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Mixed model approach for IBD-based QTL mapping in a complex oil palm pedigree

Tisne Sébastien, Denis Marie, Cros David, Pomies Virginie, Riou Virginie, Syahputra Indra, Omoré Alphonse, Durand-Gasselin Tristan, Bouvet Jean-Marc, Cochard Benoît. 2015. Mixed model approach for IBD-based QTL mapping in a complex oil palm pedigree. BMC Genomics, 16 (798), 12 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q2, Sujet : GENETICS & HEREDITY

Abstract : Background Elaeis guineensis is the world's leading source of vegetable oil, and the demand is still increasing. Oil palm breeding would benefit from marker-assisted selection but genetic studies are scarce and inconclusive. This study aims to identify genetic bases of oil palm production using a pedigree-based approach that is innovative in plant genetics. Results A quantitative trait locus (QTL) mapping approach involving two-step variance component analysis was employed using phenotypic data on 30852 palms from crosses between more than 300 genotyped parents of two heterotic groups. Genome scans were performed at parental level by modeling QTL effects as random terms in linear mixed models with identity-by-descent (IBD) kinship matrices. Eighteen QTL regions controlling production traits were identified among a large genetically diversified sample from breeding program. QTL patterns depended on the genetic origin, with only one region shared between heterotic groups. Contrasting effects of QTLs on bunch number and weights reflected the close negative correlation between the two traits. Conclusions The pedigree-based approach using data from ongoing breeding programs is a powerful, relevant and economic approach to map QTLs. Genetic determinisms contributing to heterotic effects have been identified and provide valuable information for orienting oil palm breeding strategies. (Résumé d'auteur)

Mots-clés Agrovoc : Elaeis guineensis, Locus des caractères quantitatifs, Carte génétique, Amélioration des plantes, Huile de palme, Modèle linéaire, Modèle mathématique, Vigueur hybride

Mots-clés géographiques Agrovoc : Bénin, Indonésie

Mots-clés complémentaires : QTL

Classification Agris : F30 - Plant genetics and breeding
U10 - Mathematical and statistical methods

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

Auteurs et affiliations

  • Tisne Sébastien, CIRAD-BIOS-UMR AGAP (FRA)
  • Denis Marie, CIRAD-BIOS-UMR AGAP (FRA)
  • Cros David, CIRAD-BIOS-UMR AGAP (CMR) ORCID: 0000-0002-8601-7991
  • Pomies Virginie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-5481-5120
  • Riou Virginie, CIRAD-BIOS-UMR AGAP (FRA)
  • Syahputra Indra, SOCFINDO (IDN)
  • Omoré Alphonse, SOCFINDO (IDN)
  • Durand-Gasselin Tristan, PalmElit (FRA)
  • Bouvet Jean-Marc, CIRAD-BIOS-UMR AGAP (FRA)
  • Cochard Benoît, CIRAD-BIOS-UMR AGAP (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/577772/)

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