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Genomic structure, QTL mapping, and molecular markers of lipase genes responsible for palm oil acidity in the oil palm (Elaeis guineensis Jacq.)

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Abstract

The degradation of triglycerides in oil palm fruit due to an endogenous lipase in the pulp is the main reason for acidification of palm oil, which causes major economic losses and is currently mainly associated with the FLL1 gene. We designed this study to identify all the major genes controlling differences in acidity and lipase activity in the oil palm fruit mesocarp and determine a molecular markers kit to allow marker-assisted selection of commercial varieties with low acidity. Not only one gene (FLL1) but three closely linked genes including FLL1 were found and characterized in LM2T_EgCIR184O12c, a bacterial artificial chromosome sequence of 231 kb. Intra-gene PCR-based markers were designed for these genes. A QTL gene co-localization analysis for oil acidity (percentage of fatty acids released) was performed on two mapping populations. It evidenced a single major QTL at our lipase gene loci, explaining 84 to 92% of phenotypic variation, and validating the main genetic control of palm oil acidification by FLL1 and/or by the two new lipase genes. The three lipase genes had high homology to demonstrated triacylglycerol lipases. While FLL1 shows the highest expression levels, the two other genes may also contribute to oil acidity. Our molecular markers of lipase genes and the associated major QTL is an important step towards marker-assisted selection of commercial varieties with low acidity.

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Acknowledgments

Hubert Domonhedo is a recipient of the French Embassy SCAC scholarship and the West Africa Agricultural Productivity Program (WAAPP) fellowship. The authors are grateful to the CRA-PP of INRAB for providing the plant samples and phenotypic data. We would also like to thank the Ivory Coast’s Centre National de Recherche Agronomique (CNRA) for providing the LM2T oil palm leaf material previously used to construct the oil palm BAC library. We would furthermore like to express our gratitude to the reviewers of this journal for their corrections and kind help in improving this article. Finally, we are grateful to Dr. Fabienne Morcillo (IRD, France) for providing the PCR primers for the probes of candidate gene FLL1.

Funding

This study was funded by the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), PalmElit S.A.S., and the Centre de Recherches Agricoles Plantes Pérennes (CRA-PP) of the Institut National des Recherches Agricoles du Bénin (INRAB).

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Authors and Affiliations

  1. Centre de Recherches Agricoles-Plantes Pérennes (CRA-PP). Institut National des Recherches Agricoles du Bénin (INRAB), BP 1 Pobè, Bénin

    Hubert Domonhédo, Alphonse Omoré & Léifi Nodichao

  2. Laboratoire Central des Biotechnologies Végétales et d’Amélioration des Plantes; Faculté des Sciences et Techniques (FAST), Université d’Abomey-Calavi (UAC), Cotonou, Bénin

    Hubert Domonhédo

  3. Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Bios-UMR AGAP, Bâtiment 03Bis-Bureau 063, TA A-108/03, Avenue Agropolis, 34398, Montpellier Cedex 5, France

    Teresa Cuéllar, Sandra Espeout, Gaëtan Droc, Marilyne Summo, Ronan Rivallan, David Cros & Norbert Billotte

  4. CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France

    Teresa Cuéllar, Sandra Espeout, Gaëtan Droc, Marilyne Summo, Ronan Rivallan, David Cros & Norbert Billotte

  5. PalmElit SAS, 34980, Montferrier sur Lez, France

    Bruno Nouy

  6. University of Bordeaux, CNRS, UMR5200, 33140, Villenave d’Ornon, France

    Vincent Arondel & Corneille Ahanhanzo

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  1. Hubert Domonhédo
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  2. Teresa Cuéllar
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  3. Sandra Espeout
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  4. Gaëtan Droc
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  7. David Cros
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  13. Norbert Billotte
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Correspondence to Norbert Billotte.

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Communicated by A. A. Myburg

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Data archiving statement

The published microsatellite markers used in the present study were described in Billotte et al. (2001, 2005, 2010), Durand-Gasselin et al. (2009), and Tranbarger et al. (2012).

The BAC consensus sequence and the genomic sequence of each of the three lipase genes identified are archived and publicly available at the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov/). Their accession numbers are as follows: NCBI accession no. KX588870 of BAC consensus sequence LM2T_EgCIR184O12c, NCBI accession no. KX588871 of the genomic sequence of gene EgCIR184O12c_g0040, NCBI accession no. KX588872 of the genomic sequence of gene EgCIR184O12c_g0050, and NCBI accession no. KX588873 of the genomic sequence of gene EgCIR184O12c_g0170.

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Domonhédo, H., Cuéllar, T., Espeout, S. et al. Genomic structure, QTL mapping, and molecular markers of lipase genes responsible for palm oil acidity in the oil palm (Elaeis guineensis Jacq.). Tree Genetics & Genomes 14, 69 (2018). https://doi.org/10.1007/s11295-018-1284-7

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