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High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly

Bartholomé Jérôme, Mandrou Eric, Mabiala André, Jenkins Jerry, Nabihoudine Ibouniyamine, Klopp Christophe, Schmutz Jeremy, Plomion Christophe, Gion Jean-Marc. 2015. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytologist, 206 (4), n.spéc. Featured papers on 'Eucalyptus genome' : pp. 1283-1296.

Journal article ; Article de revue à facteur d'impact
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Quartile : Outlier, Sujet : PLANT SCIENCES

Abstract : Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome.

Mots-clés Agrovoc : Eucalyptus, Eucalyptus urophylla, Eucalyptus grandis, Carte génétique, Marqueur génétique, Locus des caractères quantitatifs, Hybride, Génome, Polymorphisme génétique, Séquence nucléotidique, Dimension

Classification Agris : F30 - Plant genetics and breeding
K10 - Forestry production

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Bartholomé Jérôme, INRA (FRA) ORCID: 0000-0002-0855-3828
  • Mandrou Eric, INRA (FRA)
  • Mabiala André, CRDPI (COG)
  • Jenkins Jerry, HudsonAlpha Biotechnology Institute (USA)
  • Nabihoudine Ibouniyamine, INRA (FRA)
  • Klopp Christophe, INRA (FRA)
  • Schmutz Jeremy, DOE-JGI (USA)
  • Plomion Christophe, INRA (FRA)
  • Gion Jean-Marc, CIRAD-BIOS-UMR AGAP (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/576081/)

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