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New genomic tools to enhance discovery of functional diversity in natural populations of Populus nigra L.: Evoltree Lecture

Abstract : In a collaborative effort launched by Evoltree, INRA (F), Universities of Southampton (GB) and Udine and IGA (I), co mbined sampling of Populus nigra genetic resources at the European scale, high through put sequencing and SNP genotyping technologies, to characterize genetic diversity patterns and perform association genetics for adaptive and production traits. The Evoltree Plant Gene Repository Center’s facilities in Tulln (AT), provided DNA for the accessions sampled and maintained in a clonal archive in France (INRA, ONF). For SNP discovery, 51 individuals representative of the Western part of the European collection were resequenced with pair-end Illumina technologies. Four individuals were resequenced at high coverage (>20x) and 47 at lower coverage (2x-12x). Raw reads of the P. nigra clone 71077-308 were aligned on the P. trichocarpa genome sequence V2.0. Around 50% of the reads uniquely matched and 70% of the P. trichocarpa genome was covered. The resulting alignment was used as a framework reference genome of P. nigra to perform SNP calling after alignment of the 3 other high coverage genotype reads. SNP frequencies were then estimated after mapping of the 47 low coverage genotype reads. In the frame of FP7 projects Energy-poplar and NovelTree, over ten thousands SNP have been selectively filtered to target -15 known QTL regions -2916 expressional candidate genes related to rust resistance and wood properties -1007 genes spread out of the framework reference for the construction of a 12 K Infinium BeadChip array. The results of admixture analyses based on 7896 SNP were consistent with geographical distribution of the 14 populations under study (721 individuals). Admixture remains an important feature in many populations except the Italian ones. High clonality rates were confirmed in endangered populations in Netherlands and Germany. The successful collaborative strategy developed here has fostered large scale genetic studies on a reference association population.
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Submitted on : Wednesday, June 3, 2020 - 2:50:02 AM
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  • HAL Id : hal-02741907, version 1
  • PRODINRA : 355937

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Patricia Faivre-Rampant, Guisi Zaina, Simone Scalabrin, Véronique Jorge, Vincent Segura, et al.. New genomic tools to enhance discovery of functional diversity in natural populations of Populus nigra L.: Evoltree Lecture. Forest Tree Breeding Conference. IUFRO 2014, Aug 2014, Prague, Czech Republic. ⟨hal-02741907⟩

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