title: New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array.
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.
authors.affiliation: INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.
authors.forename: P
authors.initials: P
authors.lastname: Faivre-Rampant
authors.affiliation: DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Zaina
authors.affiliation: INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.
authors.forename: V
authors.initials: V
authors.lastname: Jorge
authors.affiliation: IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Giacomello
authors.affiliation: INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.
authors.forename: V
authors.initials: V
authors.lastname: Segura
authors.affiliation: IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Scalabrin
authors.affiliation: INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.
authors.forename: V
authors.initials: V
authors.lastname: Guérin
authors.affiliation: IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.
authors.forename: E
authors.initials: E
authors.lastname: De Paoli
authors.affiliation: INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.|INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.
authors.forename: C
authors.initials: C
authors.lastname: Aluome
authors.affiliation: Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.
authors.forename: M
authors.initials: M
authors.lastname: Viger
authors.affiliation: IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Cattonaro
authors.affiliation: Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.
authors.forename: A
authors.initials: A
authors.lastname: Payne
authors.affiliation: INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.
authors.forename: P
authors.initials: P
authors.lastname: PaulStephenRaj
authors.affiliation: INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.
authors.forename: M C
authors.initials: MC
authors.lastname: Le Paslier
authors.affiliation: INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.
authors.forename: A
authors.initials: A
authors.lastname: Berard
authors.affiliation: Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.
authors.forename: M R
authors.initials: MR
authors.lastname: Allwright
authors.affiliation: INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.
authors.forename: M
authors.initials: M
authors.lastname: Villar
authors.affiliation: Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK.
authors.forename: G
authors.initials: G
authors.lastname: Taylor
authors.affiliation: INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France.
authors.forename: C
authors.initials: C
authors.lastname: Bastien
authors.affiliation: DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.|IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Morgante
mesh_terms: D005060:Europe; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods*; D018745:Genome, Plant; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D046228:Microarray Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000145:classification* / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: HT-genotyping design; Populus nigra; large-scale SNP discovery; population genetics