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Detection of significant SNP associated with production and oil quality traits in interspecific oil palm hybrids using RARSeq

Astorkia Maider, Hernandez Mónica, Bocs Stéphanie, Ponce Kevin, León Olga, Morales Shone, Quezada Nathalie, Orellana Francisco, Wendra Fahni, Sembiring Zulhermana, Asmono Dwi, Ritter Enrique. 2020. Detection of significant SNP associated with production and oil quality traits in interspecific oil palm hybrids using RARSeq. Plant Science, 291:110366, 13 p.

Journal article ; Article de revue à facteur d'impact
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Abstract : A RARSeq based Association mapping study was performed in a population of 104 Elaeis oleifera x E. guineensis hybrids of five origins with the aim of finding functional markers associated to six productive and 19 oil quality traits. For this purpose mRNA of each genotype was isolated and double stranded cDNA was synthesized. Following digestion with two restriction enzymes and adapter ligation, a size selected pool of barcoded amplicons was produced and sequenced using Illumina MiSeq. The obtained sequences were processed with a “snakemake” pipeline, filtered and missing values were imputed. For all traits except two significant effects of the origin was observed. Genetic diversity analyses revealed high variability within origins and an excess of heterozygosity in the population. Two GLM models with Q matrix or PCA matrix as covariates and two MLM models incorporating in addition a Kinship matrix were tested for genotype-phenotype associations using GAPIT software. Using unadjusted p values (< 0.01) 78 potential associations were detected involving 25 SNP and 20 traits. When applying FDR multiple testing with p < 0.05, 25 significant associations remained involving eight SNP and six quality traits. Four SNP were located in genes with a potential relevant biological meaning.

Mots-clés Agrovoc : Elaeis guineensis, Elaeis oleifera, Hybride, amélioration génétique, Marqueur génétique, Qualité, Huile de palme

Mots-clés géographiques Agrovoc : Équateur, Colombie

Mots-clés libres : Oil palm, CDNA, RARSeq, Oil quality, Association mapping

Classification Agris : F30 - Plant genetics and breeding
J11 - Handling, transport, storage and protection of plant products

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
  • 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 (https://agritrop.cirad.fr/594787/)

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