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New Resources for genetic studies in Populus Nigra: genome-wide SNP discovery and development of a 12K Infinium array

New Resources for genetic studies in Populus Nigra: genome-wide SNP discovery and development of a 12K Infinium array
New Resources for genetic studies in Populus Nigra: genome-wide SNP discovery and development of a 12K Infinium array
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.
0962-1083
1023-1036
Faivre-Rampant, P.
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Zaina, G.
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Jorge, V.
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Giacomello, S.
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Segura, V.
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Scalabrin, S.
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Guerin, V.
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De Paoli, E.
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Aluome, C.
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Viger, M.
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Cattonaro, F.
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Payne, A.
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Paulstephenraj, P.
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Le Paslier, M.C.
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Berard, A.
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Allwright, M.R.
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Villar, M.
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Taylor, G.
Bastien, C.
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Morganye, M.
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Faivre-Rampant, P.
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Zaina, G.
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Jorge, V.
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Giacomello, S.
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Segura, V.
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Scalabrin, S.
ff064b17-8e7a-406c-8cf1-b229f5008389
Guerin, V.
37659a61-b2da-4310-948c-c7c18f22b651
De Paoli, E.
33a9a2bc-7b12-46e0-9626-ea81364a6d0c
Aluome, C.
59543230-9da2-4129-b29c-9a5e72a3738f
Viger, M.
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Cattonaro, F.
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Payne, A.
d71d18a8-874d-419f-8002-c02c2e26b001
Paulstephenraj, P.
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Le Paslier, M.C.
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Berard, A.
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Allwright, M.R.
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Villar, M.
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Taylor, G.
Bastien, C.
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Morganye, M.
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Faivre-Rampant, P., Zaina, G., Jorge, V., Giacomello, S., Segura, V., Scalabrin, S., Guerin, V., De Paoli, E., Aluome, C., Viger, M., Cattonaro, F., Payne, A., Paulstephenraj, P., Le Paslier, M.C., Berard, A., Allwright, M.R., Villar, M., Taylor, G., Bastien, C. and Morganye, M. (2016) New Resources for genetic studies in Populus Nigra: genome-wide SNP discovery and development of a 12K Infinium array. Molecular Ecology, 16 (4), 1023-1036. (doi:10.1111/1755-0998.12513).

Record type: Article

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.

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Accepted/In Press date: 22 December 2015
e-pub ahead of print date: 24 March 2016
Published date: July 2016
Organisations: Faculty of Natural and Environmental Sciences

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Local EPrints ID: 404626
URI: http://eprints.soton.ac.uk/id/eprint/404626
ISSN: 0962-1083
PURE UUID: 26c8ddac-3a56-437b-b9c1-539758aecdb9

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Date deposited: 13 Jan 2017 14:32
Last modified: 15 Mar 2024 04:11

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Contributors

Author: P. Faivre-Rampant
Author: G. Zaina
Author: V. Jorge
Author: S. Giacomello
Author: V. Segura
Author: S. Scalabrin
Author: V. Guerin
Author: E. De Paoli
Author: C. Aluome
Author: M. Viger
Author: F. Cattonaro
Author: A. Payne
Author: P. Paulstephenraj
Author: M.C. Le Paslier
Author: A. Berard
Author: M.R. Allwright
Author: M. Villar
Author: G. Taylor
Author: C. Bastien
Author: M. Morganye

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