniqKey="Jorge V" first="V" last="Jorge">V. Jorge</name><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Giacomello, S" sort="Giacomello, S" uniqKey="Giacomello S" first="S" last="Giacomello">S. Giacomello</name><affiliation wicri:level="1"><nlm:affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Segura, V" sort="Segura, V" uniqKey="Segura V" first="V" last="Segura">V. Segura</name><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Scalabrin, S" sort="Scalabrin, S" uniqKey="Scalabrin S" first="S" last="Scalabrin">S. Scalabrin</name><affiliation wicri:level="1"><nlm:affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Guerin, V" sort="Guerin, V" uniqKey="Guerin V" first="V" last="Guérin">V. Guérin</name><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="De Paoli, E" sort="De Paoli, E" uniqKey="De Paoli E" first="E" last="De Paoli">E. De Paoli</name><affiliation wicri:level="1"><nlm:affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Aluome, C" sort="Aluome, C" uniqKey="Aluome C" first="C" last="Aluome">C. Aluome</name><affiliation wicri:level="3"><nlm:affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Viger, M" sort="Viger, M" uniqKey="Viger M" first="M" last="Viger">M. Viger</name><affiliation wicri:level="1"><nlm:affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton</wicri:regionArea><wicri:noRegion>Southampton</wicri:noRegion></affiliation></author><author><name sortKey="Cattonaro, F" sort="Cattonaro, F" uniqKey="Cattonaro F" first="F" last="Cattonaro">F. Cattonaro</name><affiliation wicri:level="1"><nlm:affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author><author><name sortKey="Payne, A" sort="Payne, A" uniqKey="Payne A" first="A" last="Payne">A. Payne</name><affiliation wicri:level="1"><nlm:affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton</wicri:regionArea><wicri:noRegion>Southampton</wicri:noRegion></affiliation></author><author><name sortKey="Paulstephenraj, P" sort="Paulstephenraj, P" uniqKey="Paulstephenraj P" first="P" last="Paulstephenraj">P. Paulstephenraj</name><affiliation wicri:level="3"><nlm:affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Le Paslier, M C" sort="Le Paslier, M C" uniqKey="Le Paslier M" first="M C" last="Le Paslier">M C Le Paslier</name><affiliation wicri:level="3"><nlm:affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Berard, A" sort="Berard, A" uniqKey="Berard A" first="A" last="Berard">A. Berard</name><affiliation wicri:level="3"><nlm:affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Évry (Essonne)</settlement></placeName></affiliation></author><author><name sortKey="Allwright, M R" sort="Allwright, M R" uniqKey="Allwright M" first="M R" last="Allwright">M R Allwright</name><affiliation wicri:level="1"><nlm:affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton</wicri:regionArea><wicri:noRegion>Southampton</wicri:noRegion></affiliation></author><author><name sortKey="Villar, M" sort="Villar, M" uniqKey="Villar M" first="M" last="Villar">M. Villar</name><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Taylor, G" sort="Taylor, G" uniqKey="Taylor G" first="G" last="Taylor">G. Taylor</name><affiliation wicri:level="1"><nlm:affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton</wicri:regionArea><wicri:noRegion>Southampton</wicri:noRegion></affiliation></author><author><name sortKey="Bastien, C" sort="Bastien, C" uniqKey="Bastien C" first="C" last="Bastien">C. Bastien</name><affiliation wicri:level="3"><nlm:affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Morgante, M" sort="Morgante, M" uniqKey="Morgante M" first="M" last="Morgante">M. Morgante</name><affiliation wicri:level="1"><nlm:affiliation>DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>DI4A, University of Udine, via delle Scienze 206, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine</wicri:regionArea><wicri:noRegion>Udine</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular ecology resources</title><idno type="eISSN">1755-0998</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Europe (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genetics, Population (methods)</term><term>Genome, Plant (MeSH)</term><term>Genotyping Techniques (methods)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Microarray Analysis (methods)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Analyse sur microréseau (méthodes)</term><term>Europe (MeSH)</term><term>Génome végétal (MeSH)</term><term>Génétique des populations (méthodes)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Techniques de génotypage (méthodes)</term><term>Variation génétique (MeSH)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Europe</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genetics, Population</term><term>Genotyping Techniques</term><term>Microarray Analysis</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse sur microréseau</term><term>Génétique des populations</term><term>Techniques de génotypage</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genetic Variation</term><term>Genome, Plant</term><term>High-Throughput Nucleotide Sequencing</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>Europe</term><term>Génome végétal</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term><term>Séquençage nucléotidique à haut débit</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26929265</PMID><DateCompleted><Year>2017</Year><Month>04</Month><Day>03</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1755-0998</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><Issue>4</Issue><PubDate><Year>2016</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Molecular ecology resources</Title><ISOAbbreviation>Mol Ecol Resour</ISOAbbreviation></Journal><ArticleTitle>New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array.</ArticleTitle><Pagination><MedlinePgn>1023-36</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/1755-0998.12513</ELocationID><Abstract><AbstractText>Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra. </AbstractText><CopyrightInformation>© 2016 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Faivre-Rampant</LastName><ForeName>P</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zaina</LastName><ForeName>G</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jorge</LastName><ForeName>V</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giacomello</LastName><ForeName>S</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Segura</LastName><ForeName>V</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scalabrin</LastName><ForeName>S</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guérin</LastName><ForeName>V</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>De Paoli</LastName><ForeName>E</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Aluome</LastName><ForeName>C</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Viger</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cattonaro</LastName><ForeName>F</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Payne</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>PaulStephenRaj</LastName><ForeName>P</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Le Paslier</LastName><ForeName>M C</ForeName><Initials>MC</Initials><AffiliationInfo><Affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Berard</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Allwright</LastName><ForeName>M R</ForeName><Initials>MR</Initials><AffiliationInfo><Affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Villar</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taylor</LastName><ForeName>G</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bastien</LastName><ForeName>C</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morgante</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>SRP067688</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>03</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol Resour</MedlineTA><NlmUniqueID>101465604</NlmUniqueID><ISSNLinking>1755-098X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005060" MajorTopicYN="N" Type="Geographic">Europe</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005828" MajorTopicYN="N">Genetics, Population</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D060005" MajorTopicYN="N">Genotyping Techniques</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D046228" MajorTopicYN="N">Microarray Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">HT-genotyping design</Keyword><Keyword MajorTopicYN="Y">Populus nigra</Keyword><Keyword MajorTopicYN="Y">large-scale SNP discovery</Keyword><Keyword MajorTopicYN="Y">population genetics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>09</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>12</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>12</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>3</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>3</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>4</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26929265</ArticleId><ArticleId IdType="doi">10.1111/1755-0998.12513</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li><li>Italie</li><li>Royaume-Uni</li></country><region><li>Centre-Val de Loire</li><li>Région Centre</li><li>Île-de-France</li></region><settlement><li>Orléans</li><li>Évry (Essonne)</li></settlement></list><tree><country name="France"><region name="Île-de-France"><name sortKey="Faivre Rampant, P" sort="Faivre Rampant, P" uniqKey="Faivre Rampant P" first="P" last="Faivre-Rampant">P. Faivre-Rampant</name></region><name sortKey="Aluome, C" sort="Aluome, C" uniqKey="Aluome C" first="C" last="Aluome">C. Aluome</name><name sortKey="Aluome, C" sort="Aluome, C" uniqKey="Aluome C" first="C" last="Aluome">C. Aluome</name><name sortKey="Bastien, C" sort="Bastien, C" uniqKey="Bastien C" first="C" last="Bastien">C. Bastien</name><name sortKey="Berard, A" sort="Berard, A" uniqKey="Berard A" first="A" last="Berard">A. Berard</name><name sortKey="Guerin, V" sort="Guerin, V" uniqKey="Guerin V" first="V" last="Guérin">V. Guérin</name><name sortKey="Jorge, V" sort="Jorge, V" uniqKey="Jorge V" first="V" last="Jorge">V. Jorge</name><name sortKey="Le Paslier, M C" sort="Le Paslier, M C" uniqKey="Le Paslier M" first="M C" last="Le Paslier">M C Le Paslier</name><name sortKey="Paulstephenraj, P" sort="Paulstephenraj, P" uniqKey="Paulstephenraj P" first="P" last="Paulstephenraj">P. Paulstephenraj</name><name sortKey="Segura, V" sort="Segura, V" uniqKey="Segura V" first="V" last="Segura">V. Segura</name><name sortKey="Villar, M" sort="Villar, M" uniqKey="Villar M" first="M" last="Villar">M. Villar</name></country><country name="Italie"><noRegion><name sortKey="Zaina, G" sort="Zaina, G" uniqKey="Zaina G" first="G" last="Zaina">G. Zaina</name></noRegion><name sortKey="Cattonaro, F" sort="Cattonaro, F" uniqKey="Cattonaro F" first="F" last="Cattonaro">F. Cattonaro</name><name sortKey="De Paoli, E" sort="De Paoli, E" uniqKey="De Paoli E" first="E" last="De Paoli">E. De Paoli</name><name sortKey="Giacomello, S" sort="Giacomello, S" uniqKey="Giacomello S" first="S" last="Giacomello">S. Giacomello</name><name sortKey="Morgante, M" sort="Morgante, M" uniqKey="Morgante M" first="M" last="Morgante">M. Morgante</name><name sortKey="Morgante, M" sort="Morgante, M" uniqKey="Morgante M" first="M" last="Morgante">M. Morgante</name><name sortKey="Scalabrin, S" sort="Scalabrin, S" uniqKey="Scalabrin S" first="S" last="Scalabrin">S. Scalabrin</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Viger, M" sort="Viger, M" uniqKey="Viger M" first="M" last="Viger">M. Viger</name></noRegion><name sortKey="Allwright, M R" sort="Allwright, M R" uniqKey="Allwright M" first="M R" last="Allwright">M R Allwright</name><name sortKey="Payne, A" sort="Payne, A" uniqKey="Payne A" first="A" last="Payne">A. Payne</name><name sortKey="Taylor, G" sort="Taylor, G" uniqKey="Taylor G" first="G" last="Taylor">G. Taylor</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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