Association mapping between candidate gene SNP and production and oil quality traits in interspecific oil palm hybrids

Astorkia Maider, Hernandez Mónica, Bocs Stéphanie, Lopez de Armentia Emma, Herran Ana, Ponce Kevin, León Olga, Morales Shone, Quezada Nathalie, Orellana Francisco, Wendra Fahni, Sembiring Zulhermana, Asmono Dwi, Ritter Enrique. 2019. Association mapping between candidate gene SNP and production and oil quality traits in interspecific oil palm hybrids. Plants, 8 (10):377, 19 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
Published version - Anglais
License Licence Creative Commons.

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Quartile : Q1, Sujet : PLANT SCIENCES

Abstract : Oil palm production is gaining importance in Central and South America. However, the main species Elaeis guineensis (Eg) is suffering severely from bud rod disease, restricting the potential cultivation areas. Therefore, breeding companies have started to work with interspecific Elaeis oleifera × Eg (Eo × Eg) hybrids which are tolerant to this disease. We performed association studies between candidate gene (CG) single nucleotide polymorphisms (SNP) and six production and 19 oil quality traits in 198 accessions of interspecific oil palm hybrids from five different origins. For this purpose, barcoded amplicons of initially 167 CG were produced from each genotype and sequenced with Ion Torrent. After sequence cleaning 115 SNP remained targeting 62 CG. The influence of the origins on the different traits was analyzed and a genetic diversity study was performed. Two generalized linear models (GLM) with principle component analysis (PCA) or structure (Q) matrixes as covariates and two mixed linear models (MLM) which included in addition a Kinship (K) matrix were applied for association mapping using GAPIT. False discovery rate (FDR) multiple testing corrections were applied in order to avoid Type I errors. However, with FDR adjusted p values no significant associations between SNP and traits were detected. If using unadjusted p values below 0.05, seven of the studied CG showed potential associations with production traits, while 23 CG may influence different quality traits. Under these conditions the current approach and the detected candidate genes could be exploited for selecting genotypes with superior CG alleles in Marker Assisted Selection systems.

Mots-clés Agrovoc : Elaeis guineensis, Elaeis oleifera, amélioration génétique, Résistance aux maladies, Hybride, Huile de palme, Qualité, Analyse de données

Mots-clés géographiques Agrovoc : Amérique centrale, Amérique du Sud

Mots-clés libres : Elaeis guineensis, Elaeis oleifera, Snakemake, Lipids, Tocols, Carotene

Classification Agris : F30 - Plant genetics and breeding
H20 - Plant diseases
Q04 - Food composition

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

  • Astorkia Maider, CIRAD-BIOS-UMR AGAP (FRA) - auteur correspondant
  • Hernandez Mónica, NEIKER (ESP)
  • Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
  • Lopez de Armentia Emma, NEIKER (ESP)
  • Herran Ana, NEIKER (ESP)
  • Ponce Kevin, La Fabril (ECU)
  • León Olga, Fundación Pérez Pallarez (ECU)
  • Morales Shone, La Fabril (ECU)
  • Quezada Nathalie, La Fabril (ECU)
  • Orellana Francisco, Fundación Pérez Pallarez (ECU)
  • Wendra Fahni, PT Sampoerna Agro (IDN)
  • Sembiring Zulhermana, PT Sampoerna Agro (IDN)
  • Asmono Dwi, PT Sampoerna Agro (IDN)
  • Ritter Enrique, NEIKER (ESP)

Source : Cirad-Agritrop (

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