A new Genomic resource for Populus nigra and its deployment for genetic studies - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Conference Papers Year : 2016

A new Genomic resource for Populus nigra and its deployment for genetic studies


Black poplar (Populus nigra L., Salicaceae) is an Eurasian native species distributed within fluvial corridors. As a pioneer species, P. nigra plays an important role in the establishment of riparian ecosystems. The species has important adaptive performances that have promoted Black poplar as a parental pool in interspecific breeding programs world-wide. Until recently, there is no genomic resource in black poplar to support genetic diversities studies and breeding. INRA, University of Southampton, University of Udine and IGA were collaborating to develop genomic resources and genetic tools for black poplar. SNPs were discovered using whole genome sequencing of 51 individuals relevant of the genetic diversity of an association population covering the range of the species in Western Europe. Four individuals were selected and sequenced at coverage > 25X and 47 at coverage <25X. We had two main objectives: to maximize the genetic variation among individuals and to identify informative SNPs. More than 189 000 SNPs were identified within 15 known QTL regions related to rust resistance, wood properties, water use efficiency and phenology, 2 916 expressional candidate genes for the same traits, and 1 732 genes spread out on the genome. Because many more SNPs were detected than needed, a set of stringent parameters was applied to filter 10 331 loci for the construction of a 12K Infinium BeadChip array (Faivre Rampant et al, 2016). This new array was employed to genotype more than 1 000 unrelated individuals and progenies. The high SNP call rate over 90% provided valuable information on population genetic structure. The structure pattern was consistent with the geographical distribution of the populations under study. However, admixture is an important feature in French populations. Moreover a high rate of clonality was found in populations from Netherlands and Germany. Most polymorphic SNPs had a Minor Allele Frequency greater than 0.05, showing that the array is suitable for association studies. The array data were also used to estimate linkage disequilibrium. The r2 fell to approximately one half of the initial value within 5 to 7 kb. This new information is important to develop further whole genome association in P. nigra. The 12K Infinium BeadChip array is the first genotyping resource for black poplar, and examples of current applications in diversity studies, pedigree validation, genetic mapping, genomic evaluation and natural-population-based genetic association will be presented. It is also considered as gold standard to fine-tune parameters for SNP calling from RNAseq and whole-genome sequencing data.
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hal-02743801 , version 1 (03-06-2020)


  • HAL Id : hal-02743801 , version 1
  • PRODINRA : 357490


Patricia P. Faivre-Rampant, Véronique V. Jorge, Giusi Zaina, Stefania Giacomello, Vincent Segura, et al.. A new Genomic resource for Populus nigra and its deployment for genetic studies. IUFRO Genomics and Forest Tree Genetics, May 2016, Arcachon, France. ⟨hal-02743801⟩
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